title: Transcriptional profilling of potato during a compatible interaction with the root-knot nematode Melodoigyne javanica

city: Pretoria

first: Teresia

middle: Nyambura

last: Macharia

state: Gauteng

address: cnr Lynnwood Road and Roper Street

department: Biochemistry, Genetics and Microbiology

country: South Africa

institute: University of Pretoria

summary: The aim of this study was to elucidate the molecular basis underlying the compatible interaction between potato and root-knot nematode at early stages on infection at 3 and 7dpi.

overall_design: RNA profiles of 0, 3 and 7 dpi were seqquenced using Illumina tecnnology in two biological replicates. The sequenced reads that passed the quality asssement were mapped to the potato genome using histat2 v2.1.0 software and featureCounts used to count the raw reads in the R environment and finally the edgeR package used for differential analysis.

first: Lucy

last: Moleleki

first: Daniel

last: Rebelo


title: Transcriptome sequencing of SKA3 knockdown laryngeal squamous cell carcinoma cells

status: Public on Nov 02 2020

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

country: China

institute: Shanxi Medical University

type: Expression profiling by high throughput sequencing

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. The spindle and kinetochore associated complex subunit 3 (SKA3) protein was upregulated in LSCC and associated with poor prognosis. To understand mechanism of SKA3 regulation in LSCC, we performed high throughout transcriptome sequencing to identify SKA3-regulated genes.

overall_design: Knockdown of SKA3 in LSCC cells TU-177, and mRNA expression was examination by high throughout sequencing.

first: Wei

last: Gao

first: Binquan

last: Wang


title: G9a-mediated methylation abrogates RUNX3 tumor suppressive activity to promote cancer cell survival under hypoxia [ChIP-seq]

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chronic hypoxia inhibits apoptosis to enhance survival of cancer cells. The mechanisms that prevent apoptosis under hypoxia are unclear. Here, we show that hypoxia induced G9a, a lysine methyltransferase, which methylates a tumor suppressor, Runt-related transcription factor 3 (RUNX3) at lysines 129 and 171. G9a-mediated methylation reduced transcriptional activity of RUNX3 by inhibiting interactions with its transcriptional cofactors, the core-binding factor-beta (CBF-beta) and p300, and also decreased the protein level of RUNX3 via Smurf1-mediated proteasomal degradation. Through ChIP-seq and gene expression profiling, G9a-mediated methylation inhibited expression of genes involved in apoptosis, thereby enhancing survival and proliferation of cancer cells both in vitro and vivo. Our results suggest G9a-dependent methylation of RUNX3 as a therapeutic target to control tumor growth.

overall_design: RUNX3 binding profiles of SNU484 cells at the following three conditions (2 replicates each) were examined by ChIP-sequencing: wild-type (WT), RUNX3 K129R mutant (K129R), and RUNX3 K171R mutant (K171R).

first: Yo-Mie

last: Lee

first: Daehee

last: Hwang


title: AR-V7 targets the oncogenic genes in castration resistant prostate cancer.

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

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

overall_design: Refer to individual Series


title: G9a-mediated methylation abrogates RUNX3 tumor suppressive activity to promote cancer cell survival under hypoxia


title: AR-V7 targets the oncogenic genes in castration resistant prostate cancer. [RNA]

summary: To identify the  AR-V7 target genes in human prostate cancer, two cell lines (LNCaP, LNCaP95) were subjected to RNA-seq analysis.

overall_design: 1) LNCaP were treated with 10nM DHT, EtOH 2)LNCaP95 was treated with 10nM DHT, EtOH, siRNAs (siSLC3A2, siLAT1), shRNAs (AR-V7), 50uM JPH203, DMSO

first: Masahiro

last: Sugiura

first: Hiroaki

last: Sato

first: Atsushi

last: Okabe

first: Yasunobu

last: Mano

first: Kenichi

last: Shinohara

first: Kosuke

last: Higuchi

first: Maihulan

last: Maumaiti

first: Manato

last: Kanesaka

first: Yusuke

last: Imamura

first: Shinichi

last: Sakamoto

first: Naohiko

last: Anzai

first: Yoshikatsu

last: Kanai

first: Tomohiko

last: Ichilawa

last: Kaneda


title: Response of Pseudomonas aeruginosa to the innate immune system-derived oxidants hypochlorous acid and hypothiocyanous acid

city: London

first: Huw

middle: David

last: Williams

address: Imperial College Road

department: Department of Life Sciences

country: United Kingdom

institute: Imperial College London

summary:
Purpose: The aim of this study was to determine the transcriptional response of P. aeruginosa PA14 to HOCl and HOSCN stress, and determine genes dependent on RclR (PA14_07340) regulation.
Methods: PA14 WT and ∆rclR exponential phase cultures were exposed to sub-lethal amounts of HOCl or HOSCN (2.2 or 0.8 mM, respectively), or untreated, and after 20 minutes of exposure, RNA was extracted and gene expression analysed by RNA-seq. Reads Per Kilobase per Million mapped reads (RPKM) were determined and the log2 fold change of the RPKM values of treated WT compared to untreated WT, or treated WT compared to treated ∆rclR was calculated. Genes with a log2 fold change of >1.5 were considered upregulated and genes with a log2 fold change of <-1.5 were considered downregulated.
Results: In the WT strain, HOCl exposure resulted in upregulation of 231 genes and downregulation of 20 genes, and HOSCN exposure caused upregulation of 105 genes and downregulation of 16 genes. There was considerable overlap in the transcriptional response to HOCl and HOSCN, with 74 genes being induced in response to both oxidants. Genes upregulated by HOCl and HOSCN included those involved in sulphur and taurine transport, those encoding the type 3 secretion system, the MexEF-OprN drug efflux pump, and the putative peroxiredoxin RclX (PA14_07355). Comparison of the treated WT and treated ∆rclR strains revealed that in the presence of HOCl RclR upregulated 42 genes and downregulated 7 genes, and in the presence of HOSCN upregulated 132 genes and downregulated 213 genes. In the presence of both HOCl and HOSCN, RclR was required for upregulation of rclX as well as pyocyanin biosynthesis genes. In the presence of HOSCN, RclR downregulated a large number of genes, including those encoding chaperones.
Conclusions: Our data have identified that the transcriptional response of P. aeruginosa to HOCl and HOSCN is multifaceted and appears to be linked to antibiotic resistance and the virulence factors pyocyanin and type 3 secretion. Determination of the regulon of the transcriptional regulator RclR after HOCl and HOSCN exposure suggests RclR has a role in coordinating the P. aeruginosa response to these oxidants.

overall_design: PA14 WT and ∆rclR exponential phase cultures were either untreated, exposed to 2.2 mM HOCl or 0.8 mM HOSCN for 20 minutes, in duplicate, and then RNA from the 12 samples was extracted, cDNA libraries were constructed, and RNA-seq was carried out using the Illumina NextSeq 500 system. Untreated WT samples were used as a reference to identify genes differentially expressed in the HOCl or HOSCN treated samples, and treated WT samples were used as a reference compared to treated ∆rclR samples to identify RclR regulated genes.

first: Katie

middle: V

last: Farrant

first: Livia

last: Spiga

first: Jane

middle: C

last: Davies

middle: D


title: Gene expression profile of TRA-1-60 population in FL cell line

city: Okayama city

first: Katsuyoshi

last: Takata

address: 2-5-1, Kita-ku, Shikata-cho

department: Pathology

institute: Okayama University

summary: Objective and goals: To find a clue for the mechanism of drug resistance in TRA-1-60 positive minor cell populations

overall_design:
We examined TRA-1-60 positive and negative population in FL-18 and DOHH-2 cell line using Agilent 8 x 60K microarray to identify the specific genes that are involved in the drug resistance mechanisms.
TRA-1-60 positive and negative population were purified using FACS Aria. Total RNA was extracted and analyzed.

first: Shujiro

last: Okuda

first: Eisaku

last: Kondo


title: AR-V7 targets the oncogenic genes in castration resistant prostate cancer. [ChIP]

first: Masaki

last: Fukuyo

summary: To elucidate the AR-V7 role, we performed ChIP-seq on H3K4me1, H3K4me3, H3K27ac, and AR antibody recognizing the N-terminus of AR and AR splice variants (AR-Vs) using LNCaP and LNCaP95 cells. We showed  399 AR-V7 targeted regions in LNCaP95, most of the AR-V7 target regions could be commonly activated by hormone stimulated AR. However, 22 regions were identified as AR-V7 specific regions. In addition, we show here that AR-V7 can transcript in the ligand independent manner in LNCaP95, unlike LNCaP.  We identified the AR-V7 target gene contributing to the CRPC progression.

overall_design: 1) Examination of AR and AR-V7 target regions and 2 different histone modifications in LNCaP or LNCaP95 cells. 2) Examination of  different histone modifications in shRNA-mediated knockdown LNCaP95 cells.

first: Masahiro

last: Sugiura

first: Hiroaki

last: Sato

first: Atsushi

last: Okabe

first: Yasunobu

last: Mano

last: Shinohara


title: Transcriptome analysis of Bacillus subtilis NBRC 16449 grown on surface of boiled soybeans under the similar condition to production of Japanese traditional soybean-fermented food "natto"

city: uji

first: HASHIMOTO

last: WATARU

address: gokasho

department: Division of Food Science and Biotechnology

institute: Graduate School of Agriculture, Kyoto University

summary:
Purpose:The goals of this study are to clarify the B. subtilis NBRC 16449 response to soybeans.
Methods: B. subtilis NBRC 16449 cells were aerobically cultured in liquid LB, LB solidified with agar, or on surface of boiled soybeans to logarithmic growth phase. Total RNAs were extracted from bacterial cells by Hot-Phenol method. Samples for RNA-seq were prepared according to Illmina protocol available from the manufacture. The sequence reads that passed quality filters were analyzed at the transcript isoform level with bowtie v0.11.2.
Results: Using an optimized data analysis workflow, we mapped around 15 million sequence reads per sample to the whole genome of B. subtilis BEST195 and identified 4271 transcripts in B. subtilis NBRC 16449 with Bowtie aligner. Read count per genome was extracted from known gene annotations with HTSeq program. Compared the transcriptomes of B. subtilis NBRC 16449 grown on LB solidified with agar to that grown on surface of boiled soybeans, about 5% of genes showed the different expression levels.

overall_design: RNA profiles of B. subtilis NBRC 16449 grown under different conditions: liquid LB, LB solidified with agar, or surface of boiled soybeans.

