title: Akt inhibition with MK-2206 is associated with favorable immune profile changes within the tumor microenvironment of hormone receptor positive, HER2 negative breast cancer [PI3K panel]

city: Mineola

first: Douglas

last: Marks

address: 120 Mineola Boulevard

institute: NYU Langone Health

summary: Gene expression was assessed with Nanostring in the surgical specimens obtained from a Window of Opportunity trial with MK-2206 in early stage breast cancer. Tumor biopsies and surgical specimens were compared for patients who received MK-2206 along with a prospective untreated control group of patients. Greater expression of interferon related genes was seen in surgical specimens following MK-2206 and compared to untreated controls.

overall_design: In the study/data presented here, patients with early stage breast cancer were treated with MK-2206 for two doses in a Window of Opportunity trial. Patients had corrollary studies performed on their pretreatment and post-treatment (surgical excision) specimens to assess the effect of MK-2206 on both known direct targets of the PI3KCA/Akt pathway as well as tumor immune microenvironment. Enclosed here is the nanostring data from the PI3K panel analysis of the surgical specimens from patients treated with MK-2206 as well as surgical specimens from an untreated prospective control cohort.

first: Kevin

last: Kalinsky


title: Sequencing of mRNA with N6-methyladenosine (m6A) modification in AML cells upon ALKBH5 knockdown or overexpression

status: Public on May 26 2020

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

country: USA

institute: Beckman Research Institute of City of Hope

type: Expression profiling by high throughput sequencing

summary: To identify the potential mRNA targets of ALKBH5, we conducted m6A-seq with mRNA samples enriched from AML cells with ALKBH5 knockdown or overexpression

overall_design: AML cells (herein is NOMO1) were transduced  with lentivirus expressing shRNAs or ALKBH5 CDS, then selected with puromycin for 2 days. Polyadenylated RNAs (poly(A) RNAs) were extracted with FastTrack MAG Maxi mRNA isolation kit (Life technology) and randomly fragmented with RNA fragmentation reagents (Ambion). m6A antibody (Synaptic Systems) was used to immunoprecipitate m6A RNA. Final library preparation was constructed with TruSeq Stranded mRNA Sample Prep Kit (Illumina) and the library was quantified by BioAnalyzer High Sensitivity DNA chip. The m6A-seq was conducted on the Illumina HiSeq 2500.

first: Chao

last: Shen

first: Lei

last: Dong


title: Akt inhibition with MK-2206 is associated with favorable immune profile changes within the tumor microenvironment of hormone receptor positive, HER2 negative breast cancer

status: Public on May 25 2020

state: NY

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

overall_design: Refer to individual Series


title: RNA sequencing data of microglia isolated from brains of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice. {Reporter]

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

summary: RNA sequencing of FACS sorted microglia isolated from brain tissue of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice was performed to test for potential differences in gene expression caused by the knock-in of tdTomato and CreERT2 into the Hexb locus.

overall_design: Microglia were isolated from brain tissue and RNA expression levels between individual samples were compared.

first: Marco

last: Prinz

first: Takahiro

last: Masuda

first: Lukas

last: Amann


title: RNA sequencing data of microglia isolated from brains of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice.


title: DNA methylation changes induced by hypomethylating agent, Azacitidine (AZA); IDH1 inhibitor, BAY1436032 (BAY) and sequential and simultaneous combination of BAY and AZA in  in vitro treated human (CD45+) cells isolated from the  bone marrow of IDH1mut

city: Halle

first: Razif

last: Gabdoulline

state: Sachsen-Anhalt

address: Ernst-Grube-Straße 40

department: Innere Medizin IV Haematologie und Onkologie

institute: Universitätsklinikum Halle

type: Methylation profiling by genome tiling array

summary: Mutations in the enzymes IDH1 and IDH2 have been identified in a wide variety of tumors like glioma, chondrosarcoma, thyroid cancer, lymphoma, melanoma, and in acute myeloid leukemia. Mutated IDH1/2 produces the metabolite 2-hydroxyglutarate (2HG), which interferes with epigenetic regulation of gene expression, and thus may promote tumorigenesis.  Data for IDH1 inhibitors show that 30-40% of AML patients respond to monotherapy with a median duration of response of 8 months, suggesting that IDH1 inhibitors should be combined with other agents to improve efficacy. BAY 1436032 (BAY) is an oral pan-mutant IDH1 inhibitor currently undergoing phase 1 clinical trials. 5-Azacitidine (AZA) is a hypomethylating agent and can activate key epigenetically silenced pathways in AML cells, leading to an arrest of AML cell proliferation.

overall_design: Human AML cells isolated from  the spleen and bone marrow of IDH1 R132C (PDX1) mice were cultured in IMDM medium (Stemcell Technology Inc. Vancouver, Canada) supplemented with 10% FBS (Sigma-Aldrich, Munich, Germany), 2 mM L-Glutamine (Life Technologies, Karlsruhe, Germany), 1% Penicillin/Streptomycin (Gibco, ThermoFischer Scientific, Braunschweig, Germany) , 20 ng/ml human GMCSF, 20 ng/ml human GCSF, 20 ng/ml human IL6, 50 ng/μl, human SCF and 20 ng/μl human IL-3 (all from PeproTech, Hamburg, Germany) and were incubated at 37 °C with 5% CO2 in humidified atmosphere. Treatment was carried out with DMSO (vehicle), 500nm of azacitidine for day 1 to day 4, 50nm of BAY1436032 for day 1 to day 5, sequential combination (azacitidine for day 1 to day 4 and BAY1436032 for day 5 to day 9) and simultaneous combination (azacitidine for day 1 to day 4 and BAY1436032 for day 1 to day 5).  RNA was isolated on day 6 for cells treated with vehicle, azacitidine, BAY1436032 and simultaneous combination and on day 10 for sequential combination using AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions.

first: Anuhar

last: Chaturvedi

first: Michael

last: Heuser


title: Transcriptomics of BCR-stimulated IgG1 and IgG4 human B cell clones

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: We characterize the transcriptomic profile of a set of human IgG1 and IgG4-switched memory B cell clones

overall_design: mRNA profiles of human B cell clones were generated by deep sequencing

first: Willem

last: van de Veen

first: Mübeccel

last: Akdis


title: CCR7L-inducible lnc-Dpf3 restrains dendritic cell migration by inhibiting HIF1α-mediated glycolysis (lncRNA)

city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

country: China

institute: Zhejiang University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:  The purpose is to systemically identify long non-coding RNAs (lncRNAs) in CCR7 Ligands-stimulated mDCs
Methods: We profiled lncRNA seq in mDCs stimulated with or without CCR7 ligand CCL19 and CCL21.
Results: CCR7 stimulation induced profound lncRNAs expression in mDCs

overall_design: mDCs were stimulated with CCR7 ligand CCL19 and CCL21 (CCR7L) for 12 h or left unstimulated (Med), and then subjected to lncRNA seq.

first: Xuetao

last: Cao

first: Juan

last: Liu


title: CCR7L-inducible lnc-Dpf3 restrains dendritic cell migration by inhibiting HIF1α-mediated glycolysis (mRNA)

summary:
Purpose:  The purpose is to systemically identify RNA expression changes after lnc-Dpf3 knockdown in CCR7-stimulated mDCs
Methods: We profiled RNA seq in mDCs transfected with si-Lnc-Dpf3 or si-NC and stimulated with or without CCR7 ligand CCL19 and CCL21.
Results: CCR7 stimulation induced profound RNA expression changes in mDCs, and a set of genes were differentially expressed in lnc-Dpf3-knockdown DC

overall_design: mDCs were transfected with si-Lnc-Dpf3 or si-NC and stimulated with or without CCR7 ligand CCL19 and CCL21 (CCR7L) for 12 h or left unstimulated (Med), and then subjected to RNA seq


title: Akt inhibition with MK-2206 is associated with favorable immune profile changes within the tumor microenvironment of hormone receptor positive, HER2 negative breast cancer [IO360 panel]

first: Douglas

last: Marks

overall_design: In the study/data presented here, patients with early stage breast cancer were treated with MK-2206 for two doses in a Window of Opportunity trial. Patients had corrollary studies performed on their pretreatment and post-treatment (surgical excision) specimens to assess the effect of MK-2206 on both known direct targets of the PI3KCA/Akt pathway as well as tumor immune microenvironment. Enclosed here is the nanostring data from the IO360 panel analysis of the surgical specimens from patients treated with MK-2206 as well as surgical specimens from an untreated prospective control cohort.

first: Kevin

last: Kalinsky


title: Multimodal and multisensory coding in the Drosophila larval peripheral gustatory center

city: Fribourg

first: G. Larisa

last: Maier

address: Ch. du Musée 10

department: Department of Biology

institute: University of Fribourg

summary: The ability to evaluate food palatability is innate in all animals from insects to mammals, ensuring their survival. The external taste organ at the periphery in Drosophila larvae is composed of only few sensory neurons but displays discrimination between a wide range of chemicals as well as a high level of complexity in receptor expression and cell response profile. Taking advantage of this architecturally simple but functionally complex sensory system, we tackled dissection of taste coding at organ level with cellular resolution. We combined whole-organ calcium imaging and single-cell transcriptomics to map physiological properties and molecular features of individual sense neurons. In line with taste multimodality, about one third of gustatory sense neurons responded to multiple tastants. Reinforcing on the peripheral integration of signals, we observed neuronal deactivation events within simultaneous neighboring responses, submitting the probability of inter-cellular communication through electrical coupling. Furthermore, we identified neurons responding to both mechanical and taste stimulation, indicating potential multisensory integration. On a molecular level, chemosensory cells show heterogeneity in neuromodulator expression. In addition to a broad cholinergic profile, markers on dopaminergic, glutamatergic or neuropeptidergic pathways are present either in distinct cell populations or are seemingly co-expressed. Our data further extend the sensory capacity of the larval taste system showing a large degree of multimodal as well as multisensory coding principles.

overall_design: Fluorescently labelled sense organs were manually isolated and further treated enzymatically for single cell dissociation. We then completed DisCo workflow and generated cDNA libraries.

first: G

middle: L

first: Johannes

last: Bues

first: Marjan

last: Biočanin

first: Felix

last: Meyenhofer

first: Clarisse

last: Brunet Avalos

first: Jae

middle: Y

last: Kwon

first: Bart

last: Deplancke

first: Simon

middle: G

last: Sprecher


title: RNA sequencing data of microglia isolated from brains of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice. [Hexb-KO]

first: Ori

last: Staszewski

overall_design: Microglia were isolated from brain tissue  and RNA expression levels between individual samples were compared.

