title: Dissecting the co-transcriptome landscape of plants and microbiota

city: Cologne

first: Tatsuya

last: Nobori

address: Carl-von-Linne Weg 10, Max-Planck Institute for Plant Breeding Research

summary: Interactions between plants and each neighboring microbial species are fundamental building blocks that collectively determine the structure and function of the plant microbiota, but the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant-associated bacteria from all major phyla of the plant microbiota and profiled co-transcriptomes of plants and bacteria. These strains elicited quantitatively different plant transcriptional responses including typical pattern-triggered immunity responses. Genes of non-pathogenic bacteria involved in general metabolism and energy production were commonly suppressed in planta in contrast to a virulent pathogen. Various nutrient acquisition pathways that are frequently encoded in the genomes of plant-associated bacteria were induced in planta in a strain-specific manner, shedding light on bacterial adaptation to the plant environment and identifying a potential driving force of niche separation. Integrative analyses of plant and bacterial transcriptomes suggested that the transcriptional reprogramming of plants is largely uncoupled from that of bacteria at an early stage of interactions. This study provides insights into how plants discriminate among bacterial strains and sets the foundation for in-depth mechanistic dissection of plant-microbiota interactions.

sample_organism:
Arabidopsis thaliana
Plantibacter sp. Leaf1
Acinetobacter sp. Leaf130
Rhizobium sp. Leaf155
Pedobacter sp. Leaf176
Burkholderia sp. Leaf177
Exiguobacterium sp. Leaf187
Chryseobacterium sp. Leaf404
Arthrobacter sp. Soil763
Flavobacterium sp. Root935

overall_design: Plant RNA-seq: 20 conditions (19 commensal strains and mock control) with 3 biological replicates. Bacterial RNA-seq: 9 commensal strains both in vitro and in planta (18 conditions in total), each condition contains 3 biological replicates.

first: Kenichi

last: Tsuda


title: ibrutinib resistance mantle cell lymphoma

status: Public on Apr 26 2021

city: Tampa

first: Jianguo

last: Tao

state: Florida

address: 12902 Magnolia Dr

country: USA

institute: Moffitt Cancer Center

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Vitamin D deficiency exacerbates UV/endorphin and opioid addiction

status: Public on Apr 25 2021

city: Boston

first: Lajos

last: Kemeny

address: 149 13th Street

institute: Massachusetts General Hospitala

summary: Due to the current opioid epidemic, a better understanding of genetic and environmental factors that contribute to opioid addiction is warranted. To explore the potential causative role of VitD in opioid addiction , we used multiple pharmacologic approaches and genetic mouse models. We used profiled the transcriptome of key brain reward regions upon morphine treatment in vitamin D receptor KO and wild type mice. Our results highlight the role of VitD deficiency in the development of addiction and suggest a potential therapeutic benefit of VitD supplementation for VitD deficient individuals in the prevention and management of addiction.

overall_design:
To examine the mechanism underlying the increased morphine reward in Vdr-/- mice, we performed RNA-seq on bilateral micro-punches of the nucleus accumbens and the ventral tegmental area, key brain regions for morphine reward, from Vdr-/- and wild type mice i.p. injection of PBS or 5 mg/kg morphine sulfate. Mice were sacrificed with cervical dislocation. Brains were then immediately flash frozen in isopentane and stored in -80°C.
Punches were taken from coronal sections of the mouse brain for both NACC and VTA. For NACC, the aci and fmi white matter structures were used as landmarks to determine Bregma 1.94. 1.5 mm diameter bilateral punches were then taken 2 mm in depth with aci at the center of the punch, to ensure both the accumbens core and shell were within the punch. To reach the VTA, coronal sections were taken until white matter structures of the cingulum (cg) were rounded and the dentate gyrus of the hippocampus began to form ventrally and caudally, as observed at Bregma -2.92 mm. 1.5 mm diameter bilateral punches were then taken at ~1.0 mm in depth at a location 0.5 mm lateral and from the the midsagittal plane and 0.5 mm from the most ventral portion of the brain.

middle: V

first: Andrea

middle: L

last: Hermann

first: Phillip

last: Rivera

first: Matthew

middle: P

last: Salomon

first: Dave

middle: S

last: Hoon

first: David

middle: E

last: Fisher


title: Characterization of the adaptive transcriptional response triggered by the cell wall interfering compound Poacic acid in yeast and its effect on crosslinking enzymes.