first: Haruka

first: Wataru

last: Hashimoto


title: Negative regulation of RUNX3 activity by G9a-mediated protein methylation in hypoxia [array]

first: Do Young

last: Hyeon

summary: Chronic hypoxia inhibits apoptosis and cell cycle arrest in cancer cells, leading to cell survival, proliferation and angiogenesis. The mechanism for anti-apoptosis and cell proliferation in hypoxic cancer cells is still elusive. Here, we showed that hypoxia inactivates Runt-related transcription factor 3 (RUNX3), which is known to play as a tumor suppressor to induce apoptosis and cell cycle arrest in various cancers. RUNX3 is methylated under hypoxic conditions at lysines (K) 129 and 171 through its interaction with methyltranferase G9a. Gene expression profiling revealed that the mutations of K129 and 171 in RUNX3 induced the expression of genes related to apoptosis and cell cycle arrest under hypoxic conditions, indicating critical roles of the RNUX methylation in anti-apoptosis and cell proliferation. Moreover, K129 and 171 mutants, compared to G9a or G9a+RUNX3 control, showed significant reduction in apoptotic ability and tumor progression in xenograft models. Therefore, G9a-dependent methylation of RUNX3 is a novel target to inhibit cell proliferation and anti-apoptosis under hypoxic conditions during tumorigenesis.

overall_design: The mRNA levels were measured for two biological replicates for each condition: hypoxia-treated wild type (WT), hypoxia-treated K129R mutant (K129R), and hypoxia-treated K171R mutant (K171R).

first: You-Mie

last: Lee

first: Daehee

last: Hwang


title: Interleukin-13 drives cholestasis and compositional changes in the gut microbiome in Abcb4-deficient mice by compromising bile duct barrier integrity

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: The Th2 cytokine IL-13 has been described to be involved in biliary epithelial injury and liver fibrosis in patients as well as in animal models. IL-13 was found to reduce tight junction-associated barrier function of bile ducts, to promote cholangiocyte hyperplasia, and thus causing biliary epithelial injury. We generated Abcb4-/-- and IL-13-/- double-knockout mice on fibrosis susceptible genetic background BALB/c. Molecular and cellular mechanisms of hepatic and ileal pathology were investigated by  mRNA microarray. Depletion of IL-13 in Abcb4-/--mice resulted in a tenfold decrease of total serum bile acid concentrations at the age of 8 weeks and lead to a recovery of intrahepatic bile duct integrity. The decrease of serum bile acid in 8 week old mice went along with relative enhancement of bile acid excretion and normalization of the composition of fecal bile excretion, correction of fecal microbiome, and improved ileal integrity. Liver integrity, measured by serum ALT, was ameliorated in younger mice and strongly correlated with the concentration of serum bile acids. 52 weeks old Abcb4-/-IL-13-/--mice exhibited significantly reduced hepatic fibrosis.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent mouse whole genome catalog 8x60K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Luisa

last: Hahn

first: Elke

last: Roeb

first: Martin

last: Roderfeld


title: Dysregulated long noncoding RNAs in the brainstem of DBA/1 mouse SUDEP model

status: Public on Nov 01 2020

city: Chengdu

first: Ling

last: Liu

state: Sichuan

address: Wai Nan Guo Xue Lane 37 #

department: Department of neurology

institute: West China Hospital, Sichuan University

summary: We investigated the differential expressed lncRNA and messenger RNA (mRNA) of the brainstem between primed DBA/1 mouse SUDEP model and normal DBA/1.

overall_design: The Arraystar mouse lncRNA Microarray V3.0 (Arraystar, Rockville, MD) was applied to identify the aberrantly expressed lncRNAs and mRNAs in the brainstem of of DBA/1 mouse SUDEP model(n=4). Normol DBA/1 mice(n=4) were enrolled as control groups.

first: Lina

last: Zhu


title: Transcriptional analysis of LAG3 deficient Tregs in an inflamed CNS

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

country: USA

institute: University of Pennsylvania

summary: Transcriptonal analysis of Tregs reveal role of LAG3 in stability and function of Tregs in an inflamed CNS

overall_design: CD45+ cells or CD4 cells were sorted from CNS cells isolated at peaks of diseases in age and sex matched mice(Lag3KO and WT) in which EAE was induced were subject to Gene Expression analysis using the 10x Genomics Single Cell analysis platform.

first: Youg

middle: R

last: Thaker

first: Arlene

middle: H

last: Sharpe


title: Dual DNA/protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia (CUT&RUN)

city: Boston

first: Jonathan

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

summary: The architecture of chromatin specifies eukaryotic cell identity by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase/peroxidase approach, integrative DNA And Protein Tagging (iDAPT), which detects both DNA (iDAPT-seq) and protein (iDAPT-MS) associated with accessible regions of chromatin. In addition to direct identification of bound transcription factors, iDAPT enables the inference of their gene regulatory networks, protein interactors, and regulation of chromatin accessibility. We applied iDAPT to profile the epigenomic consequences of granulocytic differentiation of acute promyelocytic leukemia, yielding previously undescribed mechanistic insights with potential therapeutic implications. Our findings demonstrate the power of iDAPT as a discovery platform for both the dynamic epigenomic landscapes and their transcription factor components associated with biological phenomena and disease.

overall_design: CUT&RUN of newly identified open chromatin-associated proteins in the K562 cell line. Peaks are called relative to a normal rabbit IgG control.

first: Pier

middle: P

last: Pandolfi


title: A Regulatory T Cell Notch4 Switch Governs Lung Inflammation in Viral Infections

first: KLaus

last: Schmitz-Abe

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

summary: Coronavirus disease 2019 (Covid19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is associated with lung inflammation and respiratory failure. In a prospective multi-country cohort of Covid19 patients, we found that increased Notch4 expression on circulating Treg cells was associated with increased disease severity, predicted mortality, and declined upon recovery. Deletion of Notch4 in Treg cells or therapy with anti-Notch4 antibodies in conventional and humanized mice suppressed the dysregulated innate immune response and rescued disease morbidity and mortality induced by a synthetic analogue of viral RNA or by the influenza H1N1 virus in an amphiregulin-dependent manner. Notably, amphiregulin production declined in Covid19 subjects as a function of disease severity and Notch4 expression. These results identify Notch4 as an immune regulatory switch that licenses virus-induced lung inflammation by altering Treg cell-mediated tissue repair. They also suggest Notch4 as a therapeutic target in Covid19 and other respiratory viral infections.

overall_design: The mice were treated with 2.5 mg/kg of Poly I:C for 6 consecutive days intratracheally. On day 7, the lungs were digested and regulatory T-cells were isolated from either the Foxp3YFPCre mice vs. Foxp3YFPCrexNotch4fl/fl group. The T-reg cells from both groups were used for the RNA-seq analysis

first: Hani

last: Harb

first: Klaus

first: Talal

middle: A

last: Chatila


title: Gene expression profiling of wildtype and MAPK9 knockout murine knee post destabilization of the medial meniscus

city: Sheffield

first: Heba

last: Ismail

address: Firth Court, University of Sheffield, Western Bank, Sheffield

department: Infection, Immunity and Cardiovascular disease.

institute: University of Sheffield

summary: To identify the gene expression profile of knee post injury in wild type C57BL6 strain and MAPK9 knockout.

overall_design: Total RNA obtained from murine knees 6 hours post injury induction.


title: Anti-inflammatory Effects of the Commensal Bacterium Faecalibacterium prausnitzii analyzed by microarrays

city: Jouy en Josas

first: Florian

last: Chain

address: Domaine de Vilvert

department: Institut Micalis

country: France

institute: INRA

summary: The human intestinal microbiota plays an essential role in host health. Modifications in its composition and diversity could induce pathologies such as inflammatory bowel diseases (IBD). These diseases are characterized by an unbalanced intestinal microbiota (a process known as dysbiosis) and an altered immune response. Faecalibacterium prausnitzii, the most abundant commensal bacterium in the human intestinal microbiota of healthy individuals (representing more than 5% of the total bacterial population), has been reported to be lower in feces and mucosa-associated microbiota of IBD patients. In addition, we have shown that both F. prausnitzii and its culture supernatant (SN) have anti-inflammatory and protective effects in both acute and chronic colitis models. However, the host molecular mechanisms involved in these anti-inflammatory effects remain unknown. In order to address this issue, we performed DNA chip-based transcriptomic analyses in HT-29 human intestinal epithelial cells stimulated with TNF-a  and exposed to F. prausnitzii SN or to BHI (growth medium for F prausnitzii).

overall_design: A reference design with complete dye-swap including two biological replicates per sample was used to compare HT-29 cells submitted to different treatments for a total of 6 Agilent 4x44K Whole Human Genome Microarrays (Agilent Technologies, France).

first: Marion

last: Lenoir

first: Rebeca

last: Martin-Rosique

first: Philippe

last: Langella

first: Luis

middle: G

last: Bermudez-Humaran


title: Expression of immune-related genes in peripheral blood mononuclear cells of HBV infected patients and uninfected controls

city: Bethesda

first: Barbara

last: Rehermann

state: Maryland

address: 10 Center Drive

department: Liver Diseases Branch

institute: National Institutes of Health

summary: This study was conducted to assess how long-term nucleoside analogue (NUC) treatment and HBeAg loss alters the transcriptome of blood mononuclear cells from chronic HBV patients

overall_design: Cryopreserved, subsequently thawed peripheral blood mononuclear cells were subjected to NanoString nCounter expression analysis of immune-related genes

first: Akira

last: Nishio


title: Differential analysis of host small RNAs identified conserved and new miRNAs that affect nodulation and strain selectivity in the Phaseolus vulgaris- Rhizobium etli symbiosis

city: Villa Elisa-La Plata

first: Maria

middle: Eugenia

last: Zanetti

state: BUENOS AIRES

department: Instituto de Biotecnología y Biología Molecular

country: Argentina

institute: Universidad Nacional de La Plata

type: Non-coding RNA profiling by high throughput sequencing

summary: We report an small RNA sequencing (sRNA-seq) approach to identify host sRNAs involved in the nitrogen fixing symbiosis between Mesoamerican Phaseolus vulgaris and Rhizobium etli strains with different degrees in nodulation efficiency. This approach identified conserved and known microRNAs (miRNAs) differentially accumulated in Mesoamerican P. vulgaris roots in response to a highly efficient strain, to a less efficient one or to both strains.

overall_design: sRNA-seq profiling of P. vulgaris root tissues inoculated with Yeast Extract Mannitol media as a control (CTL), with the highly efficient strain of R. etli SC15 or the less effcient strain 55N1.

first: Melisse

last: Castaingts

first: Claudio

last: Rivero

first: Ulises

last: Mancini

first: Flavio

last: Blanco

first: María

middle: E


title: Dual DNA/protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia (ATAC-Seq)

first: Jonathan

last: Lee

overall_design: ATAC-seq/iDAPT-seq of leukemia cell lines.