first: Marco

last: Prinz

first: Takahiro

last: Masuda

first: Lukas

last: Amann


title: Apolipoprotein E4 Expression Causes Gain of Toxic Function in Isogenic Human Induced Pluripotent Stem Cell-Derived Endothelial Cells

status: Public on May 24 2020

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

institute: Nestle Institute Of Health Sciences

summary:
Objective: The ApoE (apolipoprotein) allele epsilon 4 is a major genetic risk factor for Alzheimer disease, cardiovascular disorders, and stroke, indicating that it significantly impacts cerebral and vascular systems. However, very little is known about how APOE genotype affects brain endothelial cells, which form a network of tight junctions to regulate communication between the brain and circulating blood factors. Approach and Results: Here, we present a novel model of endothelial dysfunction using isogenic human induced pluripotent stem cell-derived cells harboring different alleles of the APOE gene, specifically ApoE 3/3, 3/4, and 4/4. We show for the first time that ApoE4 expression by endothelial cells is sufficient to cause a toxic gain of cellular dysfunction. Using RNAseq, we found significant effects of ApoE4 on signaling pathways involved in blood coagulation and barrier function. These changes were associated with altered cell function, including increased binding of platelets to ECs with the 3/4 or 4/4 genotype. ApoE4-positive cells exhibited a proinflammatory state and prothrombotic state, evidenced by higher secretion of Aβ (amyloid-β) 40 and 42, increased release of cytokines, and overexpression of the platelet-binding protein VWF (vonWillebrand factor). Immunohistochemistry of human brain Alzheimer disease brains also showed increased VWF expression with the ApoE4/4 genotype. Finally, pharmacological inhibition of inflammation in ECs by celastrol rescued overexpression of VWF in cells expressing ApoE4.
Conclusions: These cells provide novel insight into ApoE4-mediated endothelial dysfunction and provide a new platform to test potential therapies for vascular disorders.

overall_design: Comparison between 6 replicates of ApoE 4/4 iPSC-derived endothelial cell lines versus 6 replicates of ApoE 3/3 iPSC-derived endothelial cell lines

first: Claus

last: Rieker

first: Eugenia

last: Migliavacca

first: Angelique

last: Vaucher

first: Julien

last: Marquis

first: Aline

last: Charpagne

first: Amy

last: Pooler


title: The Serratia marcescens siderophore, serratiochelin, is necessary for full virulence during bloodstream infection

city: Ann Arbor

first: Danelle

middle: Rae

last: Weakland

state: MI

address: 1150 West Medical Center Dr.

department: Microbiology and Immunology

institute: University of Michigan Medical School

summary: Serratia marcescens is a bacterium frequently found in the environment, but over the last several decades it has evolved into a concerning clinical pathogen, causing fatal bacteremia. To establish such infections, pathogens require specific nutrients; one very limited but essential nutrient is iron. We sought to characterize the iron acquisition systems in S. marcescens isolate UMH9, which was recovered from a clinical bloodstream infection. Using RNA sequencing (RNA-seq), we identified two predicted siderophore gene clusters (cbs and sch) that were regulated by iron. Mutants were constructed to delete each iron acquisition locus individually and in conjunction, generating both single and double mutants for the putative siderophore systems. Mutants lacking the sch gene cluster lost their iron-chelating ability as quantified by the chrome azurol S (CAS) assay, whereas the cbs mutant retained wild-type activity. Mass spectrometry-based analysis identified the chelating siderophore to be serratiochelin, a siderophore previously identified in Serratia plymuthica. Serratiochelin-producing mutants also displayed a decreased growth rate under iron-limited conditions created by dipyridyl added to LB medium. Additionally, mutants lacking serratiochelin were significantly outcompeted during cochallenge with wild-type UMH9 in the kidneys and spleen after inoculation via the tail vein in a bacteremia mouse model. This result was further confirmed by an independent challenge, suggesting that serratiochelin is required for full S. marcescens pathogenesis in the bloodstream. Nine other clinical isolates have at least 90% protein identity to the UMH9 serratiochelin system; therefore, our results are broadly applicable to emerging clinical isolates of S. marcescens causing bacteremia.

overall_design: Examination of differential gene expression in Serratia marcescens under iron-replete and iron-depleted conditions

middle: R

first: Sara

middle: N

last: Smith

first: Bailey

last: Bell

first: Ashootosh

last: Tripathi

first: Harry

last: Mobley


title: Chromatin state maintains human myeloid leukemia by regulating m6A demethylase ALKBH5 expression [ATAC-seq]

status: Public on May 27 2020

city: Zhengzhou

first: Jiazhen

last: Wang

address: 156 Jinshui East Road

institute: Henan University of Chinese Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ALKBH5 is the RNA N(6)-methyladenosine (m6A) demethylase. To understhand the function and mechnism of ALKBH5 in human acute myeloid leukemia, we compared the translational efficiency in wild-type and ALKBH5-knock-down MOLM-13 cells.

overall_design: ATAC-seq in wild-type or KDM4C knock-down MOLM-13 cells

first: Yicun

last: Li

first: Peipei

first: Guoqiang

last: Han

first: Haojian

last: Zhang


title: A549 Human lung cell : Control vs transfected with E6E7 HPV16

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

summary: Transcriptional profiling of A549 lung cell transfected with E6E7 HPV-16 genes using pLXSN vector. Control cells were transfected with the empty pLXSN  vector

overall_design: Two-condition experiment, A549 E6E7 vs A549 V. Two dye-swap Cy3/Cy5 replicate per array.

first: Nelson

last: Peña

last: Urzúa

first: Francisco

last: Aguayo


title: RNA sequencing data of microglia isolated from brains of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice. [Cre]

first: Ori

last: Staszewski

first: Marco

last: Prinz

first: Takahiro

last: Masuda

first: Lukas

last: Amann


title: Clinical presentation and differential splicing of SRSF2, U2AF1 and SF3B1 mutations in patients with Acute Myeloid Leukemia

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

summary: Previous studies demonstrated that splicing factor mutations are recurrent events in hematopoietic malignancies with both clinical and functional implications. However, their aberrant splicing patterns in acute myeloid leukemia remain largely unexplored. In this study we characterized mutations in SRSF2, U2AF1 and SF3B1, the most commonly mutated splicing factors. In our clinical analysis of 2678 patients, splicing factor mutations showed inferior relapse-free and overall survival, however, these mutations did not represent independent prognostic markers. RNA-sequencing of 246 and independent validation in 177 patients revealed an isoform expression profile highly characteristic for each individual mutation, with several isoforms showing a strong dysregulation. By establishing a custom differential splice junction usage pipeline, we accurately detected aberrant splicing in splicing factor mutated samples. A large proportion of differentially used junctions were novel, including several junctions in leukemia associated genes. In SRSF2(P95H) mutants we further explored the possibility of a cascading effect through the dysregulation of the splicing pathway. Furthermore, we observed a validated impact on overall survival for two junctions overused in SRSF2(P95H) mutants. We conclude that splicing factor mutations do not represent independent prognostic markers. However, they do have genome-wide consequences on gene splicing leading to dysregulated isoform expression of several genes

overall_design:
The set consists of all patients with available material treated in the AMLCG-2008 study (NCT01382147, n=205) and additional 41 patients with resistant disease that were treated in the AMLG-1999 trial (NCT00266136).
Using the Sense mRNA Seq Library Prep Kit V2 (Lexogen; Vienna, Austria) samples underwent, strand-specific, paired-end 100 bp sequencing on a HiSeq 1500 instrument (Illumina; San Diego, CA, USA) to a targeted depth of 20 million mappable paired reads per sample.

*** Submitter states that German law does not allow raw data to be submitted for public access.

first: Stefanos

middle: A

last: Bamopoulos

first: Maria

middle: C

last: Sauerland

first: Dennis

last: Görlich

first: Wolfgang

middle: E

last: Berdel

first: Bernhard

middle: J

last: Woermann

first: Jan

last: Braess

last: Hiddemann

first: Karsten

last: Spiekermann

first: Klaus

middle: H

last: Metzeler


title: Time course XBP1s ChIP-Seq in Xbp1 flx/flx (WT, wild-type) mice and AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout) mice

city: Houston

first: Huan

last: Meng

state: Texas

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: We reported the hepatic XBP1s cistrome (starting at CT0 and proceeding every four hours for three complete 12-hour cycles) in the liver of wild-type mice and XBP1 liver-specific knockout mice; we also chose liver samples at CT0 and CT8 (four hours before the dusk 12-hour rhythmic peak) for comprehensive XBP1s ChIP-Seq to interrogate the genomic binding profiles of hepatic XBP1s in vivo.

overall_design: Livers were harvested at 4-hour interval for a total of 36 hours from the male Xbp1 flx/flx and AlbCre;Xbp1flx/flx mice under the condition of constant darkness.


title: MiRNA-seq in blood of myasthenia gravis (MG) patients responder and non-responder to immunosuppressive treatment

status: Public on May 23 2020

city: Milan

first: Paola

last: Cavalcante

address: Via Celoria 11

department: Neurology IV

country: Italy

institute: Fondazione IRCCS Istituto Neurologico Carlo Besta

summary:
Purpose: to identify specific miRNAs as biomarkers associated with immunosuppressive treatment response in MG patients.
Methods: Blood miRNome profiles of 15 responder and 15 non-responder MG patients by miRNA-seq  using Illumina NextSeq 500 sequencing. Raw data were de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software. FASTQ data were checked using the FastQC tool. After mapping the data and counting to relevant entries in miRBase 20 (http://www.mirbase.org/), the numbers of known microRNAs was calculated.For statistical analysis, along with TPM normalization, the trimmed mean of M-values (TMM) normalization method was used. Validation was perfomed using TaqMan Advanced real-time PCR on microRNA array cards.
Results: An average of 9.98 million reads was obtained per sample. We identified 41 statistically significant differentially expressed miRNAs (logFoldChange from +1.371 to -1.439, p < 0.05), including 18 miRNAs up-regulated and 23 miRNAs down-regulated in non-responder versus responder MG patients. 23 miRNAs were selected for validation. Among them, three miRNAs were significantly decreased in non-responder versus responder patients, whereas two showed an opposite trend.
Conclusions: We identified a blood miRNA signature associated with drug responsiveness in MG patients, that could represent a valuable tool for therapeutic follow-up in MG.

overall_design: MiRNome profiling in responder and non-responder MG patients by miRNA-seq using an Illumina's platform.

first: Carlo

last: Antozzi


title: Identifying new signaling mediators responsible for Mesothelin (MSLN) intraperitoneal (IP) tumor growth phenotype

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

summary: Identification of new targets involved in MSLN signaling by comparing mRNA expression patterns in MSLN WT and KO in both cells grown in culture and in IP tumor tissues using RNA deep sequencing

overall_design:
Compare and contrast tanscriptome of MSLN WT and KO cells grown in culture and IP tumors tissues using RNAseq
The parent KLM1 cell line was crispr edited to make the following cell lines Mock, KO#1 and KO#2. The KO lackMesothelin.  These same human-derived cell lines were put into nude mice to form intraperitoneal tumors.

