title: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of ICAM-1 on lung ILC2 Transcriptome

status: Public on Sep 30 2020

city: Los Angeles

first: Benjamin

middle: Pierre

last: Hurrell

state: CA

address: 1450 Biggy Street

department: MMI

country: USA

institute: University of Southern California

type: Expression profiling by high throughput sequencing

summary: ICAM-1 modulates cytokine expression in ILC2s. While it downregulates the expression of ILC2 key cytokines il5, il13 and il9, it upregulates that of il10.

overall_design: mRNA profiles of sorted mouse activated lung ILC2s from C57BL/6 and ICAM-1 mice were generated by deep sequencing, in duplicates, using a NextSeq 500 (Illumina) system.

middle: P

first: Omid

last: Akbari


title: Gene expression of MOLM14 (AML cell line) transfected with shCD39 or shCTRL

status: Public on Sep 29 2020

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Relapses driven by chemoresistant leukemic cell populations are the main cause of mortality for patients with acute myeloid leukemia (AML). Here, we show that the ectonucleotidase CD39 (ENTPD1) is upregulated in cytarabine (AraC)-resistant leukemic cells from both AML cell lines and patient samples in vivo and in vitro. Similarly, CD39 cell surface expression and activity is increased in AML patients upon chemotherapy compared to diagnosis and enrichment in CD39-expressing blasts is a marker of adverse prognosis in the clinics. High CD39 activity promotes AraC resistance by enhancing mitochondrial activity and biogenesis through activation of a cAMP-mediated response. Finally, genetic and pharmacological inhibition of CD39 eATPase activity blocks the mitochondrial reprogramming triggered by AraC treatment and markedly enhances its cytotoxicity in AML cells in vitro and in vivo. Together, these results reveal CD39 as a new prognostic marker and a promising therapeutic target to improve chemotherapy response in AML.

overall_design: MOLM14 AML cells were grown and treated with doxycycline during 72 hours to express shControl and shCD39 for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene signature specific ofCD39/ENTPD1 function.

first: Aroua

last: Nesrine

first: Sarry

last: Jean-Emmanuel

first: Kaoma

last: Tony


title: Statin-induced microRNAome alterations in patients with hypercholesterolemia

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

summary: This study investigates miRNA expression profiles from peripheral blood specimens in patients with hypercholesterolemia. Our findings demonstrated that miRNA regulations could be involved in statin-induced inflammation modulation in immune cells, thereby providing an anti-inflammatory approach to reduce residual ASCVD risk in individuals with optimal lipid control.

overall_design: A total of 34 hypercholesterolemic patients were recruited to receive 2 mg/day pitavastatin or 10 mg/day atorvastatin treatment for 12 weeks. Peripheral blood mononuclear cells (PBMC) were isolated at enrollment and 12 weeks.

first: Hung-Ju

last: Lin

first: Kuo-Liang

last: Chien


title: small RNA seqencing of pig small inteseine cells samples from different treatment groups

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: small RNA seqencing of pig small inteseine cells  samples from different groups in different generations to search for weaning effect on gene expression.

overall_design: small RNA seqencing of pig small inteseine cells  samples from different groups in different generations to search forweaning effect on gene expression.

first: Bohui

last: Xiong

first: Cong

last: Zhang

first: Qingshi

last: Meng

first: Hongfu


title: Expression data from human whole blood of propionate treated MS patients

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

summary:
Short chain fatty acids were shown to affect regulatory immune response in context of autoimmune diseases like multiple sclerosis (MS). Recent studies in an animal model of MS revealed significant impact of short chain fatty acid propionate (PA) on the differentiation towards regulatory Tcells (Treg). In a translational proof of concept study, PA was administered to relapse remitting MS patients. We observed an increase of Treg in peripheral blood as well as functional improvement in Treg suppressive capacity beside a decrease of proinflammatory Thelper1 and 17 cells.
To investigate underlying mechanisms of the observed shift in immune cell balance, intensive transcriptomic analysis on whole blood of PA treated relapse remitting MS patients was performed.

overall_design: PA was supplemented on daily basis in four relapse remitting MS patients for 14 days. Blood was collected in BD PaxGene tubes for RNA isolation and subsequent microarray analysis to compare baseline and 14 days of treatment.

first: Aiden

last: Haghikia

first: Alexander

last: Duscha


title: small RNA seqencing of mouse sperm samples from different treatment groups

summary: The gole of this project was to explore the effect of NH3 and/or H2S effect on the mouse sperm small RNA expression and the trangerational effects. small RNA sequencing of mouse sperm samples from different groups (NH3 and or H2S treatment) in different generations was done to search for transgenerational effects on RNA expression.

overall_design: small RNA seqencing  of mouse sperm samples from different groups in different generations to search for transgenerational effects of NH3 and/or H2S treatment. First, three weeks of age ICR male mice were treated with NH3 and H2S for 5 weeks (F0 mice). Then the mice (F0) mated with normal ICR female mice. After delivery, F1 male mice were raised normally (without any treatments). At the 8 weeks of age, F1 male mice mated with normal female mice. The F2 male mice were raised normally without any treatment. The semen was collected for F0, F1, F2 mice for the RNA-seq to search for the transgenerational effects of NH3, H2S.


title: scRNA-seq on C57BL/6J mice retina

city: Irvine

first: Les

last: Kallestad

address: 829 Health Sciences Rd

department: Ophthalmology

institute: University of California Irvine

summary: Fresh retinatissues were harvested from 30 day old C57BL/6J mice according to published protocols. 3 retinas were pooled together to form one biological sample. Under a dissecting microscope, spring scissors were used to puncture the eye and remove the cornea, iris, and lens. The remaining eyecup had 4 radial incisions made every 90 degrees, resulting in a flat and open eye cup. The retina was then gently removed using curved tweezers and placed in a 1.5 ml microcentrifuge tube.

first: Krzysztof

last: Palczewski


title: YTHDF3 Induces the Translation of m6A-enriched Metastasis-associated Gene Transcripts to Promote Breast Cancer Brain Metastasis

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

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

overall_design: Refer to individual Series


title: GSF1635: RNA-seq data of OVCAR3-DAB2IP expressing cells vs. control

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

summary: Ovarian cancer (OC) is the leading cause of death from gynecologic malignancies in the US. Ovarian cancer stem cells (OCSCs) have been shown to drive chemoresistance and tumor  progression but the mechanism remains incompletely understood. Disabled Homolog 2-  Interacting Protein (DAB2IP) is a potent tumor suppressor identified in multiple types of cancers  and we demonstrate that DAB2IP is silenced by the repressive epigenetic mark H3K27me3 at  the DAB2IP promoter loci in OCSCs.

overall_design: In triplicate,OVCAR3 cells were transfected with DAb2IP expressing vectors and empty vectors. RNA was harvested from the adipocytes using the RNAEasy kit (Qiagen). RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina #RS-122-2101) according to manufacter's protocol.

first: Xingyue

last: Zong

first: Doug

last: Rusch

first: Fang

last: Fang

first: Aaron

last: Buechlein


title: Mouse trophoblast stem cells in KSR-based conditions

city: Bunkyo ku

first: Shuai

last: Sun

state: Tokyo

country: Japan

institute: The university of Tokyo

summary: We have constituted the serum-free culture conditions (SFC) with Knockout Serum Replacement that support growth of mouse trophoblast stem cells (TSCs). The global gene expression profile of undifferentiated TSCs was maintained in the SFC. TSCs in the SFC showed differentiation potential both in vitro and in vivo.

overall_design: mRNA expression profiles of TSC, which cultured in conventional FBS culture condition and KSR culture condition

first: Satoshi

last: Tanaka


title: RNAseq from mouse Cre-loxP-induced Ewsr1-Atf1 translocation

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

institute: China Agricutural University

summary: Mice formed tumors after a translocation induced between Ewsr1 and Atf1 genes on chromosomes 11 and 15. From total RNA, libraries were generated using the RiboZero method and sequenced on an Ilumina HiSeq instrument to permit comparison to prior datasets prepared with the same methods.

overall_design: Transcriptome sequencing for comparison to a prior dataset.

first: Kevin

last: Jones


title: RNA-seq of pig small inteseine cells samples from different treatment groups

first: Yong

last: Zhao

summary: RNA-seq of pig small inteseine cells  samples from different groups in different generations to search for weaning effect on gene expression.

first: Bohui

last: Xiong

first: Cong

last: Zhang

first: Qingshi


title: Expression profiling of ramie genes

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: To aid the annotation of the genome of cultivated (ZSZ1) and wild (QYZM) ramie and characterize the expression profiling, the root, stem and leaves from these two varieties were performed for transcriptome sequencing. Our results generated 20,693 and 19,498 predicted genes from QYZM and ZSZ1 genome. of them, 17,983 QYZM genes and 17,998 ZSZ1 expressed in at least one of these three examined tissues.

overall_design: RNA-seq for three tissues (i.e., roots, stems, and leaves) in two varieties whose genome was de novo assembled.


title: Pig small inteseine cells samples from different treatment groups


title: RNAseq comparing mouse Cre-loxP-induced EWSR1-ATF1 expression from Rosa26 versus Ewsr1-Atf1 translocation

summary: Mice formed tumors either after a TATCre-induced floxed-STOP removal from an EWSR1-ATF1 human cDNA expression vector targeted to the Rosa26 endogenous pseudogene or after an Hprt-Cre-initiated translocation between Ewsr1 and Atf1 genes on chromosomes 11 and 15. From total RNA, libraries were generated using the RiboZero method and sequenced on an Ilumina NovaSeq instrument to permit comparison to each other.

overall_design: Transcriptome sequencing for comparison


title: Transcriptomic response of Fusarium verticillioides to Bacillus mojavensis lipopeptides

city: Riverside

first: Alex

last: Blacutt

address: 3523 Webber Hall

institute: University of California, Riverside

summary: Transcriptomic data collected from cultures of Fusarium verticillioides six hours post-exposure to Bacillus mojavensis RRC101 lipopeptides (surfactins, fengycins, combined treatment)

overall_design: SRP150421, PRJNA475942 - mRNA from F. verticillioides cultures exposed to fengycin, surfactin, and a combination treatment were harvested six hours post treatment

first: Scott

last: Gold

first: Anthony

last: Glenn


title: CD73 contributes to anti-inflammatory properties of afferent lymphatic endothelial cells in humans and mice

city: Turku

first: Sirpa

last: Jalkanen

address: Tykistökatu 6a

department: Medical Microbiology and Immunology

country: Finland

institute: Univeristy of Turku

summary: The aim of this study is to compare gene expression differences between human lymphatic endothelial cells after they have been treated with siRNA or with different CD73-blocking antibodies. In addition also the gene expression differences after antibody-blocking in human blood endothelial cells are determined.

overall_design: Transcriptome profiles from four different donors of human lymphatic and blood endothelial cells after different treatments were generated by NGS using Illumina Hiseq3000.