first: Pier

last: Pandolfi


title: Characterization of Mutational Status, Spheroid Formation, and Drug Response of a New Genomically-Stable Human Ovarian Clear Cell Carcinoma Cell Line, 105C (Oncomine)

first: Gabriel

last: DiMattia

state: ONTARIO

address: 750 Base Line Rd E

department: Biochemistry

country: Canada

institute: Western University

type: Genome variation profiling by high throughput sequencing

summary: Ovarian clear cell carcinoma (OCCC) is a rare subtype of gynecological cancer for which well-characterized and authenticated model systems are scarce. We provide an extensive characterization of ‘105C’, a cell line generated from an adenocarcinoma of the clear cell histotype using targeted next-generation sequencing, cytogenetic microarrays, along with analyses of AKT/mTOR signaling. We report that that the 105C cell line is a bona fide OCCC cell line, carrying PIK3CA, PTEN, and ARID1A gene mutations, consistent with OCCC, yet maintain a stable genome as reflected by low copy number variation. Unlike KOC-7c, TOV-21G, and RMG-V OCCC lines also mutated for the above genes, the 105C cells do not carry mutations in mismatch repair genes. Importantly, we show that 105C cells exhibit greater resistance to mTOR inhibition and carboplatin treatment compared to 9 other OCCC cell lines in 3D spheroid cultures. This resistance may be attributed to 105C cells remaining dormant in suspension culture which surprisingly, contrasts with several other OCCC lines which continue to proliferate in long-term suspension culture. 105C cells survive xenotransplantation but do not proliferate and metastasize. Collectively, we show that the 105C OCCC cell line exhibits unique properties useful for the pre-clinical investigation of OCCC pathobiology.

overall_design: DNA from 105C cell line sequenced using Oncomine Comprehensive v3 assay (Thermo Fisher Scientific)

first: Bart

last: Kolendowski

first: Yudith

last: Ramos-Valdes

first: Hal

last: Hirte

first: Hiroaki

last: Itamochi

first: Wonjae

first: Mark

last: Carey

first: Trevor

last: Shepherd


title: RNA sequencing of CD8 T cells flow sorted from post-stroke brain

city: Lexington

first: Ann

middle: Marie

last: Stowe

state: Kentucky

address: 741 S. Limestone

department: Neurology

institute: University of Kentucky

summary: CD8 T cells functional profile was characterized by comparing the gene expression between the cells isolated from 3 days post-stroke, 30 days post-stroke and naïve brains.

overall_design: CD8 T cells were isolated from post-stroke mice brains at 3 days and 30 days post-stroke. CD8 T cells isolated from naïve mouse blood and brain were used as control/ reference samples. 3 samples were analyzed for each condition.

first: Uma

last: Maheswari Selvaraj

first: Xiangmei

last: Kong

first: Thomas

last: Ujas

first: Ashwani

last: Kumar

first: Erik

middle: J

last: Plautz

first: Shanrong

last: Zhang

first: Chao

last: Xing

first: Jadwiga

last: Turchan-Cholewo

last: Goldberg


title: EVI1-phosphorylation at S436 regulates interactions with CtBP1 and DNMT3A and promotes self-renewal

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

institute: University of Manchester

summary: The transcriptional regulator EVI1 has an essential role in early development and haematopoiesis. However, acute myeloid leukaemia (AML) driven by aberrantly high EVI1 expression has very poor prognosis. To investigate effects of posttranslational modifications on EVI1 function, we carried out a mass spectrometry (MS) analysis of EVI1 in AML and detected dynamic phosphorylation at serine 436 (S436). EVI1-WT (wild type), with S436 available for phosphorylation, but not EVI1-S436A, conferred haematopoietic progenitor cell self-renewal associated with significantly higher organised transcriptional patterns. In silico modelling of EVI1-S436 phosphorylation showed affinity reduction to CtBP1, and EVI1-WT showed reduced interaction with CtBP1 compared with EVI1-S463A. The target the motif harbouring S436 is targeted by CDK2 and CDK3 kinases, which both interacted with EVI1-WT. The methyltransferase DNMT3A bound preferentially to EVI1-WT compared to EVI1-S436A, and a hypo-methylated cell population associated with EVI1-WT expression is not maintained with EVI1-S436A. These data point to a role of the EVI1-S436 phosphorylation for directing functional protein interactions for haematopoietic self-renewal. Targeting EVI1-S436 phosphorylation may benefit therapy for EVI1-driven leukaemia.

overall_design: Poly-A RNA sequencing (RNAseq) analysis of Evi1-mediated modulation of gene expression RNA extracted from murine haematopoietic progenitor cells at 48 hrs after lentiviral transduction with Evi1-WT, Evi1-S436A or vector only and untransduced cells.

first: Stefan

last: Meyer


title: microRNA expression in breast cancer tumors from Chilean patients.

city: San Francisco

first: Valentina

last: Zavala

state: CA

address: 1560 3rd street Apt 201

institute: University of California San Francisco

summary:
We performed microRNA microarrays from total RNA extracted from 47 breast cancer tumors with known BRCA1 protein status to identify potential regulators of BRCA1 expression.
BRCA1 positive tumors ( H-score ≥50) were divided into two groups: “BRCA1 intermediate”, defined by an H-score between 50 and 90, both values included, and “BRCA1 positive”, including tumors with H-score above 90

overall_design: total RNA was extracted from breast cancer tumors and hibridized in the Agilents Human miRNA Microarray Release 14.0, 8 x 15K platform.


title: Melanocyte precursors in the hair follicle bulge of repigmented vitiligo skin are controlled by RHO-GTPase, KCTD10 and CTNNB1 signaling

city: Aurora

first: Stanca

last: Birlea

state: CO

department: Dermatology

institute: University of Colorado, Anschutz Medical Campus

summary:
In repigmentation of human vitiligo, the melanocyte (MC) precursors in the hair follicle (HF) bulge proliferate, migrate and differentiate to repopulate the depigmented epidermis. Here we present a comprehensive characterization of pathways and signals in the bulge that control the repigmentation process.
Using biopsies from vitiligo patients we have selectively harvested, by laser capture microdissection, MC and keratinocyte precursors from the HF bulge of untreated vitiligo skin and vitiligo skin treated with Narrow Band UVB (NBUVB). The captured material was subjected to whole transcriptome RNA sequencing. With this strategy, we found that repigmentation in the bulge MCs precursors is driven by KCTD10, a signal with unknown roles in the skin, and by CTNNB1 (encoding β-catenin) and RHO-GTPase (RHO), two signaling pathways previously shown to be involved in pigmentation biology.

overall_design: 1)Gene expression profiles of hair follicle bulge melanocyte precursor samples (MCBG) from 6 vitiligo patients undergoing active NBUVB treatment were compared to gene expression profiles of hair follicle bulge melanocyte precursor samples (MCBG) from 6 untreated vitiligo patients; 2)Gene expression profiles of hair follicle bulge outer root sheath keratinocyte samples (KCBG) from 6 vitiligo patients undergoing active NBUVB treatment were compared to gene expression profiles of hair follicle bulge outer root sheath keratinocyte samples (KCBG) from 6 untreated vitiligo patients. Both comparisons utilized F-LCM on full-thickness skin biopsies.  100 captured cells were pooled for each sample, RNA was extracted, amplified, and subjected to whole transcriptome RNA-Seq.

first: Nathaniel

middle: B

last: Goldstein


title: Characterization of Mutational Status, Spheroid Formation, and Drug Response of a New Genomically-Stable Human Ovarian Clear Cell Carcinoma Cell Line, 105C

first: Gabriel

last: DiMattia

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

overall_design: Refer to individual Series


title: A human cell atlas of fetal chromatin accessibility

city: Seattle

first: Silvia

last: Domcke

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: We devised an improved assay for single cell profiling of chromatin accessibility with three-level combinatorial indexing (sci-ATAC-seq3). We applied this method to 53 fetal tissue samples representing 15 organs, altogether profiling approximately one million single cells. We leveraged cell types defined by gene expression in the same organs to annotate these data, and built a catalog of hundreds-of-thousands of candidate gene regulatory elements exhibiting cell type-specific accessibility. Our analyses focus on the properties of lineage-specific transcription factors, organ-specific specializations of broadly distributed cell types, and cell type-specific enrichments of complex trait heritability. Additional data formats are available at atlas.brotmanbaty.org.

overall_design:
We profiled single cell chromatin accessibility in 53 human fetal samples (estimated gestational age 89-125d) spanning 15 organs. In total, we collected data on 1.6M individual cells, which were filtered down to ~800,000 cells after quality control.

Please note that the downstream analyses were carried out on combined tissues/samples, which resulted in matrices of peak, cell metadata, motif enrichments, cell type specificity and cicero scores for the full dataset (included in the records as  Series supplementary files).

The raw data is to be made available through dbGaP (controlled access; phs002003.v1.p1):
https://www.ncbi.nlm.nih.gov/gap/?term=phs002003

first: Andrew

last: Hill

first: Riza

middle: M

last: Daza

first: Darren

last: Cusanovich

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: FVSTUA is a Key Regulator of Sporulation, Toxin Synthesis and Virulence in Fusarium verticillioides

city: Athens

first: Anthony

middle: E.

last: Glenn

state: GA

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

summary: Fusarium verticillioides is one of the most important pathogens of maize, causing rots and producing fumonisin mycotoxins during infection. Ingestion of fumonisin-contaminated corn causes underperformance and even fatal toxicity in livestock and is associated with neural tube birth defects, growth stunting in children and some cancers. StuA, an APSES class transcription factor, is commonly a major developmental transcriptional regulator in fungi. It has been shown to regulate crucial developmental processes, such as sporulation, virulence and mycotoxin synthesis among others. In this study, the role of FvSTUA in F. verticillioides was examined by characterizing ∆FvstuA deletion mutants functionally and transcriptomally. The deletion mutants exhibited slower vegetative growth, stunted aerial hyphae and significant reductions in microconidiation. Macroconidiation and hydrophobicity of the deletion strains were reduced as well. Additionally, fumonisin production by and virulence of the deletion mutants were greatly reduced.  Transcriptomic analysis revealed downregulation of expression of several genes in the fumonisin and fusarin C biosynthetic clusters and differential expression of genes involved in conidiation and virulence. Nuclear localization of FvSTUA-tdTomato supported the likely function of FvSTUA as a transcription factor. Together, our results indicate that FvSTUA plays a global role in transcriptional regulation in F. verticillioides influencing morphogenesis, toxin production and virulence.

overall_design: RNA-Seq of WT Fv strain (Fusarium verticillioides M3125) and three ∆FvstuA strains, grown in GYAM medium, was performed to understand the influence of FvStuA on sporulation and virulence in Fv.

first: Manisha

last: Rath

first: Scott

last: Gold


title: Dual Targeting of G9a and DNMT1 for the Treatment of Experimental Cholangiocarcinoma

city: Pamplona

first: Maite

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

summary:
Cholangiocarcinogenesis involves epigenetic abnormalities of great relevance. Both the histone methyltransferase G9A and the DNA methyltransferase DNMT1 are overexpressed in this tumor. We used microarrays to evaluate the global programme of gene expression in the human CCA cell line EGI-1 treated with CM272. This molecule is an epigenetic inhibitor that simultaneously targets the methyltransferase activities of G9a and DNMT1.
EGI-1 cells treatment with CM272 (200nM) or vehicle (0.01% DMSO) for 48 hours.