first: Leela

last: Avula

first: Michael

last: Rudloff

first: Christine

last: Alewine

first: Xiongfong


title: Gene expression changes induced by hypomethylating agent, Azacitidine (AZA); IDH1 inhibitor, BAY1436032 (BAY) and sequential and simultaneous combination of BAY and AZA in  in vitro treated human (CD45+) cells isolated from the  bone marrow of IDH1mut

first: Razif

last: Gabdoulline

first: Anuhar

last: Chaturvedi

last: Heuser


title: DNA methylation and gene expression changes induced by hypomethylating agent, Azacitidine (AZA), BAY1436032 (BAY) and sequential and simultaneous combination of BAY and AZA in  in vitro treated human (CD45+) cells isolated from the bone marrow of IDH1mut

overall_design: Refer to individual Series


title: Elucidation of Ras homologous A: Systematic approach to identify potential signaling in gastric cancer

city: Incheon

first: Seungyoon

last: Nam

state: Incheon

address: Namdong-gu, Namdongdae-ro 774-21

country: South Korea

institute: Gachon University Colleage of Medicine

summary: Previously, we identified Ras homologous A (RHOA) as a major signalling hub in gastric cancer (GC), the third-most common cause of cancer death in the world, prompting us to rationally design an efficacious inhibitor of this oncogenic GTPase. Here, based on that previous work, we extend those computational analyses, and in silico modeling approaches, to further pharmacologically optimize anti-RHOA hydrazide derivatives for greater anti-GC potency. Two of these, JK-136 and JK-139, potently inhibited cell viability and migration/invasion of GC cell lines, and mouse xenografts, diversely expressing RHOA. Moreover, JK-136’s binding affinity for RHOA was >140-fold greater than Rhosin, a nonclinical RHOA inhibitor. Network analysis of JK-136/139-associated transcriptomes showed different functional contexts, compared to those following treatment with Rhosin. We strongly assert that identifying and targeting oncogenic signalling hubs, such as RHOA, represents an emerging strategy for the design, characterization, and translation of new antineoplastics, against gastric and other cancers.

overall_design: The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol (GeneChip Whole Transcript PLUS reagent Kit). cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit. Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16hour. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix). Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

first: Jin-Hee

last: Kim

first: Sungjin

last: Park

first: Seung

middle: M

last: Lim

first: Hyo

last: Eom

first: Curt

last: Balch

first: Jinhyuk

last: Lee

first: Gi

first: Jin-Hyun

last: Jeong

first: Yon


title: In depth quantitative proteomic and transcriptomic characterization of human adipocytes differentiation using the SGBS cell line

city: Leipzig

first: Petra

last: Büttner

address: Strümpellstrasse 163

department: Internal medicine/ Cardiology

institute: Heart Center Leipzig

summary: Most information on molecular processes accompanying and driving adipocyte differentiation are derived from rodent models. Here, a comprehensive analysis of combined transcriptomic and proteomic alterations during adipocyte differentiation in Simpson–Golabi–Behmel Syndrome (SGBS) cells is provided. The SGBS cells are a well-established and the most widely applied cell model to study human adipocyte differentiation and cell biology. However, the molecular alterations during human adipocyte differentiation in SGBS cells have not yet been described in a combined analysis of proteome and transcriptome. Here a global proteomic and transcriptomic data set comprising relative quantification of a total of 14372 mRNA transcripts and 2641 intracellular and secreted proteins is presented. 1153 proteins and 313 genes are determined as differentially expressed between preadipocytes and the fully differentiated cells including adiponectin, lipoprotein lipase, fatty acid binding protein 4, fatty acid synthase, stearoyl-CoA desaturase, and apolipoprotein E and many other proteins from the fatty acid synthesis, amino acid synthesis as well as glucose and lipid metabolic pathways. Preadipocyte markers, such as latexin, GATA6, and CXCL6, are found to be significantly downregulated at the protein and transcript level. This multi-omics data set provides a deep molecular profile of adipogenesis and will support future studies to understand adipocyte function.

overall_design: 13 samples were included in the study. Three samples represent undifferentiated cells and serve as baseline measurements for adipocyte differentiation.

first: Stefan

last: Kalkhof

first: Laura

last: Krieg

first: Martin

last: Wabitsch

first: Carolin

last: Küntzel

first: Daniela

last: Friebe

first: Kathrin

last: Landgraf

first: Martha

last: Hanschkow

first: Kristin

last: Schubert

first: Wieland

last: Kiess

first: Knut

last: Krohn

first: Matthias

last: Blüher

last: von Bergen

first: Antje

last: Körner


title: Analysis of VEEV Capsid Interaction Sites

city: Louisville

first: Kevin

last: Sokoloski

state: KY

address: 505 S. Hancock St.

institute: University of Louisville

summary: Brief assessment of VEEV TC-83 Capsid:RNA interactions.

overall_design:
Three libraries:
Library generated from total RNA immunoprecipitated with nonspecific polyclonal sera, and fragmented with RNAse A
Library generated from total RNA immunoprecipitated with anti-Capsid polyclonal sera, and fragmented with RNAse A
Library generated from total RNA immunoprecipitated with anti-Capsid polyclonal sera, and fragmented with RNAse A


title: RNA-seq from lung E18.5

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

summary: The impact of Mll3 removal on lung development was evaluated by mRNA profiling of three lung samples each from control and Mll3KO mice. Using 75-base-pair reads, 30 million reads per sample with comparable unique mapped reads (89-91%) were obtained. All biological replicates clustered into two well-separated groups according to genotype thereby lending confidence regarding data quality. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset.  As expected for an H3K4 methyltransferase, we observed that 5 times more mRNAs were down- than up-regulated at a false discovery rate (FDR) of 5%. GO term analysis by DAVID revealed that Mll3 is important for the regulation of cell differentiation and morphogenesis, and therefore for the maturation of the lung. Using GSEA we concluded that the most affected cell type was the alveolar epithelial type-I cells involved in gas exchange.

overall_design: mRNA profiles of E18.5 old wt and Mll3FDC/FDC (Mll3 KO) lungs were generated by deep sequencing in triplicates

first: Deepthi

last: Ashokkumar

first: Qinyu

last: Zhang

first: Christian

last: Much

first: Anita

middle: S

last: Bledau

first: Ronald

last: Naumann

first: Andreas

last: Dahl

first: Dimitra

last: Alexopoulou

first: Neha

last: Goveas

first: Jun

last: Fu

first: Konstantinos

last: Anastassiadis

first: A

middle: F

first: Andrea

last: Kranz


title: Reduced lipolysis is a common lipid accumulation mechanism for different subtypes of lipomas

first: Mehmet

middle: Volkan

last: Cakir

state: Saxony

address: Johannisallee 30

department: Medical Science

summary: We used RNA-seq to inquire gene expression profiles of lipomas with HMGA2-fusions and without gene fusions. We demonstrate that HMGA2-fusions lipomas are a specific subtype and that the common shared lipid accumulation mechanism is a reduction in lipolysis, with most gene-dysregulations leading to a reduced cAMP in the adipocyte.

overall_design: Characterization of lipomas and matched subcutaneous adipose tissue (SAT)

first: Diana

last: Le Duc

first: Chen-Ching

last: Lin

first: Yulia

last: Popova

first: Zuqin

last: Yang

first: Velluva

last: Akhil

middle: V

first: Sonja

last: Grunewald

first: Jan-Christoph

last: Simon

last: Dietz

first: Dirk

last: Dannenberger

first: Jürgen

last: Schiller

first: Ulrike

last: Rolle-Kampczyk

first: Martin

first: Janet

last: Kelso

first: Torsten

last: Schöneberg


title: Gene expression analysis of wild-type and Tafazzin-deficient granulocyte-monocyte progenitor (GMP) clones (ER-HOXB8 conditionally immortalized)

status: Public on May 22 2020

city: Boston

first: David

middle: B

last: Sykes

state: Massachusetts

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

summary: Evaluate changes in gene expression resulting from the loss of the gene TAZ (protein tafazzin). Tafazzin is an enzyme involved in cardiolipin maturation and cardiolipin is a phospholipid found only in the inner mitochondrial membrane. Gene expression profiling was performed in a murine granulocyte-monocyte progenitor in vitro cell system. We identified a limited number of changes in gene expression, which was not surprising given that the tafazzin protein is localized in the mitochondria and has a very specific enzymatic activity. Genes involved in cholesterol and fatty acid metabolism (Acss1, Acat2, Ldlr), apoptosis (Bcl2, Casp3, Casp6, Cycs), and ER-stress induced apoptosis (Ddit3, Atf4) were differentially expressed (with a fold change ≥ 1.2 and p value < 0.05).

overall_design: Using a technique of retroviral ER-Hoxb8 expression (Wang et al. Nature Methods 2006), we established conditionally immortalized granulocyte-monocyte progenitors (GMPs) from TAZ-deficient and wild-type murine fetal liver hematopoietic progenitors. These GMP lines are stem cell factor (SCF) dependent and grow indefinitely in the presence of active ER-Hoxb8 (which requires the addition of beta-estradiol). Single-cell cloning was used to generate individual clones and we performed RNA-sequencing across 6 wild-type and 6 knockout clones.

first: Jihee

last: Sohn


title: “Direct to Drug” screening as a precision medicine tool in multiple myeloma

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

summary: Seventy-six FDA approved oncology drugs and emerging therapeutics were evaluated in 25 multiple myeloma (MM) and 15 non-Hodgkin’s lymphoma cell lines and in 113 primary MM samples. Ex vivo drug sensitivities were mined for associations with clinical phenotype, cytogenetic, genetic mutation and transcriptional profiles. We investigated the predictive value of anti-apoptotic BCL2 family member transcriptomic ratios as biomarkers of venetoclax sensitivity. RNA-seq analysis was available in 38 primary patient samples, from which we identified the 9 most (median AUC 0.09409) and least (median AUC 0.7195) sensitive samples to venetoclax.

overall_design: Human multiple myeloma primary patient samples were sent for RNA sequencing

first: Cecilia

last: Bonolo de Campos

first: Nathalie

last: Meurice

first: A

middle: K

last: Stewart


title: Parent-of-origin effects on nuclear chromatin organization and behavior in Drosophila model of Williams-Beuren Syndrome.

city: Moscow

first: Sergei

last: Funikov

state: Moscow

address: Vavilov str. 32

country: Russia

institute: Engelhardt Insitute of Molecular Biology

summary: Development of prognostic models for neuropsychiatric disorders requires careful consideration of individual 1) parent-of-origin effects (POEs) relying on 2) nuclear 3D chromatin architecture of the nerve cells and 3) epigenetic impact of miRNAs produced in parental germ cells. The interplay of these events in shaping cognitive phenotypes in progeny is far from clear. Simple experimental model systems such as Drosophila can help to probe the causes and consequences leading to human neuropathology. Recently, we have developed a Drosophila model for Williams-Beuren Syndrome (WBS) – a mutant agnts3 of the agnostic locus (X:11AB) harboring limk1 gene for the key enzyme of actin remodeling LIM-kinase1. The mutation agnts3 drastically increases frequency of ectopic contacts (FEC) in specific regions of intercalary heterochromatin, suppresses learning acquisition and memory formation and affects locomotion. This study reveals that in reciprocal hybrids between agnts3 and the wild type strain Berlin the polytene chromosome bands are heterogeneous in manner of FEC regulation depending either on maternal or paternal gene origin. Bioinformatic analysis demonstrates that FEC between X:11AB and the other bands of the X chromosome partly depends on short (~ 30 bp) identical DNA fragments homologous to Drosophila 372 bp satellite DNA repeats. Although learning acquisition in conditioned courtship suppression paradigm is similar in hybrids, the middle-term memory formation shows patroclinic inheritance. Seemingly, this depends on changes in miR-974 expression levels. Several parameters of locomotion demonstrate heterosis. Our data indicate that agnts3 locus is capable of trans-regulating gene activity via POEs on chromatin nuclear organization, thereby affecting behavioral quantitative traits.