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramón y Cajal, S/N

department: Facultad de Farmacia, Departamento de Microbiologia II

country: Spain

institute: Universidad Complutense de Madrid

summary: We analyzed the genome-wide expression profile of the wild type strain in response to poacid acid (1 hour of treatment). In addition, we did transcription profiling on the effect of slt2 (MAPK of Cell wall intregity pathway) deletionin genes involved in poacid acid response

overall_design: For poacid acid treatment, three biological samples for wild type strain and three biological samples for slt2  mutant  were analyzed. Two RNA-seq experiments were carried out for each biological sample:  1. absence of the drug   2. presence of 100 µg/ml of poacid acid for one hour


title: SCA7 mouse cerebellar pathology reveals preferential downregulation of key Purkinje cell-identity genes and shared disease signature with SCA1 and SCA2

city: Illkirch

first: Anna

last: Niewiadomska-Cimicka

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disease mainly characterized by motor incoordination due to progressive cerebellar degeneration. SCA7 is caused by polyglutamine expansion in ATXN7, a subunit of the transcriptional coactivator SAGA, which harbors histone modification activities. Polyglutamine expansions in specific proteins are also responsible for SCA1-3, 6 and 17, however, the converging and diverging pathomechanisms remain poorly understood. Using a new SCA7 knock-in mouse, SCA7140Q/5Q, we analyzed gene expression in the cerebellum and assigned gene deregulation to specific cell types using published datasets. Gene deregulation affects all cerebellar cell types, although at variable degree, and correlates with alterations of SAGA-dependent epigenetic marks. Purkinje cells (PCs) are by far the most affected neurons and show reduced expression of 83 cell-type identity genes, including these critical for their spontaneous firing activity and synaptic functions. PC gene downregulation precedes morphological alterations, pacemaker dysfunction and motor incoordination. Strikingly, most PC genes downregulated in SCA7 have also decreased expression in SCA1 and SCA2 mice, revealing converging pathomechanisms and a common disease signature involving cGMP-PKG and phosphatidylinositol signaling pathways and long-term depression. Our study thus points out molecular targets for therapeutic development, which may prove beneficial for several SCAs. Furthermore, we show that SCA7140Q/5Q males and females exhibit the major disease features observed in patients, including cerebellar damage, cerebral atrophy, peripheral nerves pathology and photoreceptor dystrophy, which account for progressive impairment of behavior, motor and visual functions. SCA7140Q/5Q mice represent an accurate model for the investigation of different aspects of SCA7.

overall_design: Cerebellar transcriptional profiling (RNA-seq) of a knock-in mouse model of Spinocerebellar Ataxia Type 7 (SCA7).

first: Celine

last: Keime

first: Yvon

last: Trottier


title: Profiling of LNCaP-SL after circulating small extracellular vesicles treatment

city: Seoul

first: Miso

last: Park

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

summary: RNA was isolated from LNCaP-SL after 24 hours of circulating small extracellular vesicles (csEV) single dose treatment (1×10^10 particles/mL).

overall_design: Gene expression profiling of LNCaP-SL cell line after after 24 hours of csEV treatment.

first: Seungmin

last: Kang

first: Keon

middle: W


title: Mitochondrial dysfunction and immune response in pneumococcal pneumonia submitted to mechanical ventilation: impact of mesenchymal stem cells?

status: Public on Apr 24 2021

city: DIJON

first: Mathieu

last: Blot

address: 7 bd Jeanne d'Arc

institute: INSERM UMR1231

summary: The goal of this study was to evaluate the impact of mechanical ventilation on immune and mitochondrial dysfunctions, in the setting of pneumococcal pneumonia in rabbits. Then, in a randomized trial, we assessed the effect of human umbilical cord-derived mesenchymal stem cells (MSCs), either alone, or in association with an atibiotic treatment (Ceftaroline) in the setting of pneumococcal pneumonia submitted to adverse mechanical ventilation. Pulmonary gene expression was analysed in an attempt to elucidate the  effects of MSCs.