overall_design: 4 samples

first: Matias

last: Avila

first: Leticia

last: Colyn


title: Characterization of Mutational Status, Spheroid Formation, and Drug Response of a New Genomically-Stable Human Ovarian Clear Cell Carcinoma Cell Line, 105C (Affymetrix)

city: London

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Ovarian clear cell carcinoma (OCCC) is a rare subtype of gynecological cancer for which well-characterized and authenticated model systems are scarce. We provide an extensive characterization of ‘105C’, a cell line generated from an adenocarcinoma of the clear cell histotype using targeted next-generation sequencing, cytogenetic microarrays, along with analyses of AKT/mTOR signaling. We report that that the 105C cell line is a bona fide OCCC cell line, carrying PIK3CA, PTEN, and ARID1A gene mutations, consistent with OCCC, yet maintain a stable genome as reflected by low copy number variation. Unlike KOC-7c, TOV-21G, and RMG-V OCCC lines also mutated for the above genes, the 105C cells do not carry mutations in mismatch repair genes. Importantly, we show that 105C cells exhibit greater resistance to mTOR inhibition and carboplatin treatment compared to 9 other OCCC cell lines in 3D spheroid cultures. This resistance may be attributed to 105C cells remaining dormant in suspension culture which surprisingly, contrasts with several other OCCC lines which continue to proliferate in long-term suspension culture. 105C cells survive xenotransplantation but do not proliferate and metastasize. Collectively, we show that the 105C OCCC cell line exhibits unique properties useful for the pre-clinical investigation of OCCC pathobiology.
Copy number variation was determined for multiple Ovarian Clear Cell Carcinomas

overall_design: DNA from various OCCCs was analyzed using cytoscanHD and copy number was determined using Chromosome Analysis Suite (Applied Biosystems/Thermo Fisher Scientific, version 4.0.0.385)

first: Bart

last: Kolendowski

first: Yudith

last: Ramos-Valdes

first: Hal

last: Hirte

first: Hiroaki

last: Itamochi

first: Wonjae

last: Lee

first: Mark

last: Carey

first: Trevor

last: Shepherd


title: Comparison of different shear stress conditions on gene proflile modulation in HCASMC and HCAEC, in the presence or absence of BVS+Everolimus

city: Pisa

first: Federico

last: Vozzi

state: Tuscany

address: Via Moruzzi 1

department: Institute of Clinical Physiology

country: Italy

institute: CNR

summary:
We have analyzed the global gene expression modulation induced by mechanical stress (shear stress) on vascular wall cells, seeded in the Ibidi system, with and without BVS+Drug. By the comparison of the different flow conditions we obtained a small panel of genes, mainly involved  in inflammation, angiogenesis, leukocyte migration, smooth muscle cell growth, thrombosis (BMP4, SELE, HMOX1, MEOX2, SEMA3E): all these genes will be integrated in an in-silico model for the evaluation of restenosis and thrombosis development after BVS deployment.
This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 777119

overall_design: Transcriptomic analysis of human coronary artery cells (endothelial and smooth muscle cells) subjected to physiological (20 dyne/cm2) and pathological (1 dyne/cm2) shear stress, in the presence or absence of drug-eluting Bioresorbable Vascular Scaffold (BVS) together with Everolimus (Drug, 600nM)

first: Vozzi

last: Federico

first: Manuela

last: Cabiati


title: Genomewide binding analysis reveals ANAC060 directly represses sugar induced ABI5 transcription in Arabidopsis

city: Shanghai

first: Bo

last: Yu

address: Fenglin Road 300

department: Institute of Plant Physiology & Ecology

institute: SIBS, CAS


title: Microarray-Based Gene Expression Analysis of WT and anac060

summary:
Purpose:  we performed transcriptome analysis of the wild type and anac060 mutant under glucose treatment to investigated the role of ANAC060 in glucose signalling.
Methods: Agilent Arabidopsis 3.0 Oligo Microarray kit which contained nearly 40,000 features representing 28,500 genes was use to investigate of transcriptome of wild type and anac060 mutant under glucose treatment and sorbitol control.
Results: By analyzing the transcriptome data, we found that ANAC060 attenuate the glucose signaling and that ANAC060 plays an important role in maintaining the Endogenous stable state of Arabidopsis thaliana in the glucose signaling pathway. The microarray analysis identified 8350 altered genes between different material and treatment combinations. Cluster analysis revealed that ANAC060 attenuates the sugar regulated gene expression.
Conclusions:  our results demonstrated that ANAC060 directly bind to the promoter of ABI5 and repressed the sugar induced transcription of ABI5, which contributed to render sugar insensitivity.

overall_design: transcriptome analysis of the 4-day wild type and anac060 mutant under glucose treatment

first: Yuejun

last: Wang

first: Yijing

last: Zhang

first: Sheng

last: Teng


title: Genomewide identification of ANAC060 binding targets

summary: In this study, genome-wide binding analysis of ANAC060 was undertaken through chromatin immunoprecipitation sequencing assays using the transgenic lines expressing functional ANAC060-GFP fusion protein in anac060 background. A total of 3282 genes were identified to associate with ANAC060 binding sites. The G-box binding motif was highly enriched in the ANAC060 binding peaks.

overall_design: Two grams of 10-d-old whole seedlings of 35S:ANAC060-GFP/anac060 transgenic line were used for ChIP assays.The wild type (Col) grown under the same conditions were used as the control. Polyclonal anti-GFP antibodies (Abcam, ab290) were used to immunoprecipitate the chromatin complexes. Sequencing libraries were constructed according to the Illumina’s instructions.


title: Loss of TDP-43 in astrocytes leads to motor deficits by triggering A1-like reactive phenotype and tri-glial dysfunctions

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

summary: The majority of patients with amyotrophic lateral sclerosis (ALS) have abnormal TDP-43 aggregates in the nucleus and/or cytosol of their surviving neurons and glia. Although accumulating evidence indicates that astroglial dysfunctions contribute to motor neuron degeneration in ALS, the normal physiological functions of TDP-43 in astrocytes are largely unknown and whether the loss of astroglial TDP-43 contributes to ALS remains to be clarified. Here, we showed that TDP-43 deleted astrocytes showed cell-autonomously enhanced GFAP immunoreactivity without affecting astrocyte or microglia proliferation. At the transcriptomic level, TDP-43 deleted astrocytes resemble the A1-reactive astrocytes and induce microglia to increase C1q expression. These astrocytic changes do not cause the loss of motor neurons in spinal cords or denervation at the neuromuscular junctions. In contrast, there was a selective reduction of mature oligodendrocytes, but not oligodendrocyte precursor cells, suggesting a tri-glial dysfunction mediated by TDP-43-deleted astrocytes. Mice with astroglial TDP-43 deletion developed motor, but not sensory, deficits. Taken together, our results demonstrate that TDP-43 is required to maintain the protective functions of astrocytes relevant to the development of motor deficits in mice.

overall_design: Differential gene expression analysis of spinal cord sections of 3-month old mice with TDP-43 deleted in astrocytes

first: Audrey

middle: Y

last: Peng

first: Ira

last: Agrawal

first: Wan

last: Ho

first: Yi-Chun

last: Yen

first: Emma

last: Sanford

first: Greg

last: Tucker-Kellogg


title: Targeting AGTR1/NF-κB /CXCR4 axis by miR-155 attenuates oncogenesis in Glioblastoma

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: MiR-155 show conserved binding on the 3’UTR of AGTR1, subsequently confirmed by AGTR1-3’UTR-luciferase reporter assay. To determine the pathways regulated by miR-155, we overexpressed miR-155 in SNB19 glioblastoma cells using pLemiR lentiviral constructs. pLemiR vector, with turbo RFP (Open Biosystems) was used as control. Furthermore, stable miR-155 overexpressing GBM cells show a decrease in AGTR1-mediated cell proliferation, invasion, foci formation, anchorage-independent growth, Epithelial to Mesenchymal Transition and stemness.

overall_design: Global expression profile of microRNA-155 overexpressing SNB19 glioblastoma cells were compared to control. Agilent two-color experiment,Organism: Human ,Agilent Whole Genome Human 8x60K (AMADID: 072363).

first: Anukriti

last: Singh

first: Nidhi

last: Srivastava

first: Bushra

last: Ateeq


title: Expression Profiles of miRNAs in Drug-Resistant Non-small Cell Lung Cancer Cell Lines Using Next Generation Sequencing

city: Zhengzhou

first: Xiangzhen

last: Kong

address: No.1 Jianshe road

institute: The First Affiliated Hospital of Zhengzhou University

summary: The expression profiles of miRNAs in drug-resistant non-small cell lung cancer (NSCLC) cell lines were identified via next generation sequencing and the common dysregulated miRNAs in drug-resistant NSCLC cell lines were picked up for further analysis.

overall_design: Examination of the expression profiles of miRNAs in two drug-resistant NSCLC cell lines and their parent cell lines.

first: Shousen

last: Hu


title: lncRNA expression profiles inin fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients

city: Wenzhou

first: Li

last: Sun

address: South Baixiang, Ouhai District

department: Department of Rheumatology and Immunology

institute: The first Affiliated Hospital of Wenzhou Medical University

summary: This study was to investigate the lncRNA expression profiles in synovium tissues of rheumatoid arthritis (RA) patients by RNA sequencing, and to evaluate the clinical values of dysregulated lncRNAs in RA diagnosis and monitoring.

overall_design: FLSs were isolated from synovial tissues and cutured until passage 4. Total RNA was extracted from FLSs with Trizol and subjected to sequencing.

first: Xiaoru

last: Xia


title: BMP7 Signaling in TGFb Receptor-2 deficient Stromal Cells Provokes Epithelial Carcinogenesis

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

summary: Mouse forestomach fibroblasts were isolated from a wild-type (wt), a FSP-Cre;TGFBR2 lox/lox (TGFBR2cKO) mouse, and a FSP-Cre;TGFBR2 lox/lox; Smad4 lox/lox (TGFBR2/SMAD4 cKO) mouse and expanded in vitro. The cells were then harvested and processed for RNA purification. While wt and TGFBR2/SMAD4 cKO mice are healthy, the TGFBR2cKO mouse presents with forestomach cancer.

overall_design: Three samples; RNA samples from 1) wt fibroblast cell line 2) TGFbR2 cKO fibroblast cell line and 3) TGFbR2 & SMAD4 cKO fibroblast cell line.

first: Raghu

last: Kalluri


title: Differentially expressed genes in Oesophageal tumours in Grhl3 cKO mice in comparison with WT mice

city: Clayton

first: Nicholas

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

summary: RNA Seq analysis was performed on tissue from tumours from five Grhl3 knock out mice and five wild type mice treated with 4-NQO to determine the effect of 4-NQO exposure to the oseophagus on tumour formation in the context of Grhl3 knockout. Tissue were excised and microdissected for RNA Seq analysis.