overall_design: Deep-sequencing of small RNA of wild-type and Agnts3 flies and their hybrids.

middle: Y


title: Gene expression of visceral adipose regulatory T cells from mice with specific deletion of insulin receptor in the cells

city: Vancouver

first: Dan

last: Wu

address: 950 West 28th Avenue

country: Canada

institute: BC Children's Hospital Research Institute

summary: Visceral adipose tissue (VAT) regulatory T cells (Tregs) control inflammation and metabolism. Diet-induced obesity causes hyperinsulinemia and diminishes VAT Treg number and function, but whether these two phenomena were mechanistically linked was unknown. We hypothesized that excessive insulin signaling in obesity negatively impact VAT Tregs. Using Treg-specific insulin receptor deletion (Foxp3-cre;Insr-fl/fl) mice, we compared the gene expression of VAT Tregs from control and knockout mice in obesity and aging, two models of hyperinsulinemia. We found that genes associated with Treg functions were altered in Tregs lacking insulin receptor.

overall_design: Control (Foxp3-cre) and Treg-specific insulin receptor deletion (Foxp3-cre;Insr-fl/fl) male mice were fed either a high-fat diet (HFD) or normal chow diet (NCD) for 13 weeks, starting at 3 weeks old, to reach obesity and hyperinsulinemia. Alternatively, control and knockout mice were aged on NCD for 52 weeks to reach ageing-associated hyperinsulinemia. VAT Tregs were then isolated by fluorescence-activated cell sorting, and analyzed by a custom Nanostring mRNA panel.


title: Induction of a tumorigenic neural crest stem cell-like state in INK4A-expressing melanoma lines.

city: Salt Lake City

first: Robert

middle: L

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

summary: We generated a live reporter for tumor-initiating cells in the 501MEL human melanoma line. We conducted mRNA sequencing of reporter high and reporter low expressing cells.

overall_design: Reporter high and low populations were sorted directly into trizol. RNA was harvested and sequenced.


title: Regenerative landscape of intestinal organoids (bulk RNA-Seq 2)

city: Basel

first: Ilya

last: Lukonin

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute (FMI)

summary: We use RNA sequencing to describe transcriptional changes induced in intestinal organoids cultured in presence of retinoic signaling modulators

overall_design: Examination of transcriptional profiles of intestinal organoids cultured in 4 treatment conditions from 2 individual mice in duplicate, at 24, 72, 96 and 120 hours post-treatment.

first: Denise

last: Serra

first: Katrin

last: Volkmann

first: Janine

last: Baaten

first: Karyn

last: Colman

first: Rui

last: Zhao

first: Shelly

last: Meeusen

first: Michael

last: Stadler

first: Jeremy

last: Jenkins

first: Ludivine

last: Meylan

first: Francisca

last: Maurer

first: Prisca

last: Liberali


title: Regenerative landscape of intestinal organoids (scRNA-Seq)

overall_design: Examination of transcriptional profiles of intestinal organoids cultured from single cells in 4 treatment conditions by single-cell RNA sequencing. Organoids generated from 2 individual mice in duplicate, extraction at 24, and 96 hours post-treatment. Sampling of ca. 5000 single cells per treatment condition and timepoint.


title: Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles

city: Nagoya

first: Tokunori

last: Hobo

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

summary: Purpose: To confirm the effects of Prl5 and Pbl6 (APO1) on panicle length at the gene expression level, we performed RNA-seq analysis to compare the expression patterns of these genes in young panicles of the near isogenic lines (NILs).  Results: Gene Ontology (GO) representation analysis indicated that the biological functions of the two genes are quite different.  Conclusions: RNA-seq analysis revealed that these two genes independently regulate panicle length at the level of gene expression.

overall_design: mRNA profiles of 2-mm stage young panicles of Koshihikari, NIL-Prl5ST-1, NIL-Pbl6ST-1, and NIL-Prl5ST-1+Pbl6ST-1

first: Ayumi

last: Agata

first: Takamasa

last: Suzuki


title: Generation of an in vitro 3D Engineered Colorectal Cancer Patient-Derived Xenograft Model

city: Auburn

middle: W

last: Greene

state: AL

address: 260 Lem Morrison Dr

department: Nutrition

institute: Auburn University

summary: We report on the development of an vitro model of colorectal cancer using cells isolated from a patient-derived xengraft (PDX) tumor. Transcriptome profiling was performed to compare molecular characteristics of in vitro 3D engineered CRC tissues to in vivo tumors.

overall_design: mRNA profiles of 3D engineered CRC tissues cultured for 15 days and the corresponding in vivo PDX subcutaneous tumor grown in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NOD-SCID) mice.

first: Elizabeth

last: Lipke


title: Regenerative landscape of intestinal organoids (bulk RNA-Seq 1)

last: Lukonin

summary: Development of intestinal organoids from single intestinal stem cells is driven by the regenerative capacity of the intestinal epithelium. To unravel molecular mechanisms orchestrating organoid formation and self-organization, we developed a high-content image-based screening assay for an annotated compound library. We generated multivariate feature profiles for hundreds of thousands of individual organoids to quantitatively describe the phenotypic landscape of organoid development. Generated phenotypic fingerprints were then used to infer regulatory genetic interactions from a single screen, establishing a novel paradigm in genetic interaction screening applied to an emergent system. This allowed the identification of novel modules of genes that regulate cell identity transitions and maintain the balance between regeneration and homeostasis. We then characterized a crucial role of retinoic acid nuclear receptors in controlling the exit from the regenerative state and in driving enterocyte differentiation. By combining quantitative imaging with RNA sequencing we confirmed the role of endogenous retinoic acid signaling and metabolism in initiating transcriptional programs guiding intestinal epithelium cell fate transitions and identified a small molecule inhibitor of retinoid x receptor, RXR, that improved intestinal regeneration in vivo. We use RNA sequencing to describe transcriptional changes induced in intestinal organoids cultured in presence of retinoic signaling modulators.

overall_design: Examination of transcriptional profiles of intestinal organoids cultured in 4 treatment conditions from 2 individual mice in duplicate, at 6 and 24 hours post-treatment.


title: Coronavirus replication is regulated by both host and viral RNA N6–methyladenosine modifications

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

summary: N6–methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, and it plays an important role in RNA metabolism and function. Recent studies have revealed that viral RNA m6A modification can play an anti-viral or pro-viral role depending on the virus. However, whether m6A methylation can modulate replication of coronaviruses, which cause some severe human and animal diseases such as Coronavirus Disease 2019 (COVID-19), remains unknown. Here, we determined that m6A modifications of porcine epidemic diarrhea coronavirus (PEDV) are exclusively located in the N gene at the 3’-end of the genome, and that PEDV infection alters the expression pattern of some host proteins involved in m6A modification. Depletion of m6A demethylases significantly increased PEDV replication and gene expression whereas knockdown of m6A methyltransferases slightly decreased PEDV infection. Interestingly, m6A binding proteins YTHDF 2 and 3 significantly inhibited PEDV replication whereas YTHDF1 has the opposite effect. When the major m6A sites in the N gene were mutated, the resultant recombinant PEDVs and PEDV replicons had a significant increase in replication and gene expression. This study illustrates that (i) addition of m6A to PEDV RNA inhibits viral replication, and (ii) both host and viral m6A machinery regulate coronavirus replication.

overall_design: HMPV virions were purified from supernatants of hMPV-infected Hela and A549 cell lines. Virus derived mRNA as well as host mRNA were purified from total RNA, which were extracted from hMPV infected cells.

first: Mijia

last: Lu

first: Jianrong

last: Li


title: Gene expression in RpoB-P153L

city: Stanford

first: Anthony

middle: Lyndon

last: Shiver

address: 443 Via Ortega Shriram Bldg 062

department: BioEngineering

institute: Stanford University

summary: We report RNA-seq results comparing gene expression in the mutant RpoB-P153L to its parental E. coli strain and the effect of induction of relA* in both strains.

overall_design: Three categories: strain: wild-type or RpoB-P153L, plasmid: relA* (pALS13) or relA- (pALS14), induction: yes or no; Three replicates per sample.

first: Hendrik

last: Osadnik

first: Jason

last: Peters

first: Rachel

last: Mooney

first: Robert

last: Landick

first: Kerwyn

last: Huang

first: Carol

last: Gross


title: Serine-threonine Kinase, ROCK2, Regulates Germinal Center B Cell Positioning and Cholesterol Biosynthesis

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

summary: Splenic follicular B cells (FoB; B220+GL7-CD38hiCD23+) and Germinal Center B cells (GCB; B220+GL7+CD38lo) were FACS sorted from WT or CD23-Cre.Rock2 mice after 7d post-immunization with NP-CGG. RNA-seq was then employed to compare the transcriptome of GCBs from the indicated mice. Here we show that loss of ROCK2 leads to altered gene expression in GCBs. We also employed ATAC-seq analysis and found that differentially expressed genes from the ROCK2-deficient GC B cells contained loci that were enriched for IRF binding sites.

overall_design: 1. Examination of FoB and GCB transcriptome in cells isolated from WT or CD23-Cre.Rock2 Mice (run in triplicate); 2. Analysis of chromatin landscape in FoB and GCB cells from WT and CD23-Cre.Rock2 mice by ATAC-seq (run in duplicate)

first: Edd

last: Ricker

first: Alessandra

last: Pernis


title: Wild-type and tafazzin-deficient clones of granulocyte-monocyte progenitors (GMP), ER-HOXB8 conditionally immortalized, immature, in estrogen.

first: David

last: Sykes

summary: Evaluate changes in gene expression resulting from the loss of the gene TAZ (protein tafazzin). Tafazzin is an enzyme involved in cardiolipin maturation and cardiolipin is a phospholipid found only in the inner mitochondrial membrane. Gene expression profiling was performed in a murine granulocyte-monocyte progenitor in vitro cell system. We identified a limited number of changes in gene expression, which was not surprising given that the tafazzin protein is localized in the mitochondria and has a very specific enzymatic activity. Genes involved in cholesterol and fatty acid metabolism (Acss1, Acat2, Ldlr), apoptosis (Bcl2, Casp3, Casp6, Cycs), and ER-stress induced apoptosis (Ddit3, Atf4) were differentially expressed.