first: Dominik

last: Eichin


title: Transcriptomic Modifications in Developmental Cardiopulmonary Adaptations to Chronic Hypoxia Using a Murine Model of Simulated High Altitude Exposure

city: Indianapolis

first: Robert

last: Stearman

address: 950 W Walnut St

department: Medicine/Pulmonary

institute: Indiana Univeristy School of Medicine

summary: Mechanisms driving adaptive developmental responses to chronic high altitude (HA) exposure are incompletely known. We developed a novel rat model mimicking the human condition of cardiopulmonary adaptation to HA starting at conception and spanning the in utero and early life timeframe. We assessed lung growth and cardiopulmonary structure and function, and performed transcriptome analyses to identify mechanisms facilitating developmental adaptations to chronic hypoxia. To generate the model, breeding pairs of Sprague-Dawley rats were exposed to hypobaric hypoxia (equivalent to 9,000 feet elevation). Mating, pregnancy and delivery occurred in hypoxic conditions. Six weeks postpartum, structural and functional data were collected in the offspring. RNAseq was performed on right ventricle (RV) and lung tissue. Age-matched breeding pairs and offspring under room air (RA) conditions served as controls. Hypoxic rats exhibited significantly lower body weights and higher hematocrit levels, alveolar volumes, pulmonary diffusion capacities, RV mass, RV systolic pressure as well as increased pulmonary artery remodeling. RNAseq revealed multiple differentially expressed genes in lungs and RVs from hypoxic rats. While there was considerable similarity between hypoxic lungs and RVs compared to RA controls, several upstream regulators unique to lung or RV were identified. We noted a pattern of immune down-regulation and regulation patterns of immune and hormonal mediators similar to the genome from patients with pulmonary arterial hypertension. In summary, we developed a novel murine model of chronic hypoxia exposure that demonstrates functional and structural phenotypes similar to human adaptation. We identified transcriptomic alterations that suggest potential mechanisms for adaptation to chronic HA.

overall_design: Age matched 7-week old male or female Sprague Dawley rats (200-225 g) were acclimated to either room air or hypobaric for three weeks until they achieved the appropriate breeding age of 10 weeks. At 10 weeks, each mating pair was placed together in a standard cage for mating in their respective room air or hypoxic environments. A hypobaric hypoxia chamber, depressurized to an equivalent of an inspired oxygen fraction of 15%, was used to simulate a 9,000 feet HA environment. Males were removed from the cages once the female was visibly pregnant and females delivered naturally at term. Pups were weaned at 21 days and physiologic experiments and animal sacrifice with tissue harvest occurred at 6 weeks of age. Animals exposed to in utero and postnatal room air are denoted RA-RA and animals exposed in utero and postnatal hypoxia are denoted H-H. Lung and heart right ventricle (RV) tissues were flash frozen in liquid nitrogen and stored at -80C until RNA preparation. Animals from 2 separate litters at RA-RA of H-H were used approximately equal numbers of males and females. RNA-seq analysis on 29 rat lung samples (15 RA-RA; 14 H-H) and 26 RV samples (11 RA-RA; 14 H-H) was completed.

middle: S


title: Regulators of sexual commitment in Plasmodium falciparum

city: London

first: Moritz

last: Treeck

address: 1 MIdland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: The aim of this study was to identify transcriptonal responses during sexual commitment of P. falciparum mutants unable to form gametocytes.

overall_design: Sexual induction of the kinase KO lines and 3D7 control line was started with a 3% asexual ring culture (cycle I) where sexual commitment was induced by using 50% spent medium during the following intra-erythrocytic cycle (cycle II). The sexually committed merozoites were expected to invade and gametocytes develop during the next cycle of infection (cycle III). The samples were collected at 28-32 hpi during cycle II or induction cycle (Time Point I) and at 28-32 hpi after induction   of sexual commitment during cycle III  (Time Point II). The infected RBCs were collected at the respective time point, centrifuged and solubilized in ten volumes of TRIzol prewarmed to 37°C, mixed vigorously for 5 minutes at 37°C and immediately frozen at -80°C until extraction. Once all samples were collected, the frozen samples were quickly thawed and 0.2mL of chloroform added per each mL of TRIzol. After vigorous mixing the mixture was left for 3 min at room temperature. After centrifugation at 13,200 rpm for 30min at 4°C, the upper aqueous phase containing the RNA was collected into a new tube and an equal volume of ethanol 70% added. After vigorous mixing, the solution was loaded into an RNA Spin cartridge purified using the RNAeasy Quiagen. After RNA extraction and purification, the samples were treated with DNAse I (Quiagen). The synthesis of cDNA was performed using the superscript III first-strand synthesis system (Invitrogen). Only samples collected at time point I (Induction cycle) were considered for the purpose of the paper.

first: Marta

last: Tiburcio

first: Oliver

last: Billker

first: Gavin

last: Kelly

first: Mandy

last: Sanders

first: Frank

last: Schwach


title: Small RNA sequencing of H19X KD cell line

city: chengdu

first: li

last: tongtong

state: sichuan

address: sichuan

institute: xinong

summary: The H19X RNAi knockdown cell lines were generated, and  both miRNA and piRNA expression were compared in H19X KD cell line compared with control

overall_design: H19X RNAi knockdown

first: W

last: Xu


title: RNA-Seq analysis of E4FAD mouse brain cortex to evaluate the impact of omega-6 fatty acid docosapentaenoic acid on neuroinflammation

first: Qiu-Lan

last: Ma

address: 11301 Wilshire Boulevard Los Angeles, CA

institute: University Of California Los Angeles

summary:
Purpose: In this study, we report on an effective anti-inflammatory lipid, linoleic acid (LA) metabolite docosapentaenoic acid (DPAn-6) treatment of aged humanized EFAD mice with advanced AD pathology. We also report the associations of neuroinflammatory and/or activated microglial markers with neurodegeneration in vivo.
Methods: DPAn-6 was administered to the E4FAD mice by oral gavage for three weeks, then brain tissue was collected for the study. Total RNA was qualified using an Agilent BioAnalyzer of High Sensitivity RNA ScreenTapeÒ for Eukaryotic RNA Analysis and 1 µg was used for poly(A) mRNA selection and library construction with IlluminaÒ Platforms KAPA mRNA HyperPrep kit (KK8580 08098115702) according to the manufacturer's instructions (KR1352 – v4.17).
Results: We found that DPAn-6 reduced mRNA expressions of inflammatory markers of Il1rl2, Il6ra, Il6st, Tnfrsf1b, Tnfsf10, Il10rb; microglial markers of Tmem119, CD68 and TREM2; and caspase markers of Casp2, Casp6 and Casp8.  Further, DPAn-6 increased mRNA expressions of ADCYAP1, VGF, and neuronal pentraxin 2 in parallel, all of which were inversely correlated with inflammatory and microglial markers.
Conclusions: We first reportd that DPAn-6 modulated neuroinflammatory responses towards resolution and improvement of neurodegeneration in the late stages of AD models.

overall_design: Brain cortex mRNA profiles of DPAn-6-treated E4FAD mice.

first: Gregory

middle: M

last: Cole


title: Myc is required for adaptive beta cell replication in young mice but is not sufficient in one year old mice fed with a high fat

city: New York

first: Donald

middle: K

last: Scott

state: New York

address: 1428 Madison Avenue

department: Diabetes Obesity and Metabolism Institute

institute: MSSM

type: Methylation profiling by high throughput sequencing

summary:
Purpose: To test the role of Myc in adaptive expansion of beta cells
Methods: Islets were isolated from 8 week old or one year old male C57BL6 mice fed a standard or high fat diet.  RNAseq and DNA mehtylseq was performed.
Results: RNAseq showed that Myc target genes are upregulted in young, but not old mice after a short term high fat diet.  DNA methylation analysis shows hypomethylation of cell cycle genes that are Myc targets in islets from young mice fed with a HFD. Importantly, DNA hypomethylation of Myc response elements does not occur in islets from one-year-old mice fed short-term HFD
Conclusions: We conclude that Myc is required for metabolic stress-mediated beta cell expansion in young mice, but with aging Myc upregulation in beta cells is not sufficient to induce beta cell replication by, at least partly, an epigenetically-mediated resistance to Myc action.

overall_design: RNASeq and MethylSeq of selected genomic regions from islets isolated from 8 week old or 1 year old mice fed a standard or high fat diet. All groups in triplicate or quadruplicate.

first: Adoflo

last: Garcia-Ocana


title: TransMPRA sequencing data.

city: Seattle

first: Diego

last: Calderon

address: 3720 15th Ave NE

institute: University of Washington

summary: Gene regulation occurs through trans-acting factors (e.g. transcription factors) acting on cis-regulatory elements (e.g. enhancers). Massively parallel reporter assays (MPRAs) functionally survey large numbers of cis-regulatory elements for regulatory potential, but do not identify the trans-acting factors that mediate any observed effects. Here we include preliminary data from a pilot transMPRA experiment — a reporter assay that efficiently combines multiplex CRISPR-mediated perturbation and MPRAs to identify trans-acting factors that modulate the regulatory activity of specific enhancers.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: 2 spike-in fastq files with information used to associate random barcodes that identify specific gRNAs. 24 fastqs with RNA or DNA sequencing information of reads from the 2323 distinct transMPRA constructs containing many distinct barcodes. These were collected from 3 replicates at 2 library concentrations (lowMOI vs highMOI) from cells harvested at 2 time points (day 5 vs day 10).


title: Gut microbiota analysis associated with autism spectrum disorders [16S rRNA]

city: Nanjing City

first: Xingyin

last: Liu

state: Jiangsu Province

address: Long Mian Street No.1

institute: Nanjing Medical University

summary: Here we report 16S rRNA data in gut microbiota of  autism spectrum disorders compared with healthy volunteers. A total of 1322  operational taxonomic units (OTUs) were identified in the sequence data. The Bacteroidetes and Firmicutes were both dominated phylum in ausitic subjects and healthy controls. Phylum level analysis showed a clear alteration of the bacterial gut community in ASD characterized by a higher Firmicutes (P < 0.05), Proteobacteria (P < 0.001), and Actinobacteria (P < 0.001) than that in healthy controls. However, Bacteroidetes were significantly decreased in ASD patients (P < 0.001).

overall_design:
Microbial DNA from fecal samples [healthy control (n=143), ASD patients (n=143)] were amplified by PCR using universal bacterial primers.  PCR was performed to produce V4 regions of the 16S rDNA gene using the conserved primers 515F (5'-GTGCCAGCMGCCGCGGTAA-3') and 806R (5'-GGACTACHVGGGTWTCTAAT-3'). 16S rRNA were sequenced by Novogene Bioinformatics Technology Co., Ltd. (Shanghai, China).