overall_design: Tissue from tumours from Five Grhl3 knock out mice and five wild type mice treated with 4-NQO

first: Smitha

last: Georgy

first: Nick


title: Sulfate assimilation in Clostridium thermocellum

city: Oak Ridge

first: Dawn

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: Investigation of sulfur metabolism in Clostridium thermocellum DSM 1313 ∆hpt, to determine growth and gene expression when the organism is incubated with either the oxidized (i.e., sulfate) or the reduced and assimilated (i.e., cysteine) forms of sulfur.  A sulfite reductase (∆hpt ∆SO3R) knockout mutant to limit sulfur assimilation was  created to compare the resulting gene expression patterns by RNAseq transciptomics against the parental strain (∆hpt) when both are grown in the presence of sulfate. Additionally, we bypass the sulfate auxotrophy of the mutant by providing assimilated sulfur in the form of cysteine to determine whether growth is restored to normal and whether methionine can be biosynthesized by yet uncharacterized pathways in this organism.

overall_design: Samples for RNA-seq were taken from mid-exponential phase (OD ~ 0.6) batch cultures grown in MTC on 5 g/l cellobiose. Control strain (∆hpt) and sulfite-reductase-mutant strain (∆hpt∆SO3R) were grown in the presence of either 5.7mM cysteine or 28.2mM sodium sulfate as the only sulfur source

first: Alex

last: Dumitrache

first: Steven

last: Brown

first: Miguel

last: Rodriquez Jr.


title: A tumor suppressive relationship between mineralocorticoid and retinoic receptors activates a transcriptional program consistent with a reverse Warburg effect in breast cancer

status: Public on Oct 31 2020

city: Westmead

first: Tram

middle: Bich

last: Doan

state: NSW

address: 176 Hawkesbury Rd

institute: Westmead Institute for Medical Research

summary: Whole transcriptome profiling in MR inducible MCF-7 cells after combinations of ligand treatments

overall_design: MR-inducible MCF-7 breast cancer cells were cultured with RPMI + 10% charcoal-stripped heat-inactivated fetal calf serum with or without Dox (1 μg/ml) for 48 h with daily media replacement. Cells were then treated for 6 h with the pure MR agonist, aldosterone (10 nM), all-trans retinoic acid (1 μM), 17β-estradiol (10 nM) or their combination. Samples were done in triplicates.

first: Colin

last: Clyne

first: Heidi

middle: N

last: Hilton

first: Natalie

last: Eriksson

first: Morag

last: Young

first: John

middle: W

last: Funder

first: George

last: Muscat

first: Peter

last: Fuller

first: Christine

middle: L

last: Clarke

first: J

last: Graham

first: Venessa

last: Cheung


title: Expression data from mouse heart tissue ischemia/reperfusion (I/R) treated for 0,24,48,72 hours

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Myocardial Ischemia-reperfusion injury is a serious clinical problem that lacks effective therapy.However, the precise mechanism leading to myocardial I/R injury  remains unclear.Our study defined the dynamic changes of the differentially expressed genes  related myocardial I/R injury, and provide basis for comprehensive understanding of the disease at molecular level.
We investigated schemia-reperfusion –mediated gene expression alteration associated with the development of cardiac injury by microarray in a mouse model.

overall_design: All mice were euthanized by an overdose of pentobarbital on hours 6, 24 and 72 of  ischemia/reperfusion (I/R) treated. Total RNA was isolated with TRIzol (Invitrogen) from heart organs (n=4 per group) at each time point according to manufacturer’s instructions. Gene expression profiling was performed using Affymetrix GeneChip mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA). On the GeneChip Mouse Genome 430 2.0 Array, over 45,000 probe sets analyze the expression level of over 39,000 transcripts and variants from over 34,000 well characterized mouse genes.

first: Yun-Long

last: Zhang

first: Hui-Hua

last: Li


title: Single-cell and bulk sequencing of endothelial cells of WT and APP/PS1 mice

city: Boston

first: Chengyu

last: Zou

address: 240 Longwood Ave

institute: Harvard medical school

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

overall_design: Refer to individual Series


title: Single-cell sequencing of endothelial cells of WT and APP/PS1 mice

summary: We isolated cerebral endothelial cells from 6-month-old WT and APP/PS1 mice and then performed In-Drop to do single cell sequencing.

overall_design: CD31+CD45- cells were isolated from brain homogenates.

first: Junying

last: Yuan


title: A low meal frequency improves 24h metabolic and gene expression profiles in subjects with impaired glucose tolerance (muscle)

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Meal frequency regulates postprandial glucose and insulin responses, which may affect substrate partitioning and thus weight control. This study investigated the effects of meal frequency on the metabolic and transcriptomic profiles in subjects with impaired glucose tolerance (IGT). Eleven IGT (2h glucose; 9.0±0.3mmol/L) men stayed 2x 36 hours in a respiration chamber to measure substrate partitioning. All subjects randomly received two isoenergetic diets with a low meal frequency (3x-LFr) or a high meal frequency (14x-HFr) consisting of 15 En% prot, 30 En% fat, and 55 En% carb. Total glucose output (AUC), carbohydrate oxidation and whole body RQ significantly decreased, and FFA levels increased in the LFr diet. The HFr diet resulted in an up-regulation in expression of genes involved in immune function and inflammation after 24h in PBMCs and muscle tissue. Expression of genes involved in PPAR signalling, OXPHOS, and glutathione metabolism were up-regulated in the HFr diet in muscle tissue only. In conclusion, the LFr diet improved the metabolic and transcriptomic profiles, and appetite control compared to the HFr diet. This suggests that a LFr diet might be an effective dietary strategy with anti-inflammatory characteristics to increase metabolic flexibility and body weight control in IGT subjects.

overall_design: In a randomized, 2-way crossover study, 11 men with impaired glucose tolerance stayed 2x 36 hours in a respiration chamber to measure the effect of meal frequency on substrate partitioning and gene expression in peripheral blood mononuclear cells (PBMCs) and muscle tissue. This entry contains the muscle expression data.

first: Marjet

last: Munsters

first: Mark

middle: V

last: Boekschoten

first: Guy

last: Vijgen

first: Lydia

last: Afman

first: Wim

last: Saris


title: A cookbook of DNase Hi-C

city: Novisibirsk

first: Veniamin

last: Fishman

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences

summary: Hi-C technique is widely used to study 3-dimensional chromatin architecture and assemble genomes. Conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in non-uniform genomic coverage. Using sequence-agnostic restriction enzymes such as DNAse I could overcome this limitation. Here we compared different DNAse Hi-C protocols and identified several critical steps which significantly impact protocol efficiency. We proposed a new robust protocol for preparation of DNAse Hi-C libraries, supplemented with experimental controls and computational pipeline for evaluation of libraries quality and data analysis.

overall_design:
DNase Hi-C (Ma. et. al 2018 this paper) assay in the peripheral blood of humans (7 samples), and in k562 cell line (1 sample). DNase Hi-C (Ma. et. al 2018 with non homologous blunt and bridge adapters) assay in the peripheral blood of humans (3 samples), and in k562 cell line (1 sample). DNase Hi-C (Ma. et. al 2018 with single long linker) assay in the peripheral blood of humans (1 sample), and in k562 cell line (1 sample). DNase Hi-C (Romani et al. with biotin-fillin) assay in the peripheral blood of humans (9 samples), and in k562 cell line (1 sample). DNase Hi-C (Romani et al. with single long linker) assay in the peripheral blood of humans (3 samples). DNase Hi-C (Romani et al. with Ma. et. al linker) assay in the peripheral blood of humans (1 sample).
We neither used data produced by Romani et al., nor we collaborated with Dr. Romani to produce our data. The aim of our study is to compare several protocols, and we used the protocol described in Romani et al.  paper. Thus, the title "Romani et al." here refers to the specific protocol used for samples preparation.
*** Submitter declares that they do not have permission to deposit the raw data (for samples s1-s4, s6-s11, s13-s29, s31-s32) due to patient privacy concerns.

first: Evgeniy

last: Mozheiko

first: Maria

last: Gridina


title: Role of Id1 and Id3 in breast cancer

city: Sydney

first: Daniel

last: Roden

address: 384 Victoria Street

institute: Garvan Institute


title: Transcriptomic profiling of 4T1 cells depleted for Id1/3 and Robo1

summary: Id1 and its closely related family member Id3 are expressed by a diversity of stem and progenitor cells. We show that Id1/3 are required for the self-renewal and proliferation of triple negative breast cancer (TNBC) cells both in vitro and in vivo. Furthermore, we identified that Id1/3 negatively regulates the tumour suppressor gene Robo1. Depletion of Robo1 could rescue the proliferative defect induced by Id1/3 knockdown. To understand the mechanisms by which Robo1 rescues cell proliferation in Id1/3 depleted cells, we performed RNA-Sequencing on 4T1 cells with Dox-inducible Id1/3 KD and/or Robo1 depletion using siRNA. We conclude that following Id1/3 knockdown, Robo1 is induced and exerts anti-proliferative effects via suppression of a Myc transcriptional program.

overall_design: mRNA sequencing of 4T1 cells with 4 treatment groups: Control (Non-targeting siRNA [NT]), Id1/3 knockdown (NT+Dox), Robo1 knockdown (siRobo1), and Id1/3 + Robo1 knockdown (siRobo1+Dox). Experiments were performed in quadruplicate.

first: Christina

last: Konrad

first: Holly

last: Holliday

first: Chia-Ling

last: Chan

first: Radhika

last: Nair

first: Alexander

last: Swarbrick


title: Genome-wide expression profiling of 4T1 cells to identify genes that are regulated by Id1 and Id3 in breast cancer

summary: By combining RNAi-mediated knockdown of Id1 and Id3 in an aggressive mouse breast cancer cell line (4T1 cells) with genome-wide expression profiling, we identified several new Id target genes and novel pathways regulated by Id.