overall_design: Using a technique of retroviral ER-Hoxb8 expression (Wang et al. Nature Methods 2006), we established conditionally immortalized granulocyte-monocyte progenitors (GMPs) from TAZ-deficient and wild-type murine fetal liver hematopoietic progenitors. These GMP lines are stem cell factor (SCF) dependent and grow indefinitely in the presence of active ER-Hoxb8 (which requires the addition of beta-estradiol). Single-cell cloning was used to generate individual clones and we performed RNA-sequencing across 6 wild-type and 5 knockout clones.

first: Jihee

last: Sohn


title: Transcriptome Analysis of Etroplus Suratensis

city: Kochi

first: Rejish Kumar

state: Kerala

address: Assistant Professor Dept. of Aquaculture School of Aquaculture and Biotechnology

department: Aquaculture

country: India

institute: Kerala University of Fisheries and Ocean Studies

summary: we examined the transcriptome of E. suratensis and analysed the genes involved in growth, reproduction and immunity that are active in brain, pituitary, liver, kidney, spleen, muscles and gonads in both male and female through RNA Sequencing

overall_design: RNA Sequencing of growth, reproduction and immune related organs of  male and female  Etroplius suratensis

first: Rejish

last: Vattiringal Jayadradhan

first: S

last: Chandhini

first: Varsha

last: Mohanan

first: P

last: Anvar Ali

last: Fernandez


title: Requirement for Cleavage Factor IIm in the Control of Alternative Polyadenylation in Breast Cancer Cells

city: Clayton

first: Rachael

last: Turner

state: Victoria

address: Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: This experimental series concerns the position bias and extent of 3'-end choice in MCF7 cells after knock-down of the CFII subunits PCF11 and CLP1 in MCF7. Loss of either subunit results in 3'-lengthening by APA. Importantly this lengthening is toward a more 'normal-like' distribution. MCF7 cells show a native 3'-end distribution favoring short internal  adenylation sites compared to MDAMD231 cells. The difference between the two cell lines might be driven by a higher expression of the exosome in MDAMD231 cells.

overall_design: Analysis of 3'-focused PAT-seq data in human breast cancer cell-lines (MCF7 vs MDAMB231) and after siRNA depletion of the CFII subunits (CLP1 and PCF11)

first: Bernhard

last: Dichtl

first: Traude

last: Beilharz


title: Differentially expressed SE-lncRNAs and mRNA  in colorectal cancer

city: Nanjing

first: Linping

last: Yan

state: Jiangsu

address: Baizi Ting No. 42

institute: Jiangsu Cancer Hospital

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

summary: To address the role of SE-lncRNAs in CRC tumorigenesis, we performed Arraystar human SE-lncRNA microarray to profile the differentially expressed SE-lncRNAs and mRNA in four CRC and paired peritumoral tissues. According to the filter criteria of Fold Change ≥ 1.5 and P-value < 0.05, a total of 55 significantly upregulated and 29 significantly downregulated SE-LncRNs were identified. These data confirmed that the expression of SE-lncRNA undergoes a change that cannot be ignored during CRC tumorigenesis. We also identified 165 (91 up- and 74 downregulated) differentially expressed mRNA between the two groups（Fold Change > 1.5 and P-value < 0.05）(Fig.1C), which provides help for us to findpotential target genes and further explore the biological function of SE-lncRNA in CRC

overall_design: Four CRC and paired peritumoral tissues were subjected to Arraystar human microarray analysis to determine differentially expressed SE-LncRNAs and mRNA. All experiment procedures were performed following the Arraystar standard protocol.

first: Feng


title: Transcriptional profiling of hepatocytes isolated from chronically HBV-infected human liver chimeric mice

city: London

first: Efstathios

last: Giotis

address: Norfolk Place

department: Infectious Diseases

country: United Kingdom

institute: Imperial College London

summary: We generated human liver chimeric mice that were repopulated with human hepatocytes and we infected them for 11 weeks with Hepatitis B virus (HBV). Hepatocytes were isolated from the infected chimeric mouse livers and their gene expressions were compared with those from uninfected chimeric mice using RNA-sequencing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The human liver chimeric mice were generated by transplantation of thee different donor hepatocytes. RNA from four HBV-infected and three uninfected liver chimeric mice were collected from mouse livers, for library production and strand-specific RNA-sequencing at the Beijing Genomics Institute (BGI, Hong Kong).

first: Ana

last: Ortega-Prieto


title: Analysis of NPC48 overexpressing in Arabidopsis roots

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

summary: We analyze the effect of the overexpression of the lncRNA NPC48 on the transcriptome. Root apices were harvested and total RNA extracted for RNA sequencing.

overall_design: RNA-seq experiments (polyA+ RNA) in triplicates for each condition WT and 35S:NPC48 lines.

first: Aurélie

last: Christ

first: Caroline

last: Hartamnn

last: Roulé

first: Martin

last: Crespi


title: Transcriptomic Comparison of Common Nontyphoidal Salmonella Serovars Provides Greater Resolution for Understanding Differences in Virulence

status: Public on May 21 2020

city: Ithaca

first: Alexa

middle: Robyn

last: Cohn

state: NY

address: 411 Tower Rd

department: Food Science

institute: Cornell University

summary: RNA extracted from representative isolates of each serovar grown to late exponential phase in Luria-Bertani broth showed that transcript abundances of core genes were significantly higher (p < 0.05) than those of accessory genes for all three serovars. Inter-serovar comparisons demonstrated higher transcript abundances for genes related to vitamin B12 biosynthesis, and ethanolamine and 1,2-propanediol utilization in S. Cerro compared to Javiana and Typhimurium, while genes in Salmonella Pathogenicity Island (SPI) 1 had significantly higher transcript abundances in S. Javiana and S. Typhimurium.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

sample_organism: Salmonella enterica subsp. enterica serovar Cerro

sample_organism: Salmonella enterica subsp. enterica serovar Javiana

overall_design: mRNA profiles from three Salmonella serovars (Cerro, Javiana, Typhimurium) were generated by deep sequencing with an Illumina NextSeq 500 in triplicate with 75-nt stranded single-end reads.

first: Renato

last: Orsi

first: Laura

last: Carroll

first: Rachel

last: Cheng

last: Wiedmann


title: Differences in the transcriptomes of IgMhigh and IgMlow human memory B cells

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
We have previously shown that circulating human CD19+CD27+ IgMhigh IgDlow B cells are phenotypically and functionally different compared with CD19+CD27+ IgMlow IgDhigh B cells. Here, we compare their transcriptomes.
IgMhigh and IgMlow subsets of human CD27+ B cells were FACS purified from blood samples of four volunteers and RNA was extracted and processed for hybridization to the Affymetrix Human Clariom D Assay to compare their transcriptomes.

overall_design: The experiment is comprised of 16 Human Clariom D arrays, profiling RNA obtained from B cells from the blood of four healthy volunteer donors (39, 40, 41, and 42). Five populations of B cells were FACS purified from each donor: Naïve (IgD+IgM+CD27-), Switch (IgD-IgM-CD27+), IgMonly (IgD-IgM+CD27+), IgMhigh (IgD+IgM++CD27+) and IgMlow (IgD+IgM+CD27+). For volunteer 40 only the IgMlow population was included. The transcriptome from IgMlow was compared with IgMhigh and simultaneously the transcriptome of both populations were compared with other populations of B cells as controls.

first: Diana

last: Bautista

first: Camilo

last: Vasquez

first: Manuel

middle: A

last: Franco

first: Juana

last: Angel


title: Cholesterol homeostasis modulates platinum sensitivity in human ovarian cancer

city: Napoli

first: Danilo

last: Swann Matassa

address: Via Sergio Pansini 5

department: Molecular Medicine and Medical Biotechnology

institute: University of Naples “Federico II”

summary: Here we show that platinum-resistant ovarian cancer cells also show reduced cholesterol biosynthesis, and mostly rely on uptake of exogenous cholesterol for their needs. Expression of FDPS and OSC, enzymes involved in cholesterol synthesis, are decreased both in drug-resistant cells and upon TRAP1 silencing, whereas the expression of LDL receptor, the main mediator of extracellular cholesterol uptake, is increased. Strikingly, treatment with different statins to inhibit cholesterol synthesis reduces cisplatin-induced apoptosis, whereas silencing of LIPG, an enzyme involved in lipid metabolism, increases sensitivity to the drug.

overall_design: Evaluation of differentially expressed transcripts in PEA1 ovarian cancer cells following transfection with TRAP1-directed siRNA or control siRNA

first: Giovanni

last: Calice

first: Francesca

last: Maddalena


title: Identification of miR-154 downstream targets

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

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

overall_design: Refer to individual Series


title: Regenerative landscape of intestinal organoids

first: Ilya

last: Lukonin


title: Single-cell RNA-seq of the mouse lymph node lymphatic vasculature: Droplet-seq

first: Menglan

last: Xiang

state: CA

address: 450 Serra Mall

summary: Lymph nodes (LNs) serve as hubs for the interaction and communication between tissue-derived and blood-derived immune cells. Here we analyzed mouse lymph node (LN) lymphatic endothelial cells (LEC) at single cell resolution. Clustering identifies five well-delineated subsets, including two medullary sinus subsets not recognized previously as distinct. Nearest neighbor alignments in trajectory space position the major subsets in a sequence that recapitulates known and suggests novel features of LN lymphatic organization, providing a transcriptional map of the lymphatic endothelial niches and of the transitions between them. Differences in gene expression reveal specialized programs for (1) subcapsular ceiling endothelial interactions with the capsule connective tissue and cells, (2) subcapsular floor regulation of lymph borne cell entry into the LN parenchyma and antigen presentation, and (3) medullary subset specialization for pathogen interactions and LN remodeling. LEC of the subcapsular sinus floor and medulla, which represent major sites of cell entry and exit from the LN parenchyma respectively, respond robustly to oxazolone inflammation challenge with enriched signaling pathways that converge on both innate and adaptive immune responses.

overall_design: Male and female 6- to 8-week-old BALB/cJ or 8- to 12-week-old C57BL/6J peripheral LNs (inguinal, axillary and brachial) were processed by the 10x Genomics workflow and used for scRNA-seq.