Subject IDs (e.g. A3) in this study represent the same individual with identical id in GSE113540.

first: Zhou

last: Dan

first: Xuhao

last: Mao

first: Qisha

first: Zhi


title: RNA-seq of mouse small intestine samples from different treatment groups

first: Yong

last: Zhao

institute: Qingdao Agricultural University

summary: The aim of this project was to explore the role of  Alginate oligosaccharides (AOS) on the development small intestine. The mice were treated with one dose busulfan then the mice were dosed with AOS for 5 weeks. Then the small intestine were collected. The RNA from small intestine was used for the RNA-seq analysis to search the role of AOS on small intestine development. Groups: W5A0 was from AOS 0 treatment; W5A10 was from AOS 10 treatment; W5BA0 was from busulfan and AOS 0 treatment; W5BA10 was from busulfan and AOS 10 treatment.

overall_design: RNA-seq of mouse small intestine samples from different groups in busulfan and/or AOS treatments.

first: Yanni

last: Feng

first: Hongfu

last: Zhang


title: RNA-seq analysis of αPD-1 treatment outcomes in IL-34 expressing or not expressing CT26 cell line

city: Sapporo

first: Ken-ichiro

last: Seino

address: Kita-15 Nishi-7

institute: Hokkaido University

summary:
Interleukin-34 (IL-34) is an alternative ligand to colony-stimulating factor-1 (CSF-1) for the CSF-1 receptor that acts as a key regulator of monocyte/macrophage lineage. In this study, we show that cancer cells-derived IL-34 mediates resistance to immune checkpoint blockade regardless of CSF-1 existence. In a therapeutic study of a programmed death-1 and cytotoxic T-lymphocyte-associated antigen-4 blocking monoclonal antibody, the expression of IL-34 in tumors was accompanied with limited benefits compared to IL-34 non-expressing tumors in various murine cancer models. Consistent with its immunosuppressive characteristics,
the expression of IL-34 in tumors correlates with decreased frequencies of cellular (such as CD8+ and CD4+ T cells) and molecular (including various cytokines and chemokines) effectors at the tumor microenvironment. In addition, IL-34 blockade expands the M1-macrophage population. Then, a neutralizing antibody against IL-34 helped to reverse these effects and improved the therapeutic effects of the immune checkpoint blockade in combinatorial therapeutic models, including a patient-derived xenograft model of primary lung adenocarcinoma. Collectively, we revealed that tumor-derived IL-34 inhibits the efficacy of immune checkpoint blockade and proposed the utility of IL-34 blockade as a new strategy for cancer therapy.

overall_design: mRNA profile after αPD-1 treatment of tumors derived from IL-34 expressing or not expressing CT26 cells.

first: Naoki

last: Hama

first: Takuto

last: Kobayashi

first: Nanumi

last: Han

first: Fumihito

last: Kitagawa

first: Nabeel

last: Kajihara

first: Ryo

last: Otsuka

first: Haruka

last: Wada

first: Yoshinori

last: Hasegawa

first: Hideo

last: Yagita

first: Muhammad

last: Baghdadi


title: Epigenetic hallmarks of age-related macular degeneration are recapitulated in a photosensitive mouse model

first: Les

last: Kallestad

institute: University of California Irvine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Age-related macular degeneration (AMD) is a chronic, multifactorial disorder and a leading cause of blindness in the elderly. Characterized by progressive photoreceptor degeneration in the central retina, disease progression involves epigenetic changes in chromatin accessibility resulting from environmental exposures and chronic stress. Here, we report that a photosensitive mouse model of acute stress-induced photoreceptor degeneration recapitulates the epigenetic hallmarks of human AMD. Global epigenomic profiling by assay for transposase-accessible chromatin using sequencing (ATAC-Seq) revealed an association between decreased chromatin accessibility and stress-induced photoreceptor cell death in our mouse model. The epigenomic changes induced by light damage include reduced euchromatin and increased heterochromatin abundance, resulting in transcriptional and translational dysregulation that ultimately drives photoreceptor apoptosis and an inflammatory reactive gliosis in the retina. Through our findings, we identified key histone-modifying enzymes that contribute to the observed changes in global chromatin accessibility. Moreover, pharmacological inhibition of histone deacetylase 11 (HDAC11) and suppressor of variegation 3-9 homolog 2 (SUV39H2) ameliorated light damage in our mouse model, supporting a causal link between decreased chromatin accessibility and photoreceptor degeneration, thereby representing a potential new therapeutic strategy to combat AMD.

overall_design:
RNA-seq and ATAC-seq was conducted on C57BL/6J abca4-/- rdh8-/- mice in replicates of 3-4.
-------------------------------------------------
*This submission lacks processed data for the ATAC-Seq component

first: Krzysztof

last: Palczewski


title: YTHDF3 Induces the Translation of m6A-enriched Metastasis-associated Gene Transcripts to Promote Breast Cancer Brain Metastasis [m6A-seq]

first: Youqiong

last: Ye

institute: Shanghai Jiao Tong University School of Medicine

summary: Brain metastasis is a major cause of cancer mortality, but its molecular mechanisms are severely understudied. We found that YTHDF3 overexpression clinically correlates with brain metastases in breast cancer patients and is required for brain metastasis. Silencing YTHDF3 suppressed the brain metastasis of breast cancer cells in vitro and in vivo. Integrated transcriptome and m6A-seq analysis revealed alter expression of selected YTHDF3 target genes, including ST6GALNAC5, GJA1, and EGFR by promoting m6A-dependent translation of these target transcripts. Our work uncovers an essential role of YTHDF3 in controlling the interaction between cancer cells and brain microenvironment, thereby gaining brain metastatic competence.

overall_design: Overall design: m6A-seq of mRNA from MDA-MB-231Br cells

first: Suyun

last: Huang


title: Transcriptional responses of colon tissues following ex-vivo colonization with human microbiome

city: Ramat Gan

first: Nissan

last: Yissachar

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

summary:
Purpose: The goal of this study is to compare colonic transcriptional responses following ex-vivo colonization with fecal samples collected from multiple sclerosis patients, before and after Propionic acid treatment and between the patients that responded or not to the therapy.
Methods: Bulk whole-tissue mRNA profiles of 13-day-old wild-type mice colons were generated by deep sequencing, in triplicate, using Illumina NextSeq platform.

overall_design: To test whether changes to microbiome composition as a result of PA intake have functional consequences on the local gut tissue, fecal samples of patients before and after 14 days of PA intake were assessed in an intestinal organ culture system (Yissachar et al., 2017).  For the analysis, MS patients microbiome of responders (n=5) and non-responders (n=4), before- and after-PA intake, was introduced into the gut culture system at equivalent bacterial load (10^7 CFU/ml) and bulk RNA sequencing of colon tissues was conducted after 2 hours ( total of 36 colon samples, in two independent sequencing runs).

first: Alexander

last: Duscha

first: Barbara

last: Gisevius

first: Sarah

last: Hirschberg

first: Gabriele

middle: I

last: Stangl

first: Eva

last: Eilers

first: Verian

last: Bader

first: Stefanie

last: Haase

first: Johannes

last: Kaisler

first: Christina

last: David

first: Ruth

last: Schneider

first: Riccardo

last: Troisi

first: Daniel

last: Zent

first: Tobias

last: Hegelmaier

first: Nikolaos

last: Dokalis

first: Sara

last: Gerstein

last: Del Mare-Roumani

first: Sivan

last: Amidror

first: Ori

last: Staszewski

first: Gereon

last: Poschmann

first: Kai

last: Stühler

first: Frank

last: Hirche

first: Andras

last: Balogh

first: Stefan

last: Kempa

first: Jacob

last: Bak Holm

first: Megan

middle: G

last: Massa

first: Henrik

middle: B

last: Nielsen

first: Andreas

last: Faissner

first: Carsten

last: Lukas

first: Sören

last: Gatermann

first: Markus

last: Scholz

first: Horst

last: Przuntek

first: Marco

last: Prinz

first: Sofia

last: Forslund

first: Konstanze

middle: F

last: Winklhofer

first: Dominik

middle: N

last: Müller

first: Ralf

middle: A

last: Linker

last: Gold

first: Aiden

last: Haghikia


title: Skeletal muscle RNA expression following implantation of LLC1 cells in mice

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

summary: 7- week old  male and female, C57BL6 mice received subcutaneous injections of LLC1 lung adenocarcinoma cells or vehicle. Three weeks later, the mice were sacrificed and skeletal muscle was obtained for RNA-seq analysis.

overall_design: Seven-week old male or female mice received subcutaneous injections of LLC1  cells or vehicle.  Three weeks later skeletal muscle mass, strength, weight, mitochondrial function, fractional synthesis rate, and biochemical variables were assessed.  The gastrocnemius muscle was obtained for RNA isolation.

first: Rajiv

last: Kumar


title: RNAsequencing of Mla mutants

status: Public on Sep 28 2020

city: Athens

first: Matthew

last: Powers

state: GA

address: 501 DW Brooks Dr

institute: University of Georgia

summary: RNAsequencing comparing the WT and mla mutants of strains from UGA and UW

overall_design: RNAsequencing was performed on cultures grown until mid-logarthimic stage of growth

middle: J

first: M

last: Trent

first: Brent

middle: W

last: Simpson


title: Notch activity determines a common hepatocellular carcinoma subtype with unique molecular and clinicopathologic features [L-NICD]

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Hepatocellular carcinoma (HCC) is the predominant primary liver cancer and an increasing cause of cancer-related deaths worldwide, due in part through increased obesity-associated nonalcoholic steatohepatitis (NASH) and associated fibrosis. The Notch signaling pathway is inappropriately “reactivated” in hepatocytes in obesity and plays an active role in the pathogenesis of NASH-associated fibrosis. We aimed to understand the involvement of Notch in the pathogenesis of mouse and human HCC.

overall_design: 6 samples of mouse liver tissues (surrounding non-tumor livers and tumors) from 3 different NASH diet-fed Notch-overexrepssed mice (L-NICD) were analyzed.

first: Changyu

last: Zhu

first: Utpal

last: Pajvani


title: Notch activity determines a common hepatocellular carcinoma subtype with unique molecular and clinicopathologic features

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

overall_design: Refer to individual Series


title: ER alpha coregulator peptide screening profiling by MARCoNI (Microarray Assay for Real-time Coregulator-Nuclear receptor Interaction) assay from human embryonic kidney HEK293 cells after tranfected with ER alpha or Q375 mutations

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Estrogen insensitivity syndrome (EIS) arises from rare mutations in ERα resulting in the inability of estrogen to exert its biological effects. Due to the rarity, mutations in ESR1 gene and the underlying molecular mechanisms of EIS have not been thoroughly studied.
We used PamChip array with 154 coregulator motifs (PamGene #88101) array to compare the peptide profiles between the WT and 5 of Q375 mutants in HEK293 cells after transferred with ER alpha or Q375 mutatnts.  93 ligand-modulated peptides were reported here.

overall_design: HEK293 cells after tranfetced with WT ER or Q375 mutants were collected for cell lysate. cell lysate of ERα genotype expressing cells was incubated with or without ligand on a PamChip array with 154 coregulator motifs (PamGene #88101). Ligands: veh (DMSO, control), E2 (17-b-Estradiol), CME (11b-chloromethyl estradiol), Et-E2 (11b-ethyl estradiol), THC (diethyl-tetrahydrochrysene), DES (diethylstilbestrol) or Hex (meso-hexestrol).

first: Yin

last: Li

first: Rene

last: Houtman

first: Diana

last: Melchers


title: TMCO1 co-IP elutions and inputs

city: Chicago

first: Robert

last: Keenan

state: IL

address: 929 East 57th Street

department: Department of Biochemistry & Molecular Biology

institute: University of Chicago

summary: We report the total mRNA profile associated with purified membranes from WT TRex and TMCO1 KO cells, as well as mRNAs on ribosomes associated with TMCO1.