overall_design: 4 comparisons were considered (n=7 rabbits/group) = 1) Healthy rabbits vs. Pneumonia+adverse mechanical ventilation (MV); and then in the setting of pneumococcal pneumonia + adverse MV: 2) treatment NaCl. Vs. MSCs; 3) NaCl. Vs. Ceftaroline; 4) Ceftaroline vs. Ceftaroline+MSCs

first: Pierre-Emmanuel

last: Charles

first: Marine

last: Jacquier


title: Next Generation Sequencing Facilitating Quantitative Analysis of Wild Type (Kcnj11fl/fl, WT) and β-cell Specific Kcnj11 -/- (βKcnj11 -/-, bKO) Mouse Islets' Transcriptomes

city: Kobe

first: Okechi

last: Oduori

address: 3F, 1-5-6, Minatojima Minami-machi, Chuo-ku

department: Molecular and Metabolic Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

summary: β-cell Specific Kcnj11 -/-  mice and their islets exhibited a hirtherto unkown switch in the major signaling pathway of G-protein coulpled receptors from Gs to Gq, and overall  enhanced Gq signaling. That the phenomeno was also observed in their isolated islets, and that the genetic manipulation of the mice was only in the pancreatic beta-cells, we reasoned that peharps knockout of Kcnj11 in beta cells could result to a general change in the expression of genes related to G-protein coupled receptor signaling. Since New-Generation Sequencing (NGS) has revolutionized cellular based pathway analysis, we extracted total RNA from WT and bKO islets, performed  NGS and compared global changes in the expression of genes between WT and bKO islets.

overall_design: WT and bKO RNA samples, in triplicates, were processed as fragments per kilobase of transcript per million mapped reads (FPKM), and determined by the RNA-sequencing (RNA-seq) service provider Macrogen, who also mapped trimmed reads to the Mus musculus reference genome using AnnoOnly(-G) Transcriptome Resequencing NGS Advanced and then performed transcript assembly using Cufflinks-G. Data were log transformed and quantile normalization was performed with Pre-process Core’s R library by Macrogen. Samples with at least one FPKM value of 0 were removed from consideration

first: Susumu

last: Seino


title: Whole blood transcriptome analysis reveals SARS-CoV-2 ORF8 as a potential therapeutic and vaccine target

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: The open reading frame (ORF) 8 in severe acute respiratory syndrome coronaviruses (SARS-CoVs), associated with host adaptation and viral replication, is a hotspot for mutation. However, mutation effects on host immune responses remain unknown. Here, whole blood transcriptomics performed on patients infected with mutant SARS-CoV-2 (Δ382; 382-nt deletion in ORF8) show differing profiles from wildtype SARS-CoV-2. Understanding the Δ382 mechanism and effects would allow for a focused approach in vaccine and antiviral development.

overall_design: RNA was extracted from whole blood collected from 27 COVID-19 patients from the Singapore cohort after retrospective matching and 6 healthy controls. Timepoints selected for extraction were during active infection (PCR-positive, median 8 days PIO) and recovered (PCR-negative; median 21 days PIO).