overall_design: Gene expression profiling was performed on Control (C) and Id1 and Id3 depleted 4T1 cells. The gene expression profiles of four independent replicates (R1, R2, R3 and R4 ± doxycycline treatment) were compared by microarray analysis

first: Wee

middle: S

last: Teo


title: Dual DNA/protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia

first: Jonathan

middle: David

last: Lee

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC


title: The incorporation of extracellular vesicles from MSC into HSC increase their clonogenic capacity and engraftment ability

city: Salamanca

first: Silvia

last: Preciado

state: Salamanca

address: Campus Universitario Miguel de Unamuno

institute: Cancer Research Institute of Salamanca

summary: Treatment of graft failure after allogeneic stem cell transplantation with mesenchymal stromal cells (MSC) is being evaluated clinically. MSC can exert their functions by the release of extracellular vesicles (EV). Our aim is to analyze changes induced in hematopoietic stem cells (HSC) after the incorporation of MSC-EV. MSC were isolated from healthy donors. MSC-EV were isolated by ultracentrifugation and characterized by flow cytometry (FC), Western-blot, electron microscopy and Nanosight. EV incorporation into HSC was analyzed by FC and confocal microscopy. To study HSC gene expression, RT-PCR and arrays were performed. Apoptosis and cell cycle were evaluated by FC and clonal growth by clonogenic assays in methylcellulose. The engraftment capacity of HSC was analyzed four weeks after transplantation in NOD-SCID mice. Our results showed that MSC-EV presented the characteristic morphology, size and inmunophenotype and were able to be incorporated into HSC. MSC-EV incorporation induced an a down-regulation of pro-apoptotic genes, an overexpression of genes involved in colony formation and cell proliferation together with an activation of the JAK-STAT pathway in HSC. A significant decrease in apoptosis (p=0.001), an increase of the percentage of cells in phase S and an increased CD44 expression (p=0.013) were confirmed by FC in HSC with MSC-EV. In addition, these HSC displayed a higher CFU-GM clonogenic potential (p=0.010). Finally, in the xenotransplantation model, the engraftment ability of human HSC with MSC-EV was significantly higher (p= 0.027). In summary, the incorporation of MSC-EV induces genomic and functional changes in HSC, increasing their clonogenic capacity and their engraftment ability.

overall_design: To allow the incorporation of MSC-EV into human CD34+ cells, 2x105 CD34+ cells were co-cultured with MSC-EV for 24 hours in 500μl RPMI. For each co-culture EV obtained from 3x106 MSC (6 flask of 75cm2 at 60% confluence) were used.

first: Sandra

last: Muntión

first: Luis

middle: A

last: Corchete

first: Teresa

last: Ramos

first: Ana

last: Gómez de la Torre

first: Lika

last: Osugui

last: Rico

first: Natalia

last: Espinosa

first: María

last: Díez-Campelo

first: Consuelo

last: del Cañizo

first: Fermín

last: Sánchez-Guijo


title: Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription

city: Boulder

first: Dylan

last: Taatjes

address: 3415 Colorado Ave

institute: CU Boulder

summary: CDK7 associates with the 10-subunit TFIIH complex and regulates transcription by phosphorylating the C-terminal domain (CTD) of RNA polymerase II (RNAPII).  Few additional CDK7 substrates are known.  Here, using the covalent inhibitor SY-351 and quantitative phosphoproteomics, we identified CDK7 kinase substrates in human cells.  Among hundreds of high-confidence targets, the vast majority are unique to CDK7 (i.e. distinct from other transcription-associated kinases), with a subset that suggest novel cellular functions.  Transcription-associated factors were predominant CDK7 substrates, including SF3B1, U2AF2, and other splicing components.  Accordingly, widespread and diverse splicing defects, such as alternative exon inclusion and intron retention, were characterized in CDK7-inhibited cells.  Combined with biochemical assays, we establish that CDK7 directly activates other transcription-associated kinases CDK9, CDK12, and CDK13, invoking a “master regulator” role in transcription.  We further demonstrate that TFIIH restricts CDK7 kinase function to the RNAPII CTD, whereas other substrates (e.g. SPT5, SF3B1) are phosphorylated by the 3-subunit CDK-activating kinase (CAK; CCNH, MAT1, CDK7).  These results suggest new models for CDK7 function in transcription and implicate CAK dissociation from TFIIH as essential for kinase activation.  This straightforward regulatory strategy ensures CDK7 activation is spatially and temporally linked to transcription, and may apply toward other transcription-associated kinases.

overall_design: Examination of the role of CDK7 in transcriptional regulation with a focus on splicing and termination defects in addition to overall differential gene expression through deep RNA sequencing in HL60 cells where CDK7 is inhibited vs. control.

first: Jenna

middle: K

last: Rimel

first: Zachary

last: Poss

first: Benjamin

last: Erickson

last: Maas


title: Immunological properties of retinal ganglion cells derived from human induced pluripotent cells

city: Kobe

first: Ayaka

last: Edo

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Laboratory for Retinal Regeneration

institute: RIKEN Center for Biosystems Dynamics Research

summary: In recent years, research has been conducted to develop retinal ganglion cells (RGCs) transplantation therapies. Although rejection is one of the problems with transplantation therapy, the immunological properties of RGCs have not been clarified. We successfully induced RGCs from human induced pluripotent stem cells (iPSCs). We examined the gene expression patterns of iPS-RGCs using iPSC (a same donor) and peripheral mononuclear blood cells (PBMCs: a same donor) as a control.

overall_design: We induced RGCs from human iPSCs according to the previously described method with some modifications. We extracted RNA from iPS-RGCs (n=1), iPSCs (n=1), and PBMCs (n=1).


title: Gene expression profiles of LAG-3 positive and negative regulatory T cells in human healthy donors

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Regulatory T cells (Tregs) are known to exert a critical role in self tolerance. This subset of cells is also implicated in immune evasion mechanisms operated by cancer cells. In humans, it is known that Tregs are a heterogeneous population that includes different subsets of T cells with different phenotype, differentiation state and presumably exerting their suppressor activity with different modalities. We have provided data showing that a subset of human CD4+ Tregs (CD25hiFoxp3+) expressing the Lymphocytes Activation Gene 3 (LAG-3) molecule is amplified in melanoma invaded lymph nodes as compared with their tumor free counterpart, and these cells are endowed with enhanced suppressive functions (Camisaschi et al., J Immunol 2010). To gain insights into the phenotype, functional features and specificity of this population of Tregs expressing LAG-3, we performed microarrays to obtain gene expression profiles of LAG-3+ and LAG-3- Tregs.

overall_design: Tregs were purified from healthy donor PBMCs by immunomagnetic cell separation at a ≥ 96% purity and expanded in vitro according to a previous protocol (Camisaschi et al., J Immunol 2010). After 10 days of in vitro activation, cells were stained with anti-LAG-3 mAb (Clone 17b4; Apothech) and sorted using a FACSAria (BD Biosciences). From each healthy donor PBMCs we obtained 2 independent preparations of Tregs, with a total of 11 couples of LAG-3+ and LAG-3- Tregs analyzable. Total RNA was extracted with Agencourt RNA advance cell V2 system (Beckman Coulter), which allows the high recovery of pure RNA from few cells. Isolated RNA was quantified with Nanodrop (ThermoScientific) and its quality analyzed using the Agilent 2100 bioanalyzer for the RNA integrity Number (RIN) calculation. Gene expression profiles were then generated using Illumina HumanHT12_v4 WG-DASL (Illumina).

first: C

last: Camisaschi

first: L

last: Castelli


title: Gene expression profiles of melanoma tumor samples from patients treated with checkpoint inhibitors (mouse)

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

summary:
Checkpoint inhibitors have improved outcomes for patients with metastatic melanoma, but primary or acquired resistance often occurs. We used the mouse melanoma cell line B16, originally derived from C57BL6 mice, to model changes in tumor cell gene expression that occur with acquired resistance to checkpoint inhibitors. B16 cells used were engineered to express the fluorescent marker tdTomato, to assist monitoring and cell sorting.
Previously-untreated B16 cells (F0) were inoculated into C57BL6 mice, followed by treatment with triple-checkpoint inhibitor therapy (3I) with combined antibodies to CTLA4, PD-1, and PD-L1. Tumors that emerged despite immune selection pressure were harvested, grown again in vitro as a cell line, and then re-inoculated into a new generation of mice. This was repeated for 4 generations (F4) until inoculations were 100% successful at generating immune-resistant tumors.

overall_design: F0 or F4 B16 cells, obtained from in vitro culture, were inoculated into C57BL6 mice and tumors allowed to form. Mice received 3 doses of 3I. Tumors were harvested when they reached 100-400 mm3 in size, pooled from 3 mice per replicate, disaggregated into single-cell suspensions, and sorted into tumor (tdTomato-positive) and microenvironment (tdTomato-negative) fractions.

first: Ashvin

last: Jaiswal

first: R

last: Davis

first: Jennifer

last: Wargo

first: Michael

last: Curran


title: Gene expression profiles of melanoma tumor samples from patients treated with checkpoint inhibitors (human)

summary: Tumor samples were obtained from patients with metastatic melanoma before treatment with checkpoint inhibitors.


title: Gene expression profiles of melanoma tumor samples from patients treated with checkpoint inhibitors

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Single clonal glandular stem cells derived from human parotid glands do not attain malignant phenotype during long-term in vitro culture

status: Public on Oct 30 2020

city: Gwangjin-gu

first: junghwa

last: Moon

state: Seoul

address: 120 Neungdong-ro

institute: Konkuk university

summary: we compared transcriptome expression levels between adipose MSC and hpGSC using RNA-sequence analysis, resulting that 17,703 genes (68.8%) were similarly expressed, but 3635 genes (14.1%) and 4,399 genes (17.1%) were elevated in MSC and hpGSC, respectively

first: Young

middle: C

last: Lim


title: Genome-wide maps of chromatin state in renin cells [ATAC-Seq]

city: Charlottesville

first: Maria

middle: Florencia

last: Martinez

address: 409 Lane Rd. Rm 2006

institute: University of Virginia

summary: ATAC-seq was performed to identify open chromatin regions in juxtaglomerular cells, cells isolated from acutely and chronically recruited mice and in As4.1 cells

overall_design: Examination of H3K27ac

middle: F


title: Single cell RNA sequencing redefines the mesenchymal cell landscape of mouse endometrium [bulkRNAseq]

city: Edinburgh

first: Philippa

middle: TK

last: Saunders

address: 47 Little France Crescent

department: College of Medicine and Veterinary Medicine

institute: The University of Edinburgh

summary: The goal of this study was to generate an NGS-derived transcriptome profile (RNA-seq) for a population of perivascular mesenchymal cells from healthy cycling Pdgfrb-BAC-eGFP mouse uterus.  Bulk RNAseq revealed cells in the perivascular niche which express high levels of Pdgfrb (GFPhigh) also express genes previously identified in pericytes and/or vascular smooth muscle cells including Acta2, Myh11, Olfr78, Cspg4, Rgs4, Rgs5, Kcnj8 and Abcc9. Our work uncovers novel target genes for perivascular cell populations in mouse endometrium providing a platform to understand the role of these cells in endometrial physiology and disease.

overall_design: We present NGS mRNA profiles of mesenchymal cells isolated from the uteri of 12 healthy cycling mice. Pdgfrb+/GFP+ mesenchymal cells can be separated into GFPhigh perivascular cells and GFPlow stromal fibroblasts. The transcriptomic profile for GFPhigh cells was inferred by comparing GFPtotal cells (GFPhigh+GFPlow, termed Naive(N)) with GFPlow cells (termed Stromal (S)).