overall_design: Examination of mRNA profile of totol membrane associated mRNAs as well as mRNA profile of ribosomes obtained by TMCO1 IP followed by ultracentrifugation

first: S

last: Anghel


title: Large domains of heterochromatin direct the formation of short mitotic chromosome loops

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

institute: The University of Edinburgh

summary: During mitosis chromosomes reorganise into highly compact, rod-shaped forms, thought to consist of consecutive chromatin loops around a central protein scaffold. Condensin complexes are involved in chromatin compaction, but the contribution of other chromatin proteins, DNA sequence and histone modifications is less understood.  A large region of fission yeast DNA inserted into a mouse chromosome was previously observed to adopt a mitotic organisation distinct from that of surrounding mouse DNA. Here we show that a similar distinct structure is common to a large subset of insertion events in both mouse and human cells and is coincident with the presence of high levels of heterochromatic H3 lysine 9 trimethylation (H3K9me3). Hi-C and microscopy indicate that the heterochromatinised fission yeast DNA is organised into smaller chromatin loops than flanking euchromatic mouse chromatin. We conclude that heterochromatin alters chromatin loop size, thus contributing to the distinct appearance of heterochromatin on mitotic chromosomes, such as at centromeres.

overall_design: HI-C experiment on Interphase and Mitotic phase F1.1 cell line respectively

first: Maximilian

middle: H

last: Fitz-James

first: Hakan

last: Ozadam

first: Job

last: Dekker

first: Pin

last: Tong


title: IFN-b treatment of primary murine hepatocytes

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Primary murine hepatocytes were isolated from C57Bl/6J (wild type) animals and treated with 1000 U/mL IFN-b for 24h and compared to time-matched untreated controls.

overall_design: We sequenced in vitro cultured primary murine hepatocytes that were treated with IFN-b for 24 hours or left untreated.

first: Alexander

last: Lercher

first: Alexandra

last: Popa


title: Notch activity determines a common hepatocellular carcinoma subtype with unique molecular and clinicopathologic features [Venus]

first: Yu-Jui

last: Ho

overall_design: 6 samples of FACS-isolated hepatocytes (Venus-negative and -positive) from 3 different NASH diet-fed Notch-Venus reporter mice were analyzed.


title: Transcriptome profile of healthy mice bone marrow hematopoietic stem cells

city: Tianjin

first: Kaibin

last: Shi

address: 154 Anshan Rd

institute: Tianjin Medical University

summary: We conducted a NanoString analysis of flow cytometric sorted hematopoietic stem cells of healthy C57/BL6 mice, which can be used as control for related studies.

overall_design: Hematopoietic stem cells (HSCs) are sorted from bone marrow of C57/BL6 mice, cells from 3 mice group together as a single biological point. 4 samples are collected in total. Total RNA was then extracted, and subjected to NanoString analysis.

first: Samuel

middle: X

first: Qiang

last: Liu


title: A predictable conserved DNA base composition signature defines human core DNA replication origins

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

institute: University of Birmingham

summary: Here, we identify DNA replication initiation sites from 19 human samples, representing three untransformed and three immortalized cell types using SNS-seq protocol.

overall_design: SNS-seq was performed on 22 human samples, 19 of which were used to define Core human origins.

first: Ildem

last: Akerman

first: Bahar

last: Kassai

first: Benoit

last: Bellaster

first: Marcel

last: Mechali


title: A fully automated high throughput-workflow for human neural organoids

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

country: Switzerland

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

summary: Recent advances in stem cell technology have led to the development of three-dimensional (3D) culture systems called organoids, which have fueled hopes to bring about the next generation of more physiologically relevant high throughput screens (HTS). However, the adaptation of established organoid protocols for HTS applications has so far been elusive. Here, we present a fully scalable, HTS-compatible workflow for the automated generation, maintenance, whole mount staining, clearing, and optical analysis of human neural organoids generated from neural precursor cells in a standard 96-well format. By combining organoid generation and analysis steps in an automated fashion, we can perform quantitative whole-organoid high content imaging with single cell resolution. The resulting organoids are highly homogeneous with regard to their morphology, size, global gene expression, cellular composition, and structure. Calcium imaging suggests organoid-wide synchronized functional coupling. The scalability of our approach has the potential to form the basis for 3D tissue-based screening in a variety of applications including drug development, toxicology studies, and disease modeling.

overall_design: Comparison of automated midbrain organoids and established induced plurioptent stem cell (iPSC)-derived organoids through RNA sequencing.

first: Henrik

last: Renner

first: Martha

last: Grabos

first: Mandy

last: Otto

first: Dagmar

last: Zeuschner

first: Sebastian

last: Leidel

first: Hans

middle: R

last: Schöler

first: Jan

last: Bruder


title: In vitro expansion of cirrhosis derived liver epithelial cells reveals progenitor-like properties [methylation]

city: Portland

first: Bin

last: Li

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Oregon Stem Cell Center

institute: Oregon Health and Science University

type: Methylation profiling by genome tiling array

summary: By looking at the methylation sites in normal human liver hepatocytes, cholangiocytes, cultured gallbladder organoids, cirrhotic liver organoids and cirrhotic liver cells, we are looking at the cell origin of cirrhotic liver cells.

overall_design: To find the relationship between hepatocytes, cholangiocytes and cirrhotic liver cells, we did the bisulphite DNA methylation sequcing.

first: Joshua

last: Moss

first: Ruth

last: Shemer

first: Yuval

last: Dor

first: Markus

last: Grompe


title: ATAC-seq identifies chromatin landscapes linked to the regulation of oxidative stress in the human fungal pathogen Candida albicans

status: Public on Sep 27 2020

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

institute: Max Perutz Labs

summary: ATAC-seq analysis of Candida albicans SC5314 treated or not treated with hydrogen peroxide to assess the accessible chromatin landscape upon oxidative stress in comparison to normal growth in YPD at 30 °C.

overall_design: ATAC-seq data of three biological replicates of C.albicans strain SC5314 and naked genomic DNA (gDNA) prepared from SC5314 as background control. Cells were grown to the logarithmic growth phase in YPD at 300 °C, 200 rpm shaking and then further cultured in YPD at 30 °C +/- hydrogen peroxide for 15 minutes

first: Michael

last: Tscherner

first: Theresia

last: Mair

first: Karl

last: Kuchler


title: MED31 Knockdown in Human MSCs

city: Ruston

first: Jamie

last: Newman

state: Louisiana

address: 1 Adams Blvd, CTH 215, Biological Sciences

department: Biological Sciences

institute: Louisiana Tech University

summary:
siRNA-mediated knockdown of MED31 and Negative siRNA control in human mesenchymal stem cells
Total RNA was collected 72 hours after transfection with siRNA.

overall_design: This study aimed to identify significant changes in gene expression of self-renewing human bone marrow-derived mesenchymal stem cells following the loss of MED31

first: Erik

last: Beadle


title: Transcriptional identification of differentially expressed genes associated with division of labor in Apis cerana cerana

city: Fuzhou

first: Yijie

last: Chen

state: Fujian

address: No. 15, ShangxiadianRoad, Candgshan Zone

department: College of Bee Science

institute: Fujian Agriculture and Forestry University

summary: While Apis cerana cerana, like Apis mellifera, undergoes a behavioral transition from in-hive nursing to outdoor foraging duties, nothing is known about the genes underlying this social signal-triggered aged-related transition in this species. Here, we simultaneously sequenced the head transcriptomes of the 7-day-old normal nurses (N7BY), 18- and 22-day-old normal foragers (N18CJ and N22CJ), 7-day-old precocious foragers (Tq7CJ) and 22-day-old overaged or reverted nurses (Tq22BY) of A. cerana cerana by RNA-seq and made a 3-tier comparison (from pairwise to group-wise and between-group) to unravel the genes associated with this transition. Six pairwise comparisons revealed 165-492 differentially expressed genes between nurses vs. foragers. Subsequent 3 group-wise and 1 between-group comparisons narrowed the transition-associated genes down to 18 nurse- and 41 forager-unique genes and 29 (14 and 15 genes upregulated in nurses and foragers, respectively) differentially expressed genes between the 3 types of foragers and 2 types of nurses. The uniquely expressed genes are usually low-abundance long noncoding RNAs, transcription factors, transcription coactivators, RNA-binding proteins, kinases or phosphatases involved in signaling transduction and/or gene expression regulation, whereas the differentially expressed genes are often high-abundance downstream genes that directly perform the tasks of nurses or foragers, such as major royal jelly proteins for nurses and the genes involved in sugar/protein digestion, lipids/fatty acids metabolism, plant allelochemicals detoxification and defense against pathogens and predators for foragers. Mapping of the clean reads to the published A. mellifera genome uncovered that the 3 types of foragers had a greater percentage of reads from annotated exons and intergenic regions, whereas the 2 types of nurses had a greater percentage of reads from introns. Taken together, these results suggest that the reciprocal nurse-forager behavioral transition of the A. cerana cerana is regulated by a social signal-triggered intron-exon/intergenic epigenetic shift and the resulted transcriptional shift of the nurse- and forager-associated genes.

overall_design: The head transcriptomes of the 7-day-old normal nurses (N7BY), 18- and 22-day-old normal foragers (N18CJ and N22CJ), 7-day-old precocious foragers (Tq7CJ) and 22-day-old overaged or reverted nurses (Tq22BY) of A. cerana cerana

first: Shuang

last: Wu

first: Wenchao

last: Yang

first: Jing

last: Miao

first: Shaohua

last: Gu

first: Jianghong

first: Xiaoqing

first: Xianchun


title: Role of non-classical progesterone receptors in decidualization process

city: Valencia

first: Francisco

last: Domínguez

state: SPAIN

address: Avenida Fernando Abril Martorell, 106

country: Spain

institute: IVI Foundation

summary: To improve the understanding of PGRMC1 during decidualization, different in vitro decidualization protocols and global gene expression of endometrial stromal cells analysis were assessed.

overall_design: Non-decidualized EnSC and EnSC decidualized by P4/E2, P4/E2+AG205 or P4-BSA/E2 (n=4 per condition) were collected after 8 days in culture

first: Stefania

last: Salsano

first: Roberto

last: González-Martín


title: Differentially expressed genes in rough and smooth colony isolates of Clostridioides difficile

city: Chapel Hill

first: Rita

last: Tamayo

address: 125 Mason Farm Rd, CB# 7290

department: Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

summary:
Purpose: to determine the differentially expressed genes in the phase-variable rough and smooth colony isolates of C. difficile
Methods: C. difficile R20291 was grown on BHIS agar to obtain distinct colonies. Individual rough and smooth colonies were chosen for propagation on BHIS-agar for 24 hours as described in Garrett, et al., PLoS Biology, 2019. Growth was collected from n = 2 biological replicates. RNA was purified using TriSure and chloroform, beadbeating, and isopropanol/ethanol precipitation. Quality was verified with Bioanalyzer Assay. Samples were submitted to Genewiz for depletion of rRNA using the TruSeq RiboZero Gold Kit, library preparation, and single-end sequencing on the Illumina HiSeq 2500 platform. RNA sequencing analysis was done using CLC Genomic Workbench v20. Reads were mapped to C. difficile R20291  genome using the software's default menalties for mismatch, deletion, and insertion differences from the reference genome. Transcript reads were normalized as RPKM.
Results: 88 genes were differentially expressed between bacteria from rough versus smooth colonies, with equal to or greater than a 2-fold change and p < 0.05 with FDR correction.