first: Siew

last: Fong

middle: K

last: Yeo

first: Yi

middle: H

last: Chan

first: Siti

middle: N

last: Amrun

first: Bernett

last: Lee

first: Josephine

last: Lum

first: Foo

last: Shihui

first: Rhonda

last: Chee

first: Anthony

last: Torres-Ruesta

first: Cheryl

middle: Y

first: Guillaume

last: Carissimo

first: Z

last: Chang

first: Yun

last: Goh

first: Chek

middle: M

last: Poh

middle: Z

last: Tay

first: Barnaby

last: Young

first: Paul

middle: A

last: Tambyah

first: Shirin

last: Kalimuddin

first: Yee

last: Leo

middle: C

last: Lye

first: Shanshan

last: Howland

first: Laurent

last: Renia

first: Lisa

middle: F

last: Ng


title: Anti-fatigure properties of Sasa quelpaertensis leaf extracts in mice

city: Jeju

first: Mi Gyeong

last: Jang

address: 102 Jejudaehakno

institute: Jeju National University

summary: The study aimed the effects of Sasa quelpaertensis leaf hot water extract (SQH) on anti-fatigue function and the global gene expression pattern in muscle tissue. When rat skeletal muscle cells were cultured in hypoxic condition, the levels of lactate and lactate dehydrogenase (LDH) was increased approximately more than 2-fold, but SQH decreased effectively these levels. Thus, we assessed the exercise and fatigue recovery function using several physical biomarkers such as glycogen, lactate and so on in high intensity exercise mice. The mice were divided into three groups; Normal Control (NC), Exercise Control (EC), and Exercise SQH (ES) by oral administered at 50mg/kg/day for 7 days. After excessive swimming,the ES group showed increases serum glucose and decrease serum lactate than EC group. Lactate content in muscle was lower ES group than EC group. Glycogen contents in muscle and liver were higher ES group than EC group. And, SQH administration increased the expression of phospho-Acetyl-CoA (p-ACC), and reduced the expression of phospho-AMP-activated protein kinase (p-AMPK) and GLUT4 in in-vivo model. Also, genome wide expression profiles of tissue were determined by RNA sequencing. SQH up-regulates and down-regulates several genes associated with fatigue. In conclusion, this study suggested that SQH are effective for anti-fatigue agent.

overall_design: muscle tissue mRNA profiles of ICR mice were generated by QuantSeq 3' mRNA sequencing, using Illumina NestSeq 500.

first: Se

middle: J

last: Kim

first: Hana

last: Song

first: Mi

middle: G


title: Salt stress enhances early symbiotic gene expression in Medicago truncatula and induces a stress-specific set of rhizobium-responsive genes

city: Burlington

first: Jeanne

middle: Marie

last: Harris

state: VT

address: 63 Carrigan drive

department: Plant Biology

institute: University of Vermont

summary: Salt stress is a major agricultural concern inhibiting not only plant growth but also the symbiotic association between legume roots and the soil bacteria rhizobia. This symbiotic association is initiated by a molecular dialogue between the two partners, leading to the activation of a signaling cascade in the legume host and ultimately the formation of nitrogen-fixing root nodules. Here we show that a moderate salt stress increases the responsiveness of early symbiotic genes in Medicago truncatula to its symbiotic partner, Sinorhizobium meliloti, while conversely, inoculation with S. meliloti counteracts salt-regulated gene expression, restoring one-third to control levels. Our analysis of Early Nodulin 11 shows that salt-induced expression is dynamic, Nod-factor dependent, and requires the ionic, but not the osmotic, component of salt. We demonstrate that salt stimulation of rhizobium-induced gene expression requires NSP2, which functions as a node to integrate the abiotic and biotic signals. In addition, our work reveals that inoculation with Sinorhizobium meliloti succinoglycan mutants also hyperinduces ENOD11 expression in the presence or absence of salt, suggesting a possible link between rhizobial exopolysaccharide and the plant response to salt stress. Finally, we identify an accessory set of genes that are induced by rhizobium only under conditions of salt stress and have not been previously identified as being nodulation-related genes. Our data suggests that interplay of core nodulation genes with different accessory sets, specific for different abiotic conditions, function to establish the symbiosis. Together, our findings reveal a complex and dynamic interaction between plant, microbe, and environment.

overall_design: There were 4 treatments: +/- NaCl, +/- Rhizobium. Samples were either pouched directly in MNM containing 100 mM NaCl or in MNM at Day 0, and either mock-inoculated or inoculated with Sinorhizobium meliloti Rm1021 at Day 4. Whole roots were harvested and processed for RNA-seq at Day 5 (24 hours after the inoculation treatment). There are 3 biological replicates of each treatment group. Each treatment from a biological replicate includes 21 plants.