first: Phoebe

last: Kirkwood

first: Douglas

last: Gibson

first: Jamie

middle: R

last: Smith

first: John

last: Wilson-Kanamori

first: Olympia

last: Kelepouri

first: Arantza

middle: E

last: Zufiaurre

first: Ross

last: Dobie

first: Neil

last: Henderson

middle: T


title: Genome-wide maps of chromatin state in renin cells


title: Spatial transcriptome of FFPE sample by DBiT-seq

city: New Haven

first: Yang

last: Liu

state: CT

address: 300 George St., Room 8300C 8th floor

department: Pathology

institute: Yale University

summary: Here, we show that DBiT-seq (Deterministic barcoding in tissue) can be applied to FFPE samples, providing quality transcriptome information. We first studied the E10.5 mouse embryo tissue section with a 25 µm pixel size chip and identified all the major anatomical structures. Then, we analyzed the three major components of mouse heart and circulatory system: aorta, atrium, and ventricle.  Results show that major cell types in all above tissue types can be identified after integration with published scRNA-seq reference data.

overall_design: Spatial transcriptome of FFPE sample, including mosue embryo E10.5, adult mouse aorta, artrium and ventricle

first: Fan

last: Rong

first: Liu

last: Yang


title: Genome-wide maps of chromatin state in renin cells [ChIP-Seq]

summary: We generated genome-wide chromatin-state maps of mouse renin cells:  chronically recruited cells  and As4.1 cell line. We found that H3K27ac can discriminate a set of regulatory regions unique for the renin cells.

overall_design: Examination of H3K27ac, Med1 and Pol II


title: Dynamic epigenetic and transcriptional changes drive cellular plasticity in the liver

city: Philadelphia

first: Ben

middle: Z.

last: Stanger

state: PA

address: 421 Curie Boulevard

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Following liver injury, a subset of hepatocytes adopt features of biliary epithelial cells (BECs) in a process known as biliary reprogramming. The aim of this study is to elucidate the molecular events accompanying this dramatic shift in cellular identity.

overall_design: We treated RosaYFP mice (injected with AAV8-TBG-Cre to lineage label hepatocytes) with DDC to induce hepatocyte-to-biliary reprogramming, then isolated Cd45-/Cd31-/Cd11b- living cells by flow sorting. Samples were either sorted from remaining cells (bulk), which include YFP+ and YFP- cells, or by sorting for YFP+ lineage-labeled hepatocyte-derived cells (YFP). In addition, we examined the role of TGF? signaling by profiling cells undergoing reprogramming in mice with hepatocyte-specific deletion in the downstream TGF? signaling component Smad4.

first: Allyson

middle: J

last: Merrell

first: Tao

last: Peng

first: Jinyang

last: Li


title: Leptin Receptor, a Surface Marker for a Subset of Highly Engrafting Long-term Functional Hematopoietic Stem Cells

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: The hematopoietic system is sustained by a rare population of hematopoietic stem cells (HSCs), which emerge during early fetal development and then reside in the hypoxic niche of the adult bone marrow microenvironment. Although leptin receptor (Lepr)-expressing stromal cells are well-studied as critical regulators of murine hematopoiesis, the biological implications of Lepr expression on HSCs remain largely unexplored. We hypothesized that Lepr+HSCs are functionally different from other HSCs. Using in vitro and in vivo experimental approaches, we demonstrated that Lepr further differentiates SLAM HSCs into two distinct populations; Lepr+HSCs engrafted significantly higher than Lepr-HSCs and self-renewed more extensively as noted in secondary transplants. To determine how molecular pathways and gene expression profiles affect their functional differences, we performed bulk RNA-sequencing on purified Lepr+HSC/MPP and Lepr-HSC/MPP cells. Our results showed that Lepr+HSCs were characterized by a proinflammatory transcriptomic profile enriched for Type-I Interferon and Interferon-gamma (IFN-γ) response pathways, which are known to be critical for the emergence of HSCs in fetal life. Gene set analyses indicated that Lepr+HSCs were more highly enriched for genes associated with long-term HSCs whereas Lepr-HSCs’ expression profiles were more closely related to progenitors.  We conclude that although Lepr+HSCs represent a minor subset of HSCs, they are highly engrafting cells that possess embryonic-like transcriptomic characteristics, and that Lepr can serve as a useful marker for functional long term HSCs, which may have potential clinical applicability.

overall_design: BM cells were collected in ice-cold MACS buffer by crushing spines, pelvis, femurs and tibias from two mice for each replicate (n = 5 replicates). The cells were partially lineage depleted using the direct mouse lineage cell depletion kit (Miltenyi Biotec). Cells were stained for surface markers on ice for 20 min with the following antibodies: APC-mouse lineage cocktail (CD3e, CD11b, CD45R/B220, Ly-76, Ly-6G and Ly-6C; BD Biosciences), PE/Dazzle 594-anti-Ly6A/E (also known as Sca-1; clone D7; Biolegend), APC/Cyanine7-anti-CD117 (also known as c-kit; clone 2B8; Biolegend), BV421 Rat anti-mouse CD150 (clone Q38-480) , FITC-anti-CD48 (clone HM48-1; Biolegend), anti-Lepr-biotin antibody (R&D systems, BAF497, 0.2 ug per one million cells), washed in PBS, then incubated with secondary biotin-conjugated streptavidin-PE/Cy7 for another 20 minutes on ice (Biolegend, 1:500) and washed in PBS. Cells were sorted on the FACSAria or SORP Aria sorters for Lepr+ or Lepr- SLAM-HSC (LSKCD150+CD48-) and SLAM-MPP (LSKCD150-CD48-) directly into 350 uL 2-beta mercaptoethanol containing RLT Plus lysis buffer, and RNA was extract immediately after sorting using Qiagen RNeasy Plus Micro Kit. Non-stranded cDNA libraries were generated by the Indiana University School of Medicine Medical Genomics core and sequenced on a NovaSeq6000 flow cell for paired end sequencing. Data were analyzed for differential expression based on cell type and Lepr status.

first: Hal

last: Broxmeyer

first: Thao

last: Trinh


title: Epigenomic of the stress response in the European sea bass

city: Montpellier

first: Selim

last: Ben Chehida

address: 1093-1317 Route de Mende

institute: Institut des Sciences de l'Evolution de Montpellier

type: Methylation profiling by high throughput sequencing

summary: Understanding the molecular basis of stress is crucial in biology and of long standing interest in fish science. We tackled this question by modifying the epiGBS (epiGenotyping By sequencing) technique to screen for cytosine methylation and explore the genome-wide epigenomic response to a three months repeated acute stress challenge in the European sea bass (Dicentrarchus labrax). Following a minimally invasive sampling using nucleated red blood cells (RBCs), our modified epiGBS protocol retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% for unique best hits. Sequencing reads were shown to map across all linkage groups (LGs) of sea bass. A total of 47,983 CpG coordinates with a minimum 30X read depth was retained for differential methylation analysis between pre- and post-stress fish. A strong family effect was demonstrated, and fifty-seven distinct differentially methylated cytosines (DMCs) distributed on 17 of 24 LGs were found between RBCs of pre- and post-stress individuals. Twelve of them were located in intergenic regions, one in a repeated element; and forty four in gene bodies. Overall, DMCs were found inside or in the vicinity of 51 distinct genes shown previously to be related to stress. Thirty-eight of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences.

overall_design: 74 samples of sea bass (paired-end sequencing) analyzed with epiGBS

first: Madoka

last: Krick

first: Erick

last: Desmarais

first: Bruno

last: Guinand


title: A low meal frequency improves 24h metabolic and gene expression profiles in subjects with impaired glucose tolerance (PBMC)

first: Guido

last: Hooiveld

summary: Meal frequency regulates postprandial glucose and insulin responses, which may affect substrate partitioning and thus weight control. This study investigated the effects of meal frequency on the metabolic and transcriptomic profiles in subjects with impaired glucose tolerance (IGT). Eleven IGT (2h glucose; 9.0±0.3mmol/L) men stayed 2x 36 hours in a respiration chamber to measure substrate partitioning. All subjects randomly received two isoenergetic diets with a low meal frequency (3x-LFr) or a high meal frequency (14x-HFr) consisting of 15 En% prot, 30 En% fat, and 55 En% carb. Total glucose output (AUC), carbohydrate oxidation and whole body RQ significantly decreased, and FFA levels increased in the LFr diet. The HFr diet resulted in an up-regulation in expression of genes involved in immune function and inflammation after 24h in PBMCs and muscle tissue. Expression of genes involved in PPAR signalling, OXPHOS, and glutathione metabolism were up-regulated in the HFr diet in muscle tissue only. In conclusion, the LFr diet improved the metabolic and transcriptomic profiles, and appetite control compared to the HFr diet. This suggests that a LFr diet might be an effective dietary strategy with anti-inflammatory characteristics to increase metabolic flexibility and body weight control in IGT subjects.

overall_design: In a randomized, 2-way crossover study, 11 men with impaired glucose tolerance stayed 2x 36 hours in a respiration chamber to measure the effect of meal frequency on substrate partitioning and gene expression in peripheral blood mononuclear cells (PBMCs) and muscle tissue. This entry contains the PBMC expression data.

first: Marjet

last: Munsters

first: Mark

last: Boekschoten

first: Guy

last: Vijgen

first: Lydia

last: Afman

first: Wim

middle: H

last: Saris


title: A low meal frequency improves 24h metabolic and gene expression profiles in subjects with impaired glucose tolerance

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

overall_design: Refer to individual Series


title: The effect of beta-glucan - induced trained immunity on the epigenetic profile of bone marrow granulocyte-macrophage progenitors (GMP) and neutrophils

city: Dresden

first: Triantafyllos

last: Chavakis

address: Fiedlerstraße 42

department: Klinische Pathobiochemie

institute: Medizinische Fakultät der TU Dresden

summary: Induction of trained immunity by beta-glucan affects myeloid cells and their bone marrow progenitors. In particular, broad epigenetic alterations in  trained myeloid cells have been demonstrated.  In this study, we performed single cell ATAC sequencing in GMP and neutrophils from beta-glucan treated mice, as compared to control-treated mice, in order to investigate the impact of trained immunity on the epigenetic profile of GMP and neutrophils.

overall_design: WT mice were treated with a single dose of 1 mg of β-glucan from Trametes versicolor (Invivogen) in PBS or with PBS vehicle alone (control) and after seven days bone marrow GMP (Lin—c-Kit+Sca1—CD16/32+CD34+) and splenic neutrophils (CD11b+Ly6c-Ly6g+) were sorted and ATAC sequencing analysis was performed.