overall_design: C. difficile R20291 rough vs. smooth isolate bacteria, n = 2 biological replicates

first: Elizabeth

last: Garrett


title: Differential gene expression analysis of Plasmodium falciparum PfCDP KO and WT

status: Public on Sep 26 2020

city: Chennai

first: Arumugam

last: Rajavelu

state: Tamil Nadu

address: Adayar

country: India

institute: IITM

summary:
Purpose: We identified novel methyl reader domain protein in P. falciparum. Using Next Generation Sequencing, we studied the differential gene expression in PfCDP conditionally deleted P. falciparum versus wild type.
Methods: Transcriptome analysis of PfCDP KO vs WT P. falciparum using high throughput RNA sequencing in triplicate (Three controls and three KO samples). The total RNA was isolated from P. falciparum WT and PfCDP KO lines, the quality of RNA was assessed using Nanodrop2000, and Bioanalyzer 2100. RNA  sequencing  libraries  were  prepared  with  Illumina-compatible  NEBNext®  Ultra™  II Directional  RNA  Library  Prep  Kit.  The  double  stranded  cDNA  was  purified using  JetSeq  Beads and the purified  cDNA  was  end-repaired, adenylated and ligated to Illumina multiplex barcode adapters as per NEBNext® Ultra™ II Directional  RNA  Library  Prep  protocol. The  libraries  were  sequenced  on  IlluminaHiSeq  4000  sequencer  for  150  bp  paired-end  chemistry. The  data obtained  from  the  sequencing  run  was  de-multiplexed  using  Bcl2fastq  software  v2.20  and FastQ  files  were  generated  based  on  the  unique  dual  barcode  sequences. The sequencing quality was assessed using the FastQC software ver. 0.11.9. The adaptor sequences and low quality bases (phred quality cutoff set at 30) were trimmed from the reads using the Trim Galore tool ver. 0.6.5. The reads that survived quality check were aligned to the Plasmodium falciparum 3D7 isolate genome (ver. 46) using the Hisat2 read alignment tool. The library strandedness was set as firststrand in accordance with the strand specific library preparation protocol. The alignement output files in the sam format were sorted and converted to the bam format using the Samtools utilities (ver 1.10).
Results: The transcript abundance count data was generated using the HTSeq-count function (ver. 0.12.4). Differential gene expression analysis was performed using the DESeq2 package (ver. 3.11) in R programming environment. Genes were classified as deregulated on the basis of log2fold-change cutoff of +1 (for upregulation) and -1 (for downregulation) and p-value cutoff of 0.05. Gene Ontology analysis was performed using the GO tool hosted by the PlasmoDB web database. Data visualisation of the DGE was performed using custom scripts in R programming environment and with DESeq2 package utilities. The DGE analysis has revealed that up regulation of a subsets virulence genes family with significant p values.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Plasmodoum falciparum transcriptome profile of WT and PfCDP lines

first: Devadathan

last: Valiyamangalath Sethumadhavan


title: Cortical kidney bulk RNA Sequencing in the reversible unilateral ureter obstruction model.

first: Laura

last: Denby

address: Queen's Medical Research Institute, 47 Little France Cres

institute: University of Edinburgh

summary: The kidney has limited capacity to regenerate following injury and preferentially repairs chronic injury with secreted extracellular matrix proteins.  This can be a progressive process with functioning kidney tissue being replaced detrimentally with fibrotic scar tissue, ultimately leading to kidney failure.  Using the reversible unilateral ureteric obstruction model, a model of reversable injury, we describe the transcriptomic changes that occur during obstructive renal injury and subsequent repair.

overall_design: All animals used are male C57/blk mice.  All aged 8-9 weeks at start, culled after 1 week, 2 weeks or 4 weeks. N=10 animals were used per group of which 4 were selected for RNA Seq study.  Kidney injury is induced by UUO surgery by ligating the ureter.  Reversal surgery allows reimplantation of ureter after 7 days of UUO and animals are culled 1, 2, and 4 weeks post reversal of injury during which time the kidney slowly repairs.   Using the rUUO model for each timepoint (n=4/group) RNA library preparation was done via polyA selection.  Sequencing was performed on the Illumina HiSeq2500 platform in High Output mode (V4 chemistry) with a total of at least 250 million reads per lane.   GENEWIZ multiplexed 20 standard RNA libraries across 3 lanes of sequencing in 2x100bp PE configuration

first: Bryan

last: Conway

first: Jeremy

last: Hughes

first: Carolynn

last: Cairns


title: Polyadenylation site  mapping of  xrn1∆ in Sacchromyces cerevisiae

status: Public on Sep 25 2020

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

summary: The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we use the internal version of our previously developed protocol (PMID:  23295673), to characterize the polyA sites in a xrn1∆ strain.

overall_design: PolyA tail mapping at high resolution of a XRN1 deletion strain, with two biological replicates.

first: Stefan

last: Wilkening

first: Aino

last: Järvelin

first: Lars

last: Steinmetz


title: RNA sequencing - Microglial A20 is a critical gatekeeper of CNS homeostasis

city: Mainz

first: Ari

last: Waisman

address: Obere Zahlbacher Straße 67

institute: Institute for Molecular Medicine

summary: The goal of this study is to elucidate the role of microglial A20 in maintaining brain homeostasis, comparing fully deficient to partially deficient microglia tissue

overall_design: Microglia from tamoxifen-injected mice, either fully deficient (ko_del) or partially deficient (control) for A20 (Tnfaip3)

first: Alma

last: Mohebiany

first: Franziska

last: Härtner

first: Federico

last: Marini

first: Matthias

last: Klein


title: Profiling of Granzyme B Secreting B cells

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

summary: B cells with regulatory functions have been described both in immune homeostasis in healthy volunteers and in different pathological conditions. Whereas Il-10 secreting B cells represent the main subset described, recently, a subset of B cells secreting granzyme B (GZMB+) was evidenced in a growing numbers of immunological contexts, autoimmunity, chronic infections and neoplasias. Until now, no phenotype has been evidenced for these GZMB+ B cells and their regulatory functions as well are still to clarify.

overall_design: Purified B cells from human PBMC were differentiate into GZMB secreting cells in vitro. After 3 days of enrichment, induced GZMB+ B cells and GzmB- B cells were sorted.

first: Chesneau

last: Mélanie

first: Brouards

last: Sophie


title: Short RNAs associated to Cauliflower mosaic virus infections in Canola and Turnip

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

summary: Three plants of two species in Brassica genus, i.e. B. rapa cv. "Purple To White Globe" and B. napus cv. "SariGol", highly susceptible and tolerant hosts of Cauliflower mosaic virus (CaMV), respectively, were mechanically inoculated with CaMV strain NY8153.Phosphate buffer was used as control in mock-inoculated plants.  RNAs, in three biological repeats, were extracted 20 days post-inoculation (dpi) collecting ten leaves from mock-inoculated and virus-infected plants using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. Five µg of total RNA were resolved in 15% SDS-PAGE gel. Total RNA pattern was visualized upon Ethidium Bromide staining and sRNAs in the size range of 20-30 nt were eluted from gel. sRNAs replicates were quantified and mixed in equal molarity. Libraries were obtained using NEXTflex Small RNA-Seq Kit v3 (Bio Scientific) according to manufacturer’s instructions. Libraries were eluted from a 6% non-denaturing PAGE. The quality of libraries was checked by BioPharma QC, and then, submitted for sequencing with a HiSeq 2500 Illumina platform.

sample_organism:
Brassica napus
Brassica rapa

platform_organism:
Brassica napus
Brassica rapa

overall_design: Short RNA fractionation and characterization

first: Aysan

last: Ghasemzadeh


title: RNA-sequencing analysis of Ly6Chi macrophage and Ly6Clo macrophage harvested from infarcted heart

city: Chiba City

first: Akihiko

last: Kubota

state: Chiba

address: 1-8-1 Inohana

department: Department of Cardiovascular Medicine

institute: Graduate School of Medicine, Chiba University

summary: C57BL/6 J mice were subjected to ligation of the left anterior descending coronary artery. Ly6Chi macrophages and Ly6Clo macrophages were collected from infarcted hearts at 3 days after MI.

overall_design: We compared transcriptome between Ly6Chi macrophage and Ly6Clo macrophage harvested from infarcted heart.

first: Akira

last: Suto


title: Trypanosoma brucei brucei Doxycycline induced DRBD18 knockdown whole cell RNA and cytoplasmic RNA

city: Buffalo

first: Laurie

last: Read

state: NY

address: 955 Main St

institute: Jacobs School of Medicine and Biomedical Sciences

summary: DRBD18 (Tb927.11.14090) was knocked down by 19 hour doxycycline treatment.  Whole cell RNA and cytoplasmic RNA was isolated and sequenced.

overall_design: We compared the transcriptomes of uninduced and induced DRBD18 knockdown cells.  This was done on both the RNA population from whole cells and in RNA samples isolated from cytoplasm following nuclear/cytoplasmic fractionation.

first: Daniel

last: McSkimming

first: Amartya

last: Mishra

first: Jan

last: Kaur

first: Brianna

last: Tylec


title: Using Next Generation Sequencing to identify molecular pathways that are regulated by cardiac lymphatics during heart development

city: Chicago

first: Xiaolei

last: Liu

address: 303 e superior street

institute: Northwestern University

summary: Our study has identified a novel regulatory role of cardiac lymphatics in heart development, particularly in cardiomyocyte proliferation and survival. To investigate the molecular basis of this cardiac lymphatics-dependent effects,  We then performed RNA sequencing (RNA-seq) of the ventricular portions of E17.5 controls and Prox1 conditional nulls (embryos devoid of cardiac lymphatic development). Gene set expression analysis (GSEA) revealed that in Prox1 conditional null hearts, genes and pathways related to cell cycle were greatly reduced; instead, expression of genes and pathways involved in apoptosis were enriched.   Our study has identified a novel regulatory role of cardiac lymphatics in heart development, particularly in cardiomyocyte proliferation and survival. To investigate the molecular basis of this cardiac lymphatics-dependent effects,  We then performed RNA sequencing (RNA-seq) of the ventricular portions of E17.5 controls and Prox1 conditional nulls (embryos devoid of cardiac lymphatic development). Gene set expression analysis (GSEA) revealed that in Prox1 conditional null hearts, genes and pathways related to cell cycle were greatly reduced; instead, expression of genes and pathways involved in apoptosis were enriched.

overall_design: heart ventricular mRNA profiles of E17.5 control and Prox1 conditional nulls

first: Guillermo

last: Oliver


title: miRNA profiling analysis in high-risk intestinal GIST

first: Antonio

last: Fernandez-Serra

address: Beltraan Baguena, 8-11

department: Molecular Biology Lab

institute: Fundacion Instituto Valenciano de Oncologia

summary: Prognosis in Gastrointestinal Stromal Tumors (GIST) depends on clinical and pathological parameters that may be little objective, thus it is necessary to have other molecular biomarkers in the management of the disease.