first: Sanhita

last: Chakraborty

first: Juan

last: Abrahante

first: Heather

last: Driscoll

first: Fan

last: Zhang

first: Robert

last: Fisher


title: Defining the AHR-regulated transcriptome in NK cells reveal gene expression programs relevant to development and function

city: Columbus

first: Dean

last: Lee

state: Ohio

address: 700 Children’s Drive

department: Hematology & Oncology

institute: Nationwide Children’s Hospital

summary: Aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that plays a critical role in shaping innate and adaptive immune responses. However, the molecular mechanism by which AHR regulates the function of human NK cells remains largely unknown. Here, we use RNA sequencing on IL21-expanded NK cells in the presence of AHR agonists and antagonist to demonstrate that AHR directly regulates the expression of known regulators of phenotype, development, metabolism, and function.

overall_design: NK cells were isolated from leukopak of healthy volunteer donors using NK cell RosetteSep. NK cells were expanded using irradiated feeder cells overexpressing membrane bound IL21 (FC21) for period of 14-21 days. NK cells from 3-donors (NK1, NK124 and NK126) were expanded using human interleukin-2 (IL2-50 IU/ml) alone, IL2+stemregenin (SR1-1uM) or IL2+kynurenine (Kyn-25uM). The media was changed every 2-3 days. The samples for RNA were collected on days 0, 7, 14 and 21 (D0, D7, D14 and D21). RNA was isolated using RNeasy kit all the samples were DNase treated and concentrated using RNA concentrator kit. We compared gene expression profiling between IL2 vs SR1 and IL2 vs Kyn on days 7 and 14.

first: Prashant

last: Trikha

first: Jena

last: Moseman

first: Aarohi

last: Thakkar

first: Amanda

last: Campbell

first: Jennifer

last: Foltz

first: Nitin

last: Chakravarti

first: James

last: Fitch

first: Elaine

last: Mardis


title: Identification of intermediate transcriptome states and synergistic effects of Isl1 in Atoh1-mediated cochlear hair cell conversion

city: Omaha

first: Jian

last: Zuo

state: Nebraska

address: 2500 California Plaza

institute: Creighton University

summary: Single cell RNA expression profiling by high throughput sequencing

overall_design: Atoh1-HA was ectopically expressed in mouse supporting cells to convert into hair cells. The converted hair cells were labeled with tdTomato as well as Chrna9-GFP.

first: Tetsuji

last: Yamashita

first: Fei

last: Zheng

first: David

last: Finkelstein

first: Zoe

last: Kellard

last: Carter

first: Celeste

middle: D

last: Rosencrance

first: Ken

last: Sugino

first: John

last: Easton

first: Charles

last: Gawad


title: Transcriptome analysis of Pyrus pyrifolia watercore by comparing susceptible and non-susceptible F1 sib pairs

city: Tsukuba

first: Chikako

last: Nishitani

state: Ibaraki

institute: National Institutes of Fruit Tree Science

summary: Watercore is a physiological disorder develops in the Japanese pear fruit showing a watery translucent area in the flesh while on the tree and lead to the loss of commercial value. The sustainability to watercore is one of the most important characterization to be studied it the breeding of the Japanese pear. However, even in susceptible cultivars like ‘Hosui’, the degree of watercore development is significantly different from year to year, this makes it difficult to analyze the characteristic phenomena prior to watercore development. We’d obtained two reproducible sib strains, that is, susceptible strains developed severe watercore in all of the fruit every year while no watercore was found in the non-sustainable ones even when they were overmatured. They are originated from ‘Hosui’ x ‘Hogetsu’ and ‘Akiakari’ x ‘Taihaku’. In order to search the genes related to watercore, we used these susceptible and non-susceptible F1 sib strain pairs. By using pear custom microarray, the genes that differed in expression level prior to watercore development were extracted. The sugar-metabolism, hormone, and cell wall related genes were identified in the 105 differentially expressed genes. Some of them showed different expression levels only in the immature stages prior to watercore development.

overall_design: The gene expression profiles between watercore susceptible pears and sustainable pears

first: Eiichi

last: Inoue

first: Natsumi

last: Ogata

first: Toshiya

last: Yamamoto

first: Toshihiro

last: Saito


title: Responses of Atlantic salmon to vaccination and challenge with salmon alphavirus (SAV) and Moritella viscosa

status: Public on Apr 23 2021

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Salmon alphavirus (SAV) and Moritella viscosa causing respectively pancreatic disease and winter ulcer are among the most important pathogens threatening Atlantic salmon aquaculture. Fish is protected by vaccination with different rate of success. Here, responses to vaccination were assessed followed with pathogen challenges of vaccinated salmon and saline injected control.