first: Maria

last: Ulvmar

first: Eugene

middle: C

last: Butcher

first: Kevin

last: Brulois

first: Sofia

last: Nordling


title: Differential activation of P-TEFb complexes in the development of cardiomyocyte hypertrophy following activation of distinct GPCRs

city: Montreal

first: Jason

last: Tanny

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

institute: McGill University

summary: Pathological cardiac hypertrophy is driven by neurohormonal activation of specific G protein-coupled receptors (GPCRs) in cardiomyocytes and is accompanied by large-scale changes in cardiomyocyte gene expression. These transcriptional changes require activity of positive transcription elongation factor b (P-TEFb), which is recruited to target genes by the bromodomain protein Brd4 or the Super Elongation Complex (SEC). Here we describe GPCR-specific regulation of these P-TEFb complexes and a novel mechanism for activating Brd4 in primary neonatal rat cardiomyocytes. The SEC was required for the hypertrophic response downstream of either the α1-adrenergic receptor (α1-AR) or the endothelin receptor (ETR). In contrast, Brd4 inhibition selectively impaired the α1-AR response. This was corroborated by the finding that activation of α1-AR, but not ETR, increased Brd4 occupancy at promoters and super enhancers of hypertrophic genes. Transcriptome analysis demonstrated that activation of both receptors initiated similar gene expression programs, but that Brd4 inhibition attenuated hypertrophic genes more robustly following α1-AR activation. Finally, we show that protein kinase A (PKA) is required for α1-AR stimulation of Brd4 chromatin occupancy. The differential role of the Brd4/P-TEFb complex in response to distinct GPCR pathways has potential clinical implications as therapies targeting this complex are currently being explored for heart failure.

overall_design: RNA-seq of neonatal rat cardiomyocytes

first: Ryan

middle: D

last: Martin

first: Yalin

last: Sun

first: Sarah

last: MacKinnon

first: Luca

last: Cuccia

first: Viviane

last: Pagé

first: Terence

middle: E

last: Hébert


title: mir-154 in mouse lung development - E18.5 in vivo data

summary: Transcription profiles from mice over expressing miR-154 (overExpr) were compared to profiles from mice with normal expression (control).

overall_design: Two groups with 9 mice each (control and overExpr), RNAs from 3 mice (extracted from lungs of E18.5 embryos) each were pooled, leading to 3 hybridizations per group.

first: Gianni

last: Carraro


title: RNA-sequencing study on DSS-induced ulcerative colitis in mice of wild type and intestinal epithelial cell-sepific NCoR1 deletion.

city: La Jolla

first: Shujuan

last: Chen

address: 9500 Gilman Drive

department: Pharmacology

institute: University of California, San Diego

summary: Purpose: The goal of this study is to investigate the role of NCoR1 in protecting colon from ulcerative colitis.

overall_design: Methods: NCoR1F/F (F/F) and NCoR1DIEC (DIEC ) mice were treated with water (naive) or 2.5% DSS. On day 3 post DSS treatment, RNA was prepared from colon tissue. This experiment consisted of 4-groups. 1) Water only for NCoR1F/F mice (F/F_naive). 2) DSS treated NCoR1F/F mice (F/F_DSS). 3) Water only for NCoR1DIEC mice (DIEC _naive). 4) DSS treated NCoR1DIEC  mice (DIEC_DSS). RNA from three mice per group were combined as one sample, with four samples from each group subjected for RNA-seq

first: Chris

last: Bener


title: Effects of BMPER, CXCL10 and HOXA9 on neovascularization during early-growth stage of primary high-grade glioma

city: Chongqing

first: Xue

last: Wei

address: 10# Changjiangzhilu

institute: Daping Hospital,  Army Medical University

summary: Neovascularization is required in high-grade glioma (HGG). The objective of this study was to explore neovascularization-related genes and their corresponding MRI biomarkers during the early-growth stage of HGG. Tumor tissues from 30 HGG patients underwent perfusion MRI scanning prior to surgery were used to establish orthotopic xenograft models, pathologically analyze the tumor vasculature and perform transcriptome sequencing. The cases were divided into two groups based on whether the xenograft was successfully established. Microvascular density and BMPER, CXCL10 and HOXA9 expression of surgical specimens in the xenograft-forming group was significantly elevated and the microvascular diameter was significantly reduced, In vitro inhibition of BMPER, CXCL10 or HOXA9 in the glioma stem cell significantly suppressed its tube formation abilities. The in vivo experiment showed that BMPER was highly expressed in the early tumor growth phase (20 days), CXCL10 and HOXA9 expression was elevated with tumor progress, and spatially associated with tumor vasculature.

overall_design: We collected 30 tumor samples from 30 cases of high-grade glioma patients to establish orthotopic xenograft models, these cases were divided into two groups based on whether the xenograft was successfully established. Then mRNA was extracted from these samples, after quality inspection 22 samples were performed RNA-sequencing (RNA-Seq). 8 samples in xenograft-forming group and 14 samples in nonxenograft-forming group.

first: Wei

last: Xue

first: Junfeng

last: Zhang

first: Haipeng

last: Tong

first: Tian

last: Xie

first: Xiao

first: Bo

last: Zhou

first: Pengfei

last: Wu

first: Peng

middle: Z

last: Du

first: Yu

last: Guo

first: Youyuan

last: Yang

first: Heng

last: Liu

first: Jingqin

last: Fang

first: Shunan

last: Wang

first: Hao

first: Kai

last: Xu

first: Weiguo


title: Gene expression profiling of Male and Female adult mouse liver using RNA-seq

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

summary: Liver sex-specific long noncoding RNAs (lncRNAs) were identified based on three pools of male and three pools of female ribosomal RNA-depleted total liver RNAs, as well as three pools of male and three pools of female ribosomal RNA-depleted nuclear liver RNAs from CD-1 mice. This dataset is part of a larger study, entitled "Sex-biased lncRNAs inversely correlate with sex-opposite gene co-expression networks in Diversity Outbred mouse liver", Endocrinology (2019) 160:989-1007, PMID:30840070.

overall_design: Identification of liver sex-specific lncRNAs and RefSeq genes using rRNA-depleted total and nuclear RNA isolated from male and female mouse liver.

first: Dana

last: Lau-Corona

first: Tisha

last: Melia

middle: J


title: RNA-Sequencing of drought-stressed leaves of watermelon

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

summary: Purpose: The goals of this study are to compare differentially expressed transcripts in leaves of watermelon during drought stress using transcriptome profiling (RNA-seq)

overall_design: Methods: Leaf samples for RNA Seq analysis were collected from three independent plants at 8 days after initiation of drought stress from control (CT1_1, CT1_2, CT1_3) and drought-stressed plants (DT_1, DT_2, DT_3) were flash-frozen in liquid nitrogen for further analysis. Results: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer's instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq platform, and 150 bp paired-end reads were generated. Raw reads of fastq format were processed to obtain clean reads by removing the adapter, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30, and GC content, the clean data were calculated. Watermelon reference genome (cultivar Charleston Gray) and gene model annotation files were downloaded from CuGenDB (http://cucurbitgenomics.org/). Index of the reference genome was built using Bowtie v2.2.3, and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. : HTSeq v0.6.1 was used to count the reads mapped to each gene. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts. Differential expression analysis of control and drought-stressed conditions (three biological replicates per tissue per treatment) was performed using the DESeq R package (1.18.0) (Anders and Huber, 2010). Genes with P-value < 0.05 found by DESeq were assigned as differentially expressed. Conclusions: The transcriptomic changes induced by drought stress in leaf tissue at 8DAT was used for RNA-Seq analysis. A total of six libraries from leaf tissue (CT-1, CT-2, CT-3 for control and DT-1, DT-2, DT-3 for drought stress) were sequenced using the Illumina HiSeq platform. On average, 45.53 to 43.47 million raw reads were generated from leaf tissues in both treatments. Across all reads for both control and drought samples, the Q20 and Q30 percentage was more than 98 and 94%, respectively (sequencing error rate was less than 0.02%), and GC content for the libraries was ~45%.  Among all the libraries, the ratio of total mapped reads was above 97%, of which ~92 % reads uniquely mapped to the reference watermelon genome for control and drought-stressed samples. The data generated from all libraries provided a foundation for quality analyses. The RNA-Seq analysis identified 3971 differentially expressed (p <0.05) genes in the leaf tissue of drought-stressed plants, of which a total of 1513 genes were upregulated and 2458 genes were downregulated.


title: Gene-expression profiles of primary and metastatic lesions in head and neck squamous cell carcinoma

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous group of malignancies arising from different sites and the 8th most common type of cancer in the world.  While the advent of new techniques and multimodality therapy have improved prognosis of locally HNSCC, the appearance of distant metastases (DM) remains a challenge both for prognosis and treatment. To date, the genomic landscape of dissemination of HNSCC has to be further studied, in order to predict whether a patient will develop distant metastases. Therefore, knowing that the risk of disease spread to DM is directly correlated to initial staging, it suggested the hypothesis that the development of DM could be linked to the biologic characteristics of the primary tumor.  The aim of our work is to compare gene expression profile of primary tumors of patients who develop and not develop DM. Additionally, we studied the expression profile of matched  distant metastasis.

overall_design: We identified and matched histologically confirmed primary tumor of 49 HNSCC patients, divided in 24 without metastasis (“T-without”) and 25 with distant metastasis (“T-with”), collected from 2006 to 2016. In 23 of the 25 selected T-with cases, we collected matched FFPE samples of the distant metastasis (M). The following criteria have been used to match T-with versus T-without based on clinical and radiological staging: i) cT1 has been matched with cT1 or cT2 and viceversa for staged cT2 tumors; ii) cT3 has been matched with cT3 or cT4 and viceversa for cT4; iii) cN1 has been matched with cN0 or cN1; cN2 has been matched with cN3 and viceversa for cN3. T-with and T-without were well balanced per age, sex and previous radiotherapy performed in the curative setting on the head and neck area. Among T-with patients, the majority had lung metachronous metastases.


title: Microarray analysis of miRNA in breast cancer cell lines

city: Ourimbah

first: Judith

last: Weidenhofer

state: NSW

address: 10 Chittaway Rd

department: School of Biomedical Sciences & Pharmacy

institute: University of Newcastle

summary: The project aimed to identify miRNA that varied with tumourigenicity in human breast cell lines. The second objective was to identify miRNA that had differential expression between cell lines that varied in accordance with the abundance of the tetraspanin CD9 in the cell lines and the degree to which endogenous factors within these cell lines interacted with the 3'UTR of CD9 as determined by dual luciferase assay. These miRNA were considered potential regulators of the abundance of CD9 in breast cancer.

overall_design: Total RNA was isolated from commercial breast cancer cell lines and non-tumourigenic breast cell lines and the abundance of each miRNA was determined by hybridisation to affymetrix miRNA microarrays. RNA was combined from 3 independent cultures of each cell line prior to labelling for hybridisation to each array. Each cell line was therefore only assayed once by microarray.

first: Danielle

middle: R

last: Bond

first: Murray

last: Cairns

first: Leonie

last: Ashman


title: Transcriptional profiling of the probiotic E. coli Nissle 1917 strain under simulated microgravity and normal gravity

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: We performed comparative transcriptomic profiling of E. coli Nissle 1917 (EcN) to determine the effect of microgravity (MG) on cell growth and metabolism.

overall_design:
Growth phase: Exponential and stationary growth phase.
Culture condition: MG and normal gravity (NG) condition, in duplicate, M9 minimal media with glucose, 37°C, total 8 samples
MG condition can be simulated by rotary cell culture system (RCCS) from Synthecon Inc. (Houston, TX, USA) when it is rotated around the horizontal axis. On the other hand, NG condition can be simulated by RCCS when it is rotated around the vertical axis.