overall_design: Analysis of 6 samples of good prognosis and 8 of bad prognosis in intestinal GIST

first: Jose

last: Lopez-Guerrero


title: Intracranial aneurysm sequencing data

first: Yi

last: Sun

address: Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, 350122, China

institute: Fujian Medical University

summary: Based on sequencing technology to evaluate the differential lncRNA and mRNA expression of intracranial aneurysms. Provide ideas for the study of epigenetic regulation of intracranial aneurysms

overall_design: Sequencing data of 4 patients with intracranial aneurysm and 4 healthy controls

first: Qing

last: Huang


title: Electroacupuncture alleviates mechanical allodynia of a rat model of CRPS-I and modulates gene expression profiles in dorsal root ganglia

city: Hangzhou

first: Chengyu

last: Yin

state: Zhejiang

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

summary: Complex regional pain syndrome type-I (CRPS-I) is chronic neurological disorder accompanied with devastating pain. Most conventional medical treatments lack effectiveness, making CRPS-I a challenging clinical condition. Electroacupuncture (EA) showed effectiveness in alleviating the pain symptoms of CRPS-I patients. However, the molecular mechanisms underlying EA’s therapeutic effect are still not well understood. Here, we established the rat chronic post-ischemic pain (CPIP) model to mimic CRPS-I and performed repetitive EA on bilateral hind limbs of the CPIP model rats. We then performed RNA-sequencing (RNA-Seq) to study the differences in gene expression, gene networks and molecular pathways in ipsilateral DRGs innervating the hind limb of the CPIP model rats with and without repetitive EA treatment. Our results found that repetitive EA treatment significantly alleviated mechanical allodynia in bilateral hind limbs of CPIP model rats. RNA-Seq analysis indicated that EA modulated the expression of multiple genes and gene networks in the DRGs of CPIP model rats. Further bioinformatics analysis identified the up-regulation of an array of genes involved in biological process such as neutrophil chemotaxis and immune response in the DRGs of CPIP model rats after EA treatment. Thus, these results suggest that EA may alleviate pain response in CPIP model rats via regulating multiple genes.  Our work may help to further advance the understandings of the molecular mechanisms underlying EA’s therapeutic effects on CRPS-I and help to identify novel targets for CRPS-I treatment

overall_design: Examination of 3 different groups mRNA profiles in DRG：control group, CPIP group and CPIP+EA group

first: Jie

last: Wang

first: Xiaoli

last: Zheng

first: Boyu

first: Boyi


title: Whole transcriptome analysis of T11 treated with FPP-1746-Omomyc

city: Nedlands

first: Pilar

last: Blancafort

state: WA

address: 6 Verdun Street

department: Cancer and Cell Biology

country: Australia

institute: Harry Perkins Institute of Medical Research

summary: RNA Sequencing of claudin-low triple negative breast cancer cells T11 treated with FPP-1746-Omomyc, Omomyc, FPP-1746 and vehicle control (PBS) to determine differentially regulated genes induced by FPP-1746-Omomyc

overall_design: T11 treated with PBS, Omomyc, FPP-1746 and FPP-1746-Omomyc at 5µM for 3 and 6 hours.

first: Blancafort

last: Pilar

first: Paul

last: Watt


title: The Histone Methyltransferase Setd2 Modulates Oxidative Stress to Attenuates Colonic Inﬂammation and Tumorigenesis [ChIP-Seq]

city: shanghai

first: min

last: liu

address: huashan road

institute: shanghaijiaotong university

summary:
Inflammatory bowel disease (IBD) is a complex and relapsing inflammatory disease, and patients with IBD exhibit a higher risk of developing colorectal cancer (CRC). Epithelial barrier disruption is one of the major causes of inflammatory bowel disease (IBD) in which epigenetic modulations are pivotal elements. However, the epigenetic mechanisms underlying the epithelial barrier integrity regulation remain largely unexplored. Here, we investigated how SETD2, a histone H3K36 trimethyltransferase, maintains intestinal epithelial homeostasis under inflammatory conditions.
GEO public database and IBD tissues were used to investigate the clinical relevance of SetD2 in IBD. To define the role of SetD2 in the colitis, we generated mice with epithelial-specific deletion of Setd2 (Setd2Vil-KO mice). Acute colitis was induced by 2% dextran sodium sulfate (DSS), and colitis-associated CRC was induced by injecting azoxymethane (AOM), followed by three cycles of 2% DSS treatments. Colon tissues were collected from mice and analyzed by histology, immunohistochemistry and immunoblots. Organoids were generated from Setd2Vil-KO and control mice, and were stained with 7-AAD to detect apoptosis. We isolated intestinal epithelial cells (IECs), performed RNA-seq and H3K36me3 ChIP-seq analysis to uncover the mechanism. Results were validated in functional rescue experiments by N-acetyl-l-cysteine (NAC) treatment and transgenes expression in IECs.
SETD2 expression was decreased in IBD patients and DSS-treated colitis mice. Setd2Vil-KO mice had abnormal loss of mucosa-producing goblet cells and antimicrobial peptide (AMP)-producing Paneth cells, and promoted early intestinal inflammation development. Consistent with the reduced SETD2 expression in IBD patients, Setd2Vil-KO mice exhibited increased susceptibility to DSS-induced colitis, accompanied by more severe epithelial barrier disruption. Intestinal permeability was markedly increased in Setd2Vil-KO mice. Setd2 ablation drived inﬂammation-associated CRC. Deletion of Setd2 resulted in excess reactive oxygen species (ROS), which led to cellular apoptosis and the defects in barrier integrity. N-acetyl-l-cysteine (NAC) treatment in Setd2Vil-KO mice rescued epithelial barrier injury and apoptosis. Moreover, overexpression of antioxidase PRDX6 in Setd2Vil-KO IECs largely alleviated the overproductions of ROS and improved the cellular survival.
Deficiency of Setd2 specifically in the intestine aggravates epithelial barrier disruption and inflammatory response in colitis via a mechanism dependent on oxidative stress. More importantly, we show that Setd2 depletion results in excess ROS by directly down-regulating PRDX6, an antioxidant protein that inhibit excess ROS. Thus, our results highlight an epigenetic mechanism by which Setd2 mediates oxidative stress to modulate intestinal epithelial homeostasis.

overall_design: ChIP assays of two-month-old Setd2f/f and Setd2Vil-KO IECs were generated by deep sequencing

first: Min


title: The Histone Methyltransferase Setd2 Modulates Oxidative Stress to Attenuates Colonic Inﬂammation and Tumorigenesis [RNA-Seq]

overall_design: mRNA profiles of two-month-old Setd2f/f and Setd2Vil-KO IECs were generated by deep sequencing


title: Short term (16 hour) treatment of ER+ breast cancer cell lines with low doses of CDK4/6 inhibition

status: Public on Sep 24 2020

city: Ann Arbor

first: Andrea

last: Pesch

state: MI

address: 1301 Catherine

department: Radiation Oncology

country: USA

institute: University of Michigan

summary: Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors have improved progression free survival for metastatic, estrogen receptor positive (ER+) breast cancers, but their role in the non-metastatic setting remains unclear. We sought to understand the effects of CDK4/6 inhibition (CDK4/6i) and radiation (RT) in multiple preclinical breast cancer models. Transcriptomic and proteomic analyses were used to identify significantly altered pathways after CDK4/6i. Clonogenic assays were used to quantify the RT enhancement ratio (rER). DNA damage was quantified using γH2AX staining and the neutral comet assay. DNA repair was assessed using RAD51 foci formation and non-homologous end joining (NHEJ) reporter assays. Orthotopic xenografts were used to assess the efficacy of combination therapy. Palbociclib significantly radiosensitized multiple ER+ cell lines at low nanomolar, sub IC50 concentrations (rER: 1.21 – 1.52) and led to a decrease in the surviving fraction of cells at 2 Gy (p < 0.001). Similar results were observed in ribociclib- (rER: 1.08 - 1.68) and abemaciclib-treated (rER: 1.19 - 2.05) cells. Combination treatment decreased RAD51 foci formation (p < 0.001), leading to a suppression of HR activity, but did not affect NHEJ efficiency (p > 0.05). Immortalized breast epithelial cells and cells with acquired resistance to CDK4/6i did not demonstrate radiosensitization (rER: 0.94 – 1.11) or changes in RAD51 foci. In xenograft models, concurrent palbociclib and RT led to a significant decrease in tumor growth. These studies provide preclinical rationale to test CDK4/6i + RT in women with locally-advanced ER+ breast cancer at high risk for locoregional recurrence.

overall_design: Samples were performed in biological triplicate and all treated samples were compared to vehicle controls.

first: Benjamin

middle: C

last: Chandler

first: Anna

last: Michmerhuizen

first: Christina

middle: L

last: Gersch

last: Larios

first: Corey

last: Speers

first: James

last: Rae


title: Transcriptomic analysis of feline chronic gingivostomatitis (FCGS)

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: The purpose of this study was to characterize the transcriptomic alterations accompanying the inflammation involved in feline chronic gingivostomatitis (FCGS). Towards this goal next-generation sequencing (NGS)-based gene expression profiling (RNA-Sequencing; RNA-Seq) was performed on matched pairs of FCGS diseased and healthy tissues obtained from three feline subjects.

overall_design: A total of 6 total RNA samples were analyzed in this study. The study included matched pairs of inflamed feline chronic gingivostomatitis (FCGS; diseased) and adjacent healthy mucosal tissues from the area lateral to the palatoglossal folds from 3 individual feline subjects: Bart, Jerome, and Sadie. Full-thickness 6-8 mm biopsies were obtained from inflamed and adjacent healthy oral mucosa and were collected under general anesthesia. Tissues were snap-frozen in liquid nitrogen, total RNA was isolated, and then samples submitted for RNA-sequencing analysis.

first: Dori

last: Borjesson

first: Natalia

last: Vapniarsky-Arzi


title: Phenotypic modifications of bacteria-plasmid coevolution facilitate gut colonization

city: tianjin

first: Peng

last: Zhang

state: Tianjin

address: No.38 Tongyan Road, Jinnan

institute: Nankai University

summary: Purpose: We investigate the evolutionary footprints of a bacteria-plasmid association consisting of Escherichia coli K-12 MG1655 and plasmid RP4 undergoing a long-term sub-MIC antibiotic stress.  Methods: Bacterial mRNA profiles of evolved RP4-carrying strains (E:H:p) and ancestral RP4-carrying strains (A:H:p) were generated by deep sequencing on an Illumina Hiseq platform. The sequence reads that passed quality filters were analyzed by Burrows–Wheeler Aligner (BWA), followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays  Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads of E:H:p and 12 million sequence reads of A:H:p to the E. coli MG1655 genome (GCF_000801205.1) and differential expressed genes were identified with TopHat workflow. RNA-seq data showed that approximately 15% of the transcripts showed differential expression between the E:H:p and A:H:p strains, with a fold change ≥1 and p value <0.005. Altered expression of 26 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Data analysis with bowtie and TopHat workflows provided complementary insights in transcriptome profiling.  Conclusions: Our study showed the coevolved bacteria-plasmid pairs has colonization traits superior to the wild-type parent strain. Antibiotic stress was necessary for bacterial evolution and evolved strains mostly employed transcriptional modifications to reduce plasmid-related cost in evolutionary adaptations. Several genes related to chromosome-encoded efflux pumps were transcriptionally upregulated, while most plasmid-harboring genes were downregulated based on RNA gene sequencing. These transcriptional modifications endowed evolved strains with resistant phenotype modifications, including the enhanced bacterial growth and biofilm formation.