first: Ioannis

last: Kourtzelis

first: Panayotis

last: Verginis


title: Modulation of microRNA processing by 5-lipoxygenase

city: Frankfurt am Main

first: Marius

last: Kreiss

address: Max-von-Laue-Str. 9

department: Pharmaceutical Chemistry

institute: Goethe-University

summary: Here, we describe the modulation of miRNA processing as a novel noncanonical function of the 5-lipoxygenase (5-LO) enzyme in monocytic cells. In differentiated Mono Mac 6 (MM6) cells, we found an in situ interaction of 5-LO with Dicer, a key enzyme in miRNA biogenesis. RNA sequencing of small non-coding RNAs revealed a functional impact, knockout of 5-LO altered the expression profile of several miRNAs. Our observations suggest that 5-LO regulates the miRNA profile by modulating the Dicer-mediated processing of distinct pre-miRNAs. 5-LO inhibits the formation of let-7e which induces cell differentiation and promotes the generation of the oncomirs miR-99b and miR-125a which induce cell proliferation and the maintenance of leukemic stem cell functions.

overall_design: Small RNA profiling of differentiated Mono Mac 6 (ACC 124) wild type (WT) and 5-Lipoxygenase knockout (5-LO KO) cells

first: Stella

last: Uebbing

last: Kreiß

first: Frederike

last: Scholl

first: Ann-Kathrin

last: Häfner

first: Duran

last: Sürün

first: Ulrike

last: Garscha

first: Oliver

last: Werz

first: Devaraj

last: Basavarajappa

first: Bengt

last: Samuelsson

first: Olof

last: Rådmark

first: Beatrix

last: Suess

first: Dieter

last: Steinhilber


title: DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines

first: Alexandre

last: Duprey

address: 295 congress avenue

department: Microbial pathogenesis

institute: Yale university

summary: DNA supercoiling is essential for all living cells because it controls all processes involving DNA. In bacteria, global DNA supercoiling results from the opposing activities of topoisomerase I, which relaxes DNA, and DNA gyrase, which compacts DNA.  These enzymes are widely conserved, sharing >91% amino acid identity between the closely related species Escherichia coli and Salmonella enterica serovar Typhimurium. Why, then, do E. coli and Salmonella exhibit different DNA supercoiling when experiencing the same conditions? We now report that this surprising difference reflects disparate activation of their DNA gyrases by the polyamine spermidine and its precursor putrescine. In vitro, Salmonella DNA gyrase activity was sensitive to changes in putrescine concentration within the physiological range, whereas activity of the E. coli enzyme was not. In vivo, putrescine activated the Salmonella DNA gyrase and spermidine the E. coli enzyme. High extracellular Mg2+ decreased DNA supercoiling exclusively in Salmonella by reducing the putrescine concentration. Our results establish the basis for the differences in global DNA supercoiling between E. coli and Salmonella, define a signal transduction pathway regulating DNA supercoiling, and identify potential targets for antibacterial agents.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Comparison of gene expression of WT S. Typhimurium in minimal media at 800 μM Mg2+ or 10 mM Mg2, 2 replicates each.

first: Eduardo

last: Groisman


title: Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

summary: SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally-conserved coronavirus structural RNA elements have been identified to date. Here, we performed RNA structure probing to obtain single-base resolution secondary structure maps of the full SARS-CoV-2 coronavirus genome both in vitro and in living infected cells. Probing data recapitulate the previously described coronavirus RNA elements (5′ UTR and s2m), and reveal new structures. Of these, ∼10.2% show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. Secondary structure-restrained 3D modeling of these segments further allowed for the identification of putative druggable pockets. In addition, we identify a set of single-stranded segments in vivo, showing high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: SHAPE-MaP, DMS-MaPseq

first: Ilaria

last: Manfredonia

first: Chandran

last: Nithin

first: Almudena

last: Ponce-Salvatierra

first: Pritha

last: Ghosh

first: Tomasz

last: Wirecki

first: Tycho

last: Marinus

first: Natacha

last: Ogando

first: Eric

last: Snijder

first: Martijn

last: van Hemert

first: Janusz

middle: M

last: Bujnicki


title: The effect of beta-glucan - induced trained immunity on the transcriptomic profile of bone marrow granulocyte-macrophage progenitors (GMP) in tumor-bearing mice

first: Triantafyllos

last: Chavakis

summary: Induction of trained immunity by beta-glucan has been shown to promote transcriptomic alterations in myeloid cells. Progenitors in the bone marrow are also affected by trained immunity and also regulate anti-tumor immune responses . In this study, we performed RNA sequencing in GMP from tumor-bearing mice in order to investigate the impact of trained immunity on the transcriptomic profile of myeloid progenitors in the tumor setting.

overall_design: WT mice were pretreated with a single dose of 1 mg of β-glucan from Trametes versicolor (Invivogen) in PBS or with PBS vehicle alone (control) and were then injected subcutaneously with 3 x 105 B16-F10 melanoma cells into the right flank. Bone marrow GMP (Lin—c-Kit+Sca1—CD16/32+CD34+) were sorted 14 days after tumor cell injection and RNA sequencing analysis was performed.

first: Ioannis

last: Kourtzelis

first: Panayotis

last: Verginis


title: Adipose Mesenchymal Cells-Derived Extracellular Vesicles Alleviate DOCA-salt-Induced Hypertension by Promoting Cardio-Renal Protection

city: Padova

first: Federica

last: Collino

state: TO

address: via Ugo Bassi, 58/B

department: Department of Biomedical Sciences

institute: UNIPD

summary: By applying miRNA microarray profile of the kidney of DOCA-salt rats, we identified a selective miRNA signature associated with epithelial-mesenchymal transition (EMT)

overall_design: Renal cortex was isolated from DOCA-salt rats treated for 8-week with deoxycorticosterone acetate and high salt diet in the presence or not of EVs and compared with nephrectomized animals (UNX) and SHAM animals

first: Renata

last: Binato


title: Acute CD8+ T cell responses to viral infection harbor Tcf1-dependent stem-like cells that quantitatively yield central memory [RNA-seq]

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Central memory CD8+ T cells (TCM) can protect from secondary pathogen infection, from chronic infection and cancer as a result of their stem cell-like properties. However, the developmental origin of central memory cells and consequently the basis of their stemness have not been resolved. By monitoring the expression of the transcription factor Tcf1 (Tcf7), which is essential for central memory formation, we identified a small subset of CD8+ T cells present during the acute response to primary infection. These cells lacked cytotoxic effector function, resembled TCM both transcriptionally and epigenetically, had stem cell-like properties, and quantitatively yielded TCM. Stemness effector phase Tcf7+ CD8+ T cells depended on Tcf1 protein expression and on a set of Tcf1-dependent genes associated with adult stem cells. Stemness was thus not acquired subsequent to antigen clearance but was maintained in rare CD8+ T cells responding to acute infection and these cells quantitatively yielded TCM.

overall_design: Tcf7GFP P14 cells (either wild-type (Wt) or Tcf7-/- (Ko) (CD45.2+) were flow sorted from the spleen of naive mice based Tcf7GFPhi and CD62L+ (Naive). Naïve Tcf7GFPhi  P14 cells were transferred into B6 recipient mice  (CD45.1) prior to infection with LCMV Armstrong  (Arm). Tcf7GFPhi and Tcf7GFP-  P14 cells  were flow sortedfrom the spleen on day 8 or day 30 post infection using CD45.1- CD45.2+. Total RNA was extracted, cDNA libraries prepared and sequencing was performed using Illumina HiSeq 2500 technology.

first: Daniela

last: Pais Ferreira

first: Werner

last: Held


title: The effect of beta-glucan - induced trained immunity on the transcriptomic profile of tumor-associated neutrophils (TAN)

summary: Induction of trained immunity by beta-glucan has been shown to promote transcriptomic alterations in myeloid cells. Neutrophils are involved in the immune response against tumors and can promote or inhibit tumor growth. In this study, we performed RNA sequencing in TAN from mice in order to investigate the impact of trained immunity on the transcriptomic profile of neutrophils in the tumor setting.

overall_design: WT mice were pretreated with a single dose of 1 mg of β-glucan from Trametes versicolor (Invivogen) in PBS or with PBS vehicle alone (control). After 7 days, mice were injected subcutaneously with 3 x 105 B16-F10 melanoma cells into the right flank. Neutrophils (CD45+CD11c-CD11b+Ly6c-Ly6g+) that were infiltrated in the tumor were sorted 14 days after tumor cell injection and RNA sequencing analysis was performed.


title: The effect of beta-glucan - induced trained immunity on the transcriptomic profile of bone marrow granulocyte-macrophage progenitors (GMP)

summary: Induction of trained immunity by beta-glucan affects myeloid cells and their bone marrow progenitors. In particular, broad alterations in the transcriptome of  trained myeloid cells have been demonstrated.  In this study, we performed RNA sequencing in GMP from beta-glucan treated mice, as compared to control-treated mice, in order to investigate the impact of trained immunity on the transcriptomic profile of GMP.

overall_design: WT mice were treated with a single dose of 1 mg of β-glucan from Trametes versicolor (Invivogen) in PBS or with PBS vehicle alone (control) and after seven days bone marrow GMP (Lin—c-Kit+Sca1—CD16/32+CD34+) were sorted and RNA sequencing analysis was performed.


title: Cystic Fibrosis Keystone Species

city: San Diego

first: Cynthia

last: Silveira

state: CALIFORNIA

address: 5500 Campanile Dr, North Life Sciences 302

department: Biology

institute: San Diego State University

summary: This project shows that the use of antibiotics targeting gram-positive, anaerobic bacteria can improve patient's health by removing the main nutritional sources of classic pathogens. These antibiotics, traditionally not used in CF therapy, target anaerobes that efficiently degrade mucus providing metabolic products that feed and stimulate the expression of virulence factors in Pseudomonas. They work as keystone groups sustaining the stability of the entire microbial community, and their control drives a decrease in Pseudomonas abundance and virulence.

overall_design: 9 transcriptomes from longitudinal sampling of the same patient.


title: The effect of beta-glucan - induced trained immunity on the transcriptomic profile of tumor-associated monocytes

summary: Induction of trained immunity by beta-glucan has been shown to promote transcriptomic alterations in myeloid cells. Monocytes are involved in the immune responses against tumors. In this study, we performed RNA sequencing in tumor-infiltrated monocytes from mice in order to investigate the impact of trained immunity on the transcriptomic profile of monocytes in the tumor setting.

overall_design: WT mice were pretreated with a single dose of 1 mg of β-glucan from Trametes versicolor (Invivogen) in PBS or with PBS vehicle alone (control). After 7 days, mice were injected subcutaneously with 3 x 105 B16-F10 melanoma cells into the right flank. Monocytes (CD45+CD11c-CD11b+Ly6g-Ly6c+) that were infiltrated in the tumor were sorted 14 days after tumor cell injection and RNA sequencing analysis was performed.


title: DNA copy number alterations in neutron- or gamma-ray-induced rat mammary carcinomas

status: Public on Oct 29 2020

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

summary: To investigate DNA copy number changes in rat mammary carcinomas induced by neutron or gamma-ray irradiation.

overall_design: DNA copy number changes in neutron- or gamma-ray-induced rat mammary carcinomas were analyzed using array-CGH microarray.

last: Daino

first: Shizuko

last: Kakinuma