first: Jaewoo

last: Yim

first: Sung

last: Cho

first: Beomhee

last: Kim

first: Sungwoo

last: Park

first: Yong

middle: H

last: Han

first: Sang


title: Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria

city: Singapore

first: Xiaolin

last: Wu

state: Singapore

address: 1 CREATE Way

country: Singapore

institute: Singapore-MIT Alliance for Research and Technology (SMART)

sample_organism:
Salmonella enterica
Escherichia coli K-12
Escherichia coli BW25113


title: Male mice brain transcriptome in Bahd1 +/+ and Bahd1 -/- at adult and E16.5 embryo stages

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA


title: RNA-seq analysis for E.coli dnd and dam derivatives

summary: To get a global view of PT modification’s function in ∆dam mutant, we did an RNA-seq to compare the gene expression change after dam knocks out and test whether PT could restore the changes.

sample_organism:
Escherichia coli K-12
Escherichia coli BW25113

overall_design: We selected mid-log-phase cultures of E.coli  ∆dam mutant with or without expressing dndBCDE, to perform RNAseq analysis with wild-type E.coli BW25113 as the reference.

first: Chao

last: Chen

first: Susu

last: Jiang

first: Lianrong

last: Wang

first: Shi

first: Peter

last: Dedon


title: RNA-seq data from submiligram porcine myocardial tissue

city: Solna

first: Staffan

last: Holmin

state: Non US/Canada

address: Visionsgatan 4, J5:20

country: Sweden

institute: Karolinska Institutet

summary: Endomyocardial biopsy (EMB) is the gold standard for diagnosis of several heart diseases, yet its use is limited by relatively low diagnostic yield and significant complication risks. To address this, we have developed an endovascular micro-biopsy (Micro-EMB) device with an outer diameter of 0.4 mm in order to minimize procedural risk, sampling trauma, and increase sampling specificity. We have performed RNA-seq on the resulting submilligram tissue as well as controls. The gene expression signatures were compared between Micro-EMBs and conventional EMB controls, as well as negative controls such as blood and skeletal muscle.

overall_design: 32 micro-biopsy samples from 5 different individual pigs, of which 20 were taken on the naive heart (baseline) and 12 were taken one week after (follow-up).  10 heart control samples, of which 6 baseline and 4 follow-up, from 2 different animals. 6 blood samples at baseline, from 2 different animals. 6 skeletal muscle samples at baseline, from 2 different animals.

first: Arvin

last: Chireh

first: Rikard

last: Grankvist


title: mir-154 in mouse lung development - pull-down RNA

first: Jochen

last: Wilhelm

summary: RNA isolated from MLE12 cells was subjected to a pull down assay with biotinilated miR-154 to enrich for miR-154 target mRNAs

overall_design: RNA obtained from a single pull-down experiment using MLE12 cells with mir-154 (pmiR) and with a scrambled (random) sequence (pscra) were hybridized on two Agilent Whole Mouse Genome Microarrays. The experiment includes no replicates.

first: Gianni

last: Carraro


title: High-throughput single-cell RNA sequencing of tumor-infiltrating NK cells

city: Nanjing

first: Xi

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: High-throughput single-cell RNA-seq of tumor-infiltrating NK cells uncovered an NK subset, exhibiting elevated expression of activation markers, cytolytic molecules, chemokines and cytokines when Hif1a was absent in NK cells.

overall_design: Single cell transcrptome profiling of tumor-infiltrating NK cells from NK-Hif1a defecient mice and WT mice.

first: Qin

last: Zhang

first: Jing

last: Ni


title: mir-154 in mouse lung development

summary: miR154-3p and -5p are mainly expressed in the lung epithelium pre- and postnatally in mice and are significantly higher expressed upon hyperoxia (BPD mouse model). In normoxia in vivo overexpression of miR154 (CCSPrtTA;tetOmiR154, P0-P16) leads to increased Fgf10 signaling and Tgf- signaling. Furthermore, avleolar morphometry revealed increased MLI indicating interference with alveologenesis at P16. In hyperoxia (P0-P8) in vivo overexpression of miR154 (CCSPrtTA;tetOmiR154, P0-P16) leads to decreased Fgf10 signaling and Tgf- signaling.

overall_design: 2 groups, each with 4 biological replicates

first: Cho-Ming

last: Chao


title: Expression data of H838 KRAS mutation isogenic cell lines

city: Tapei

first: Peishan

last: Hung

state: State...

address: NO.1 JEN AI ROAD SECTION 1 TAIPEI 100 TAIWAN R.O.C.

country: Taiwan

institute: Graduate Institute of Oncology

summary:
To explore the distinct mechanism of KRAS G12V and G12D mutation.
We used microarray to explore the distinct  differences in gene expression profiles of H838 KRAS mutation isogenic cell lines

overall_design: The RNA of H838 isogenic cell lines were collected in triplicate

first: Pei-Shan

first: James

last: Yang


title: A class II-restricted chlamydia-specific CD8ɣ13 T cell clone protects the genital tract during Chlamydia muridarum infection

city: New Haven

first: Raymond

middle: Morris

last: Johnson

state: CT

department: Med/Infectious Diseases

country: USA

institute: Yale University

summary: The T cell response to Chlamydia genital tract infections in humans and mice is unusual in that the majority of antigen-specific CD8 T cells are not restricted by HLA/MHC class I and therefore have been referred to as “unrestricted” or “atypical”.   We previously reported that a subset of unrestricted murine Chlamydia-specific CD8 T cells had an unusual cytokine polarization pattern that included IFN-ɣ and IL-13.  For this report, we investigated the transcriptome of Chlamydia-specific CD8ɣ13 T cells, comparing them to Chlamydia-specific multifunctional Tc1 clones using gene expression micro array analysis.  The molecular study revealed that CD8ɣ13 polarization included IL-5 in addition to IFN-γ and IL-13.  Adoptive transfer studies were performed with Tc1 clone and CD8ɣ13 T cell clones to determine whether either influenced bacterial clearance or immunopathology during Chlamydia muridarum (Cm) genital tract infections.  To our surprise, an adoptively transferred CD8ɣ13 T cell clone was remarkably proficient at preventing chlamydia immunopathology while the multifunctional Tc1 clone did not enhance clearance or significantly protect from immunopathology.  Mapping studies with MHC class I- and class II-deficient splenocytes showed our previously published Chlamydia-specific CD8 T cell clones are MHC class II-restricted.   MHC class II-restricted CD8 T cells may play important roles in protection from intracellular pathogens that limit class I antigen presentation or deplete the CD4 T cell compartment.

overall_design: CD8γ13 T cell clones were compared to Tc1 T cell clones and an alloreactive conventional CD8 T cell clone in dormant resting state and after activation with immobilized anti-CD3 antibody for 14 hours.

middle: M


title: Mapping PT modifications in bacteria

first: Xiaolin

last: Wu

summary: One microbial organism always contains multiple DNA modification systems as defense strategies or epigenetic controls. Here, we describe crosstalk between two distinct DNA modifications with different target sequence motif: DNA phosphorothioation (PT, GPSAAC/GPSTTC by DndACDE proteins) and N6-methyl-adenine methylation (m6A, G6mATC by Dam protein). By using a newly developed DNA modification sequencing method PT nick-seq, we found that half of PT modifications change from GAAC/GTTC to GATC sites after bacteria have lost Dam.

sample_organism:
Salmonella enterica
Escherichia coli K-12

overall_design:
Map the PT modification sites in bacteria and ∆dam mutant
To further confirm this result and get a full understanding of where the new modifications are, we exploited PT-nick-seq method to get the single-base resolution of PT modification map of E.coli BW25113 and ∆dam mutant harboring S. enterica DndBCDE proteins.With PT-nick-seq technology, PT modifications on DNA were turned into strand breaks after iodine cleavage and were inferred through the higher read coverage ratio compared to their neighbor nucleotides and negative controls.To further get the PT modification site information in the same ChIP-seq samples, PT-nick-seq was adopted to sequence the genomic DNA of the same strain used for ChIP-seq experiment.

first: Bo

last: Cao


title: Exogenous NAD+ induces mucin secretion in LS 174T goblet cells via the PLC-delta/PTGES/PKC-delta/ERK1/2/CREB signalling pathway

city: seoul

first: seongho

last: ma

address: Anamro 145

institute: Korea university

summary: Mucin, one of family of glycoprotein that is a major component of the mucus layer in the intestine, is associated with antimicrobial activity and gut immune system function. Currently, mucin is mainly known for its critical function in defence against toxic molecules and pathogens. In this study, we investigated the stimulatory effects of exogenous nicotinamide adenine dinucleotide (NAD+) on the expression of MUC2, the main mucin subtype in the intestine, in LS 174T goblet cells. NAD+ significantly stimulated MUC2 expression at the transcriptional and translational levels. Through RNA sequencing, we found that the expression of genes involved in arachidonic acid metabolism was increased in NAD+-treated cells compared with the negative control cells. For example, NAD+ treatment increased phospholipase C (PLC)-δ and prostaglandin E synthase (PTGES) expression, which was inhibited by the appropriate inhibitors. Among the protein kinase C (PKC) isozymes, PKC-δ was involved in the increase in MUC2 expression. In addition, extracellular signal-regulated kinase (ERK)1/2 and cyclic AMP (cAMP) response element-binding protein (CREB) transcript levels were higher in NAD+-treated cells than in the negative control cells, and the enhanced levels of phosphorylated CREB augmented MUC2 expression. In conclusion, exogenous NAD+ increases MUC2 expression by stimulating the PLC-δ/PTGES/PKC-δ/ERK1/2/CREB signalling pathway.

overall_design: 2 samples in triplicate, total 6 samples; negative control and NAD+ 200 uM treated LS 174T

first: Seongho

last: Ma

first: Jiah

last: Yeom

first: Young-Hee

last: Lim


title: ChIP-seq study on Dnd proteins

summary: Tto get the DNA PT modification proteins binding regions on the genome, ChIP with anti-Flag antibody followed by Illumina sequencing was applied.

overall_design: We performed six ChIP experiments, including three biology replicates of Flag-DndC in YF11 (S. enterica 87∆dndC mutant), three different strains expressing DndBCDE in WXL1 (S. enterica 87∆dndBCDE mutant) with Flag tag fused to DndC, DndD, and DndE respectively (Supplementary Fig. 1a), and reproducible patterns were identified in all six ChIPs . For each ChIP, three negative controls were performed: the same strain without antibody control, Dnd protein without Flag tag control, and Flag tag not fused to Dnd protein control.