overall_design: Bacterial mRNA profiles of 150-day evolved RP4-carrying strains (E:H:p) and ancestral RP4-carrying strains (A:H:p)

first: Huihui

last: Gao

first: Yi

last: luo

first: Daqing

last: Mao


title: Host-induced spermidine production in motile Pseudomonas aeruginosa triggers phagocytic uptake

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

institute: Helmholtz Centre for Infection Research

summary: Exploring the complexity of host-pathogen communication is vital to understand why microbes persist within a host, while others are cleared. Here, we employed a Dual-sequencing approach to unravel conversational turn-taking of dynamic host-pathogen communications. We demonstrate that upon hitting a host cell, motile Pseudomonas aeruginosa induce a specific gene expression program. This results in the expression of spermidine on the surface, which specifically activates the PIP3-pathway to induce phagocytic uptake into primary or immortalized murine cells. Non-motile bacteria are more immunogenic due to a lower expression of arnT upon host cell contact, but do not produce spermidine and are phagocytosed less. We demonstrate that not only the presence of pathogen inherent molecular patterns induces immune responses, but that bacterial motility is linked to a host-cell induced expression of additional immune modulators. Our results emphasize on the value of integrating microbiological and immunological findings to unravel complex and dynamic host-pathogen interactions.

sample_organism:
Mus musculus
Pseudomonas aeruginosa UCBPP-PA14

overall_design:
DualSeq (RNASeq) of RAW264.7 macrophages infected with Pseudomonas aeruginosa PA14 wild-type and different motility mutants.
RNASeq of Pseudomonas aeruginosa PA14 wild-type and different motility mutants - planctonic growth in LB medium.
RNASeq of RAW264.7 macrophages treated with spermidine.

first: Sebastian

last: Felgner

first: Ulrike

last: Beutling

first: Stephanie

last: Stahnke

first: Vinay

last: Pawar

first: Manfred

last: Rohde

first: Mark

last: Brönstrup

first: Theresia

last: Stradal

first: Susanne

last: Häussler


title: Transcriptome analysis of valosin-containing protein effect on cardiac hypertrophy and dysfunction

city: Atlanta

first: Hongyu

last: Qiu

state: GA

address: 100 Piedmont Ave

department: Center of Molecular and Translational Medicine

institute: Georgia State University

summary: This sstudy was designed to investigate the gene netweork regulated by valosin-containing protein (VCP), an ATPase-associated protein, whic acts as a novel regulator against the cardiac stress of pressure overload. We performed transcriptome analyses to compare cardiac-specific VCP overexpression transgenic (TG) mice and wild-type (WT) mice in a series of pathological models. The left ventricular (LV) tissues were collected from both WT and VCP TG mice at 2w post TAC and at 2w post sham operations. mRNA was extracted and sequenced to generate gene expression profiles. Multiple comparisons were performed between VCP TG and WT mice at two treatment conditions: sham and 2w post TAC. Our studies revealed novel molecular mechanisms by which VCP protects heart against pressure overload-induced cardiac hypertrophy and the transition to the heart failure.

overall_design:
Left ventricular tissue of WT and VCP TG mice at 2w post sham operations (n=4 for both) and at 2w (n=4 for WT, n=3 for VCP TG) post TAC were collected for transcriptome analysis.
Left ventricular tissue of WT and VCP TG mice at 5w (n=4 for WT, n=3 for VCP TG) post TAC were collected for transcriptome analysis.

first: Xin

last: Chen

first: Charles

last: Wang


title: Cyclodextrin-derived Nano-medicine Suppresses the Progression of Colorectal Cancer

first: Harrison

last: Bai

address: Tianmu Road 148#

institute: Zhejiang University

summary:
The malignancy of colorectal cancer is connected with inflammation, which poses great therapeutic challenges. To integratetherapeutic targets with anti-inflammation strategy, wedeveloped a biocompatible, non-covalent channel-type nanoparticles that was fabricated through host-guest complexation and multiple assemble of mannose-modified ?-cyclodextrin (M-?-CD) with Regorafenib (RG), denoted as RG@M-?-CD.  For in vivo application, the channel-type formulation optimized the pharmacokinetics and bio-distribution of RG. In colitis-associated cancer (CAC) and CT26 models, RG@M-?-CD was proven to be a targeted, safe and effective anti-tumor nanomedicine that suppressed tumor cells proliferation, lesioned neovascularization, and attanuated inflammation. To investigate the therapeutic mechanism of RG@M-?-CD nanomedicine, small pieces of colon tissue with tumors from control group and treatment group were used to perform the microarray for gene expression anaylsis.
The RGnanomedicine is constructed through the host-guest assemble between mannose-modified ?-cyclodextrin (M-?-CD) and TKI Regorafenib (RG). With multiple assemble, the host-guest system is transformed into nanoparticle, denoted as RG@M-?-CD (or RG nanomedicine).

overall_design:
Colitis-associated colon cancer model is established using AOM-DSS in C57 mice. The CAC mice are then treated with Rgnanomedicine or PBS.
After treatment, the tumor loading colon tissues are selected to perform the mRNA expression evaluation.

first: J

last: Zhou

first: H

middle: Z


title: Onco-fetal reprogramming of endothelial cells drives immunosuppressive macrophages in Hepatocellular Carcinoma (Nanostring)

city: Singapore

first: Ankur

last: Sharma

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute Of Singapore

summary: Liver dysfunction is associated with diseases ranging from metabolic disorders to hepatocellular carcinomas (HCC). Here we employed single-cell RNA-sequencing to extensively characterise the cellular landscape of human liver, from development to disease. We analysed ~212,000 cells representing human fetal liver, HCC and mouse liver. Our analysis revealed a remarkable fetal-like reprogramming of the tumor microenvironment (TME). Specifically, the HCC ecosystem displayed features reminiscent of fetal development, including the re-emergence of fetal-associated endothelial cells (PLVAP+/VEGFR2+), and fetal-like (FOLR2+) tumor-associated macrophages (TAMs). In a cross-species comparative analysis, we discovered remarkable similarity of gene expression and regulatory networks between mouse embryonically-seeded, fetal-liver and FOLR2+ tumor macrophages. Spatial transcriptomics further corroborated a shared onco-fetal ecosystem between fetal-liver and HCC. Furthermore, gene regulatory analysis, spatial transcriptomics, and in vitro functional assays implicated VEGF and NOTCH signaling in maintaining onco-fetal ecosystem. Taken together, we report a shared immunosuppressive onco-fetal ecosystem between the human fetal-liver and HCC. Our results unravel a previously unexplored onco-fetal reprogramming of tumor ecosystem, provides a novel target for therapeutic interventions in HCC and also opens up avenues for identifying similar paradigms in other cancers and disease states.

overall_design:
Analysis of hepatocellular carcinoma (HCC) and human fetal liver samples
Tissue slides from 3 HCC patients (adjacent normal & tumor section for each) and 3 human fetal liver samples were used for this experiment. 12 regions of interests were selected for each of the 9 samples so a total of 108 regions of interests were analysed. The samples were stained with 96 targets (immune, stromal, epithelial and onco-fetal markers).

first: Jia

last: Seow

first: Charles-Antoine

last: Dutertre

first: Rhea

last: Pai

first: Camille

last: Blériot

first: Archita

last: Mishra

first: Regina

middle: M

last: Wong

first: Gurmit

middle: S

last: Singh

first: Samydurai

last: Sudhagar

first: Shabnam

last: Khalilnezhad

first: Sergio

last: Erdal

first: Hui

last: Teo

first: Ahad

first: Svetoslav

last: Chakarov

first: Tony

last: Lim

first: Alexander

middle: Y

last: Chung

first: Alfred

last: Kow

first: Peng

last: Cheow

first: Glenn

last: Bonney

first: Brian

last: Goh

first: Jerry

last: Chan

first: Pierce

last: Chow

first: Florent

last: Ginhoux

first: Ramanuj

last: DasGupta


title: Effect of transient focal ischemia on circular RNAs

city: Nanjing

first: Fangfang

last: Wu

state: Jiangsu

address: Dingjia Qiao 87#

department: Department of Pharmacology

institute: Southeast University

summary: To investigate the potential involvement of circRNA in ischemic pathophysiology, we performed a circRNA microarray in an established transient middle cerebral artery occlusion (MCAO) mouse model of stroke. We evaluated the expression of 1797 circRNAs in adult mice brain after tMCAO. In our study, 5 of the 1178 circRNAs analyzed in the circRNA array were up-regulated significantly, ≥1.5-fold, in ischemic cortex at 12 hours of reperfusion after MCAO compared with their levels in sham group.

overall_design: Ischemia induced circular RNA expression in ipsilateral ischemic cortex in mice was measured at 12 hours of reperfusion after 1 hour occlusion of middle cerebral artery (MCA). Sham-operated mice served as control. Sham-operated mice received the same surgery except for the insertion of the filament. Three independent samples from tMCAO group and three independent samples from sham group were employed in Arraystar Mouse circRNA Array (8x15K, Arraystar) analysis.

first: Honghong

last: Yao


title: Rod photoreceptors degeneration in the rd1 model of retinitis pigmentosa involves a cascade of events leading to proteasome dysfunction

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

institute: Institut de la Vision

summary:
Retinitis pigmentosa is an inherited disease with sequential retinal degeneration of rod then cone photoreceptors leading to blindness. As in this human syndrome the rd1 mouse model carries a recessive mutation in the rod-specific cGMP phosphodiesterase beta subunit gene leading to rod followed by cone photoreceptor death. The cascade of early events leading to the induction of rod cell death through apoptosis remains unknown.
We report a differential whole-genome expression profiling analysis of the wild-type and rd1 mouse retinal transcriptional program using high-density oligonucleotide microarrays with a time series experiment spanning the entire rod photoreceptor degeneration process. Among the 1252 genes found to be significantly differentially expressed, a key group of 19 loci showed distinct differences in expression early in development, suggesting that these genes of clinical interest may play a fundamental role in the induction of the rod photoreceptor degeneration.

overall_design: Samples from purified retinal RNA from mice aged at different post-natal days were taken

first: Emmanuelle

last: Clérin

first: François

last: Delalande

first: Frédéric

last: Chalmel

first: Ludivine

last: Perrocheau

first: Najate

last: Aït-Ali

first: Danièle

last: Thiersé

first: Géraldine

last: Millet-Puel

first: Amandine

last: Langelé

first: Marie-Laure

last: Niepon

first: Wolfgang

last: Raffelsberger

first: Naomi

last: Berdugo

first: Céline

last: Jaillard

first: Saddek

last: Mohand-Saïd

first: Valérie

last: Fraulob

first: Flavie

last: Robert

first: Françoise

last: Gofflot

first: Pascal

last: Dollé

first: George

last: Lambrou

first: Michael

last: Primig

first: Raymond

last: Ripp

first: Donald

last: Zack

first: José-Alain

last: Sahel

first: Olivier

last: Poch

first: Alain

last: Van Dorsselaer

first: Thierry

last: Léveillard


title: Real time PCR array for mouse tumor metastasis on mice with liver metastasis treated with miR-122 delivery vs miRNC delivery

status: Public on Sep 23 2020

city: Chapel Hill

first: Hossein

last: Sendi

state: NC

address: 125 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary: This experiment was done to compare mouse metastasis gene profile between liver tissues of mice with liver metastasis which treated with miR-122 delivery compared with those treated with miRNC delivery as control.

overall_design: RT PCR array of 84 genes in mouse tumor metastasis. Four replicates of RNA samples from mice with liver metastasis treated with miR122 were compared with four RNA replicates from mice treated with miRNC as control


title: Colorectal mucosa exposed to free and complement opsonized HIV

city: Linköping

first: Rada

last: Ellegård

state: Ostergotlands Lan

address: Vallmogatan 16

institute: Linköping University

summary: Whole transcriptome amplification of RNA purified from colon explants cultured with different forms of HIV (free, complement opsonized and complement and antibody opsonized HIV) or mock treated for 24h.

overall_design:
3 donors
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*Authors state "Raw files cannot be uploaded according to GDRP law (Sweden) - human samples".

first: Pradyot

last: Bhattacharya

first: Mohammad

last: Khalid

first: Cecilia

last: Svanberg

first: Melissa

last: Govender

first: Åsa

last: Keita

first: Johan

last: Söderholm

first: Pär

last: Myrelid

first: Esaki

last: Shankar

first: Sofia

last: Nyström

first: Marie

last: Larsson


title: Real time PCR array for cancer inflamation and immunity on mice with liver metastasis treated with miR-122 delivery vs miRNC delivery

summary: This experiment was done to compare cancer inflamation and immunity profile between liver tissues of mice with liver metastasis which treated with miR-122 delivery compared with those treated with miRNC delivery as control.

overall_design: RT PCR array of 84 genes in cancer inflammation and immunity cross talk. Five replicates of RNA samples from mice with liver metastasis treated with miR122 were compared with five RNA replicates from mice treated with miRNC as control


title: DCA-TGR5 signaling activation alleviates inflammatory response and improves cardiac function in myocardial infarction

city: Beijing

first: Jiaxing

last: Wang

address: No. 49 Huanyuan Nortk Road

institute: Peking University Third Hospital

summary: The progression of myocardial infarction (MI) involves multiple metabolic disorders. Bile acid metabolites have been increasingly recognized as pleiotropic signalling molecules that regulate multiple cardiovascular functions. G protein-coupled bile acid receptor (TGR5) is one of the receptors sensing bile acids to mediate their biological functions. In this study, we aimed to elucidate the effects of bile acids-TGR5 signaling pathways in myocardial infarction (MI).Mice underwent either the LAD ligation model of MI or sham operation. Both MI and sham mice were gavaged with 10 mg/kg/d DCA or vehicle control since 3-day before the operation. Administration of DCA improved cardiac function at the 3th-day post-MI. The effects of DCA in the heart were determined by RNA-sequencing experiments.

overall_design: heart mRNA profiles of mice at 1-day post-MI

first: Jianshu

last: Zhang

first: Xianjuan

last: Lin

first: Yupeng

first: Xiang

last: Wu

first: Fan

last: Yang

first: Wei

last: Gao

first: Yan

first: Jinpeng

last: Sun

first: Changtao

last: Jiang

first: Ming

last: Xu


title: Expression profile of circRNA and mRNA in lacrimal glands of AQP5-/- mice with primary dry eye

city: Qingdao

first: Peng

last: Chen

address: 308 Ningxia road, Qingdao

institute: Qingdao University

summary:
Purpose: Identify the differentially expressed circular RNA (circRNA) and elucidate their potential function in AQP5 knockout (AQP5-/-) mice with primary dry eye phenotype.
Methods: A slit lamp examination was performed on AQP5 knockout mice to assess corneal epithelial defect by fluorescein sodium staining. Hematoxylin-eosin staining and transmission electron microscope analysis were performed to access the structure of lacrimal gland epithelial cells. The expression profiles of circRNA and messenger RNA (mRNA) were determined by microarray analysis. The selected circRNA was verified by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to predict biological functions and potential pathways of parental genes involved in lacrimal gland epithelial cell changes. According to the bioinformatics analysis of identified circRNA, we can predict a circRNA-miRNA-mRNA network.
Results: AQP5-/- mice exhibit spontaneous dry eye symptoms. AQP5 deficiency obviously changes the structure of lacrimal gland epithelial cells. Analysis showed that compared to AQP5+/+ mice, 30 circRNAs in the lacrimal glands of AQP5‑/- mice had differential expression (fold change ≥ 2.0, P < 0.05). Nine upregulated circRNAs were identified by qRT-PCR; nine upregulated validated circRNAs, 40 altered microRNAs (miRNAs), and nine upregulated mRNAs were involved in the network analysis. KEGG analysis showed these nine target genes were expressed in phagosomes.
Conclusions: AQP5-/- mice have primary and stable dry eye phenotypes from birth. The study identified different expressed circRNAs in lacrimal glands between AQP5-/- and AQP5+/+ mice, predicting a circRNA-miRNA-mRNA network of phagosomes. CircRNA likely plays an important role in lacrimal gland epithelial cell pathogenesis. Therefore, it is reasonable to use circRNA as a potential therapeutic target for dry eyes.

overall_design: Lacrimal gland circRNA and mRNA profiles of wild type (WT) and AQP5-/- mice were generated by high-throughput sequencing, in triplicate.

first: Yaning

last: Liu

first: Guohu

last: Di

first: Shaohua

last: Hu


title: Real time PCR array for cancer inflamation and immunity and tumor metastasis on mice with liver metastasis treated with miR-122 delivery vs miRNC delivery

first: Hossein

last: Sendi

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

overall_design: Refer to individual Series


title: Expression analysis after co-treatment of GSK126 and pomalidomide

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: To determine combination effect of GSK126 and pomalidomide at the RNA levels in EZH2 Y641 mutant DLBCL, We performed gene expression profiling in WSU-DLCL2 cell line after co-treatment of GSK126 and pomalidomide

overall_design: Lmphoma cell lines WSU-DLCL2 were co-treated by 1μM of GSK126 and 1μM of pomalidomide for 2day and total RNA was analysed

first: Seung-Hyun

last: Jo

first: Sungryul

last: Park

first: Jong-Hwan

first: Seon-Young


title: EZH2 identifies the precursors for trained immunity of human natural killer cells

city: Tianjin

first: Jian

last: Zheng

address: QiXiangTai Road，He Ping district

department: Immunology

country: China

institute: TIanjin Medical University

summary: Human NK cells were treated with IL-12/15/18 to induce trained immunity.  scRNA-seq and TotalSeqTM were performed to map the development pathway of trained NK cells.

overall_design: scRNA-seq and TotalSeqTM of human NK cells

first: Long

last: Li

first: Xiubao

last: Ren

first: Jie

last: Yin

first: Chen


title: Transcriptomic analysis of hyperglycemic stress induced myeloid neoplasms associated with Tet2 haploinsufficiency

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

summary: Purpose: To identify potential mediators of myeloid neoplasms driven by Tet2 haploinsufficiency and hyperglycemic stress. Methods: Lin-negative bone marrow cells from WT, Tet2+/-, Ins2Akita/+ and Tet2+/-;Ins2Akita/+ were used for total RNA purification and RNA-seq. Results: Using unbiased Gene Set Enrichment Analysis (GSEA), we identified that innate immune pathway, IL-6 signaling pathway and TLR4-NFkB pathway were significantly enriched in the compound mutants (Tet2+/-;Ins2Akita/+) while controls (Tet2+/- or Ins2Akita/+) were similar to WT mice.

overall_design: Bone marrow Lin-negative RNA profile in four genotypes: WT, Tet2+/-, Ins2Akita/+ and Tet2+/-;Ins2Akita/+.

first: Zhigang

last: Cai

first: Kapur

last: Reuben


title: Inhibition of histone deacetylation by MS-275 alleviates colitis by activating the vitamin D receptor

city: Hanghou

first: Chunxiao

address: 79 Qingchun Road

department: Department of Gastroenterology

institute: The First Affiliated Hospital, College of Medicine, Zhejiang University

summary:
BACKGROUND: Ulcerative colitis (UC) is a common chronic inflammatory bowel disease without curative treatment.
METHODS: We conducted gene set enrichment analysis to explore potential therapeutic agent for UC. Human colon tissue samples were collected to test H3 acetylation in UC. Both in vivo and in vitro colitis models were constructed to verify the role and mechanism of H3 acetylation modification in UC. Intestine-specific vitamin D receptor (VDR)-/- mice and VD (vitamin D)-deficient diet-fed mice were used to explore downstream molecular mechanism accordingly.
RESULTS: According to the Connectivity Map database, MS-275 (class I histone deacetylase inhibitor) was the top-ranked agent, indicating potential importance of histone acetylation in the pathogenesis of UC. We then found that histone H3 acetylation was significantly decreased in the colon epithelium of UC patients and negatively associated with disease severity. MS-275 treatment inhibited histone H3 deacetylation, and subsequently attenuated nuclear factor kappa B (NF-?B)-induced inflammation, reduced cellular apoptosis, maintained epithelial barrier function, and thereby reduced colitis activity in a mouse model of colitis. We also identified VDR to be a downstream effector of MS-275. The curative effect of MS-275 on colitis was abolished in VDR-/- mice and in VD-deficient diet-fed mice and VDR directly targeted p65. In UC patients, histone H3 acetylation, VDR and zonulin-1 expression showed similar downregulation patterns and were negatively associated with disease severity.
CONCLUSION: We demonstrate that MS-275 inhibits histone deacetylation and alleviates colitis by ameliorating inflammation, reducing apoptosis and maintaining intestinal epithelial barrier via VDR, providing new strategies for UC treatment.

overall_design:
Examination of histone H3K9 modifications in HCT116 cells.
Chromatin immunoprecipitation followed by sequencing in HCT116 cellular colitis model was adopted to discover the downstream target of MS-275.

first: Zhe

last: Shen

first: Jing

last: Sun

first: Youming

first: Min


title: Metformin improves cognition of aged mice by promoting cerebral angiogenesis and neurogenesis [hADSCs]

city: Shanghai

first: Hailiang

address: NO 1239, siping road

institute: Tongji university

summary: We implemented transcriptomic analyses of hADSCs treated with metformin 6 days

overall_design: hADSCs treated with metformin 6 days


title: Metformin improves cognition of aged mice by promoting cerebral angiogenesis and neurogenesis [blood]

summary: We implemented transcriptomic analyses of blood of 8-10M mice; These mice with the treatment of metformin for 30 days.