first: Patricia

last: Aquino

last: Galagan

first: Peter

last: Dedon


title: Transcriptome analysis of whole brain tissue from Bahd1+/+ (WT) and Bahd1-/- (KO) mouse embryos (stage E16.5)

first: Jouneau

last: Luc

summary: Comparisons of brain gene expression profiles of Bahd1-KO mouse embryos to those of wild-type littermates

overall_design: RNA-seq of 3 samples of Bahd1-/-  embryonic brains and 3 samples of Bahd1+/+ embryonic brains

first: Renaud

last: Pourpre

first: Luc

last: Jouneau

first: Hugo

last: Varet

first: Rachel

last: Legendre

first: Olivia

last: Wendling

first: Caroline

last: Proux

first: Jean-Yves

last: Coppée

first: Hélène

last: Bierne


title: Heat-evolved microalgal symbionts increase coral bleaching tolerance

city: Canberra

first: Patrick

last: Buerger

address: Clunies Ross St, S1.03, Bldg 101,

institute: CSIRO

summary: We tested the thermal tolerance of coral larvae with heat-evolved and wild-type strains and explored the molecular mechanisms for the differential thermal tolerance with gene expression patterns. This archive provides the raw data of the RNA sequencing.

sample_organism:
Acropora tenuis
Cladocopium goreaui

platform_organism:
Acropora tenuis
Cladocopium goreaui

overall_design: We sequenced the gene expression patterns of the coral host and the algal symbionts in hospite, dual RNA-seq. The sequencing was performed on a NovaSeq 6000 and yielding 2 billion reads. Each file contains data from the coral host and algal symbiont. For further methodological details please check the associated research paper (Science Advances).

first: Carlos

last: Alvarez Roa

first: Chris

last: Coppin

first: Stephen

last: Pearce

first: Leela

last: Chakravarti

first: John

middle: G

last: Oakeshott

first: Owain

last: Edwards

first: Madeleine

last: van Oppen


title: Genome-wide maps of ARR12 transcription factor in root apical meristems cell of A. thaliana

status: Public on May 20 2020

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: We performed a genome binding/occupancy profiling by high throughput sequencing (ChIP-seq) of  root meristems of 3 days post germination old transgenic lines expressing GFP-tagged ARR12 (ARR12-GFP) as well as Col-0 as negative control to identify ARR12 direct target genes.

overall_design: ARR12-GFP ChIP was performed with an anti-GFP antibody in two independent biological replicates for each genotype (ARR12-GFP (ARR12) and Col-0  (control)). An aliquot of the total amount of the extracted DNA (INPUT) was kept and sequenced as a reference for each sample in each biological replicate.

first: Elena

last: Salvi

first: Rodolfo

last: Negri

first: Sabrina

last: Sabatini


title: Transcriptome analysis of half-brain tissue from Bahd1+/+ (WT) and Bahd1-/- (KO) mice (about 70 weeks old)

first: Jouneau

last: Luc

summary: Comparisons of brain gene expression profiles of Bahd1-KO mice to those of wild-type littermate mice

overall_design: RNA-seq of 3 samples of Bahd1-/-  half brains and 3 samples of Bahd1+/+ half brains

first: Renaud

last: Pourpre

first: Luc

last: Jouneau

first: Hugo

last: Varet

first: Rachel

last: Legendre


title: Glutamine depletion regulates Slug to promote EMT and metastasis in pancreatic cancer [mouse]

city: San Diego

first: Brian

middle: Patrick

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Tumor cells rely on glutamine to fulfill their metabolic demands and sustain proliferation. The elevated consumption of glutamine can lead to intratumoral nutrient depletion, causing metabolic stress that has the potential to impact tumor progression. Here, we show that nutrient stress caused by glutamine deprivation leads to the induction of epithelial-mesenchymal transition (EMT) in pancreatic ductal adenocarcinoma (PDAC) cells. Mechanistically, we demonstrate that glutamine deficiency regulates EMT through the upregulation of the EMT master regulator Slug, a process that is dependent on both MEK/ERK signaling and ATF4. We find that Slug is required in PDAC cells for glutamine deprivation-induced EMT, cell motility and nutrient stress survival. Importantly, we decipher that Slug is associated with nutrient stress in PDAC tumors and is required for metastasis. These results delineate a novel role for Slug in the nutrient stress response and provide insight into how nutrient depletion might influence PDAC progression.

overall_design: We performed RNA sequencing in KPC cells control or glutamine starved. We also evaluated the effect of Slug knockdown using two Slug targeting shRNA hairpins and shLuc as control in glutamine starved conditions. Five replicates per group were evaluated.

first: Maria

middle: V

last: Recouvreux

first: Cosimo

last: Commisso


title: The tumor suppressor BRCA1 is a translational regulator

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

institute: university Lyon1

summary: BRCA1 inactivation is a hallmark of familial breast cancer, often encountered in aggressive triple negative breast cancers. BRCA1 is a tumor suppressor with known functions in DNA repair, transcription regulation, cell cycle control, and apoptosis. In the present study, we demonstrate that BRCA1 is also a translational regulator. Based on the combination of RNA-binding protein immunoprecipitation and microarray analysis, as well as polysome profiling, we identified a subset of mRNAs translationally regulated by BRCA1 and coding for proteins whose functions play major role in cancer. We found that the level of these key proteins is similarly controlled in human mammary tumors according to their BRCA1-status. Therefore, our results propose translational control as a novel molecular mechanism with clinical relevance through which BRCA1 is a tumor suppressor.

overall_design: The experiment is realised on breast carcinoma MCF-7 cell line and is based on the combination of RNA-binding protein immunoprecipitation and transcriptome analysis with microarray technology, as well as polysome profiling

first: Nicole

last: Dalla-Venezia

first: Jean-Jacques

last: Diaz

first: Elise

last: Berthel

first: Anne

last: Vincent

first: Lauriane

last: Eberst

first: Estelle

last: Dacheux

first: Catherine

last: Rey

first: Virginie

last: Marcel

first: Joel

last: Lachuer

first: Frédéric

last: Catez

first: Isabelle

last: Treilleux


title: Transcriptome analysis of neural progenitor cells derived from Lowe Syndrome induced pluripotent stem cells

city: Bronx

first: Hequn

last: Liu

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: Lowe Syndrome (LS) is caused by loss-of-function mutations in the X-linked gene OCRL that codes for a 901 amino acid protein, inositol polyphosphate 5-phosphatase, which plays a key role in endosome recycling, clathrin coated pit formation and actin polymerization. It is characterized by congenital cataracts, intellectual and developmental disability, and renal proximal tubular dysfunction. Patients are also at high risk for developing glaucoma and seizures. We recently developed induced pluripotent stem cells (iPSCs) from three patients with LS who have hypomorphic variants affected the 3’ end of the gene, and their neurotypical brothers to serve as controls. In this study, we used RNA sequencing (RNA-seq) to obtain a transcriptome profile in neural progenitor cells (NPCs). Thirty-six differentially expressed genes (DEGs) were found in patient/control comparisons that were shared across all three sets of sibling pairs. Interestingly, two-thirds of these genes have previously been found to be involved in neuropsychiatric and neurodevelopmental disorders. Furthermore, 14 of the DEGs are strong candidate genes for a variety of eye disorders, including glaucoma development. The most notable example is EFEMP1, which was significantly increased in LS NPCs. These DEGs found in NPCs could reflect similar alterations occurring in eye tissues or their progenitor cells from LS. Overall, the RNA-seq findings present several molecular pathways that could explain the underlying basis for the neurodevelopmental and eye problems seen in boys with LS.

overall_design: Three Lowe Syndrome patients and 3 sibling controls were analyzed in duplicate, using the Illumina HiSeq 2500 system.

first: Jesse

last: Barnes

first: Erika

last: Pedrosa

first: Nathaniel

middle: S

last: Herman

first: Franklin

last: Salas

first: Deyou

last: Zheng

first: Herbert

last: Lachman


title: Glutamine depletion regulates Slug to promote EMT and metastasis in pancreatic cancer

first: Brian

last: James

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

overall_design: Refer to individual Series


title: As an unfavorable prognostic factor, LACTB promotes metastasis of nasopharyngeal carcinoma via activation of ERBB3/EGFR-ERK signaling

status: Public on May 19 2020

city: Guangzhou

first: Qi

last: Zhao

state: Guangdong

address: No. 651, Dongfengdong Road

department: Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: Nasopharyngeal carcinoma (NPC) is a malignant tumor originating from the nasopharyngeal epithelium and has the highest metastatic rate among head and neck cancers, NPC metastasis has become the main cause of treatment failure. The molecular basis regulating NPC metastasis remains obscure. Here we discovered a gene named LACTB Highly expressed in NPC tissues and aimed to investigate its role and regulatory mechanism in the metastasis of NPC.LACTB was found to promote NPC cellular motility in vitro and metastasis in vivo via the activation of the ERBB3/EGFR-ERK pathway on a histone H3 depending manner. Also, the elevated expression of LACTB in the primary NPC correlated with patient poor survival, indicating LACTB as a potential prognostic predictor and an anti-metastasis therapeutic target.

overall_design: To explore the mechanism of histone H3 alteration regulated by LACTB, S18 scrambled, sh581 and sh1069 cells were compared by RNA-sequencing.

first: Li-Xia

last: Peng

first: Chao-nan

last: Qian


title: Transcriptome analysis of Prunus spp. plants under flooding stress

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

summary:
Purpose: The State of Rio Grande do Sul is the largest producer of peaches from Brazil. However, it still has low values of productivity when compared to other States. One of the problems associated to it this is the occurrence of drainage soils problems, which can suffer flooding situations potentially hampering the development and productivity such culture. For studies to assist in the selection of flood tolerant genotypes, it is essential to understand the physiological and molecular changes of the plants in situations of oxygen deprivation. Using Illumina Hiseq2500 we performed transcriptome analysis of leaves from ‘Capdeboscq’ (Prunus persica) and ‘Julior’ (Prunus insititia x Prunus domestica) rootstocks under flooding for 48 hours.
Methods: The mRNA of Prunus spp. plants cv. Capdeboscq e Julior was generated using deep sequencing, in triplicate, using Illumina Hi-Seq 2500, for the following treatments:I) control: plants received irrigation daily until field capacity; and II) plants exposed to flood stress, maintaining a water level of approximately 3 cm above the ground. The sequence reads that passed quality filters were analyzed at the transcript level using this method: Mapping using STAR and identification of differentially expressed genes (DEGs) was performed with the edgeR (false discovery rates - FDRs of <0.05). RT–qPCR validation was performed using SYBR Green assays.
Results: Flooding stress causes important high transcriptional changes in the ‘Capdeboscq’ compared to 'Julior' and this is mainly due to their sensitivity/tolerance levels. ‘Capdeboscq’ had photosynthesis as the most affected physiological process at the molecular level, showing a large number of down-regulated enriched GOs, even though it activated cellular signaling pathways under flooding. 'Julior' was more efficient in defense responses, which include the activation of flavonoid biosynthesis pathways.
Conclusions: The analysis of two Prunus spp. rootstocks contrasting to the level of tolerance / sensitivity provide new insights into the process of plant flood stress tolerance.

sample_organism: Prunus domestica x Prunus domestica subsp. insititia

overall_design: mRNA profiles of Prunus spp. plants under flooding stress were generated by deep sequencing, in duplicate, using Illumina Hi-seq 2500.

first: Elsa

middle: K

last: Klumb

first: Luís

middle: W