overall_design: Salmon was smoltified and vaccinated with a commercial multicomponent vaccine according to standard protocols, control group received saline injection. After 9 weeks, fish was challenged by co-habitation with shedders. Tissues samples were collected after respectively 21 dpi (SAV) and 42 dpi (M. viscosa).

first: Anne

last: Bakke

first: Hege

last: Lund


title: Asymptomatic COVID-19: disease tolerance with efficient anti-viral immunity against SARS-CoV-2

first: Nicholas

last: Ang

summary: The immune responses and mechanisms limiting symptom progression in asymptomatic cases of SARS-CoV-2 infection remain unclear. We comprehensively characterized transcriptomic profiles, cytokine responses, neutralization capacity of antibodies and cellular immune phenotypes of asymptomatic patients with acute SARS-CoV-2 infection to identify potential protective mechanisms. Compared to symptomatic patients, asymptomatic patients had higher counts of mature neutrophils and lower proportion of CD169+ expressing monocytes in the peripheral blood. Systemic levels of pro-inflammatory cytokines were also lower in asymptomatic patients, accompanied by milder pro-inflammatory gene signatures. Mechanistically, a more robust systemic Th2 cell signature with a higher level of virus-specific Th17 cells and a weaker yet sufficient neutralizing antibody profile against SARS-CoV-2 was observed in asymptomatic patients. In addition, asymptomatic COVID-19 patients had higher systemic levels of growth factors that are associated with cellular repair. Together, asymptomatic patients mount less pro-inflammatory and more protective immune responses against SARS-CoV-2 indicative of disease tolerance. Insights from this study highlight key immune pathways that could serve as therapeutic targets to prevent disease progression in COVID-19.

overall_design: RNA was extracted from whole blood collected from 30 asymptomatic patients from the Singapore cohort. Timepoints selected for extraction were during active infection (PCR-positive). Bridging samples were used for data comparison to previous dataset (GSE155454; transcriptomic signatures of WT SARS-CoV-2 infection).

first: Yi-Hao

last: Chan

first: Siew-Wai

last: Fong

first: Chek

last: Poh

first: Guillaume

last: Carissimo

last: Yeo

first: Siti

last: Amrun

first: Jackwee

last: Lim

first: Weili

last: Xu

first: Rhonda

last: Chee

first: Anthony

last: Torres-Ruesta

first: Cheryl

last: Lee

first: Matthew

last: Tay

first: Zi

last: Chang

first: Seow-Yen

last: Tan

first: Shirin

last: Kalimuddin

first: Barnaby

last: Young

first: Yee-Sin

last: Leo

first: Bernett

first: Olaf

last: Rötzschke

last: Lye

first: Laurent

last: Renia

first: Lisa

last: Ng


title: Differential gene expression and pathway analysis by RNA sequencing in human OPTN(E50K) astrocytes

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

summary: Retinal ganglion cell (RGC) degeneration is a primary characteristic of glaucoma, although non-cell autonomous mechanisms have been implicated in RGC dysfunction. Astrocytes closely associate with RGCs in the nerve fiber layer of the retina and optic nerve, where they can contribute to RGC neurodegeneration. However, the mechanisms by which astrocytes promote neurotoxicity and contribute to glaucoma remain unclear. Here we present data describing disease phenotypes in astrocytes and their ability to modulate RGC health.

overall_design: Examination the differential gene expression from mRNA in human pluripotent stem cell-derived astrocytes underlying OPTN E50K mutation in comparison with wild-type OPTN

first: Catia

last: Gomes

first: Kirstin

last: VanderWall

first: Jason

last: Meyer


title: RNA sequencing (RNA-SEQ) of ER-α36 knockdown by siRNA in cervical cancer cells

city: Jinan

first: Chunyan

last: Wang

state: Shandong

address: Wenhua West  No. 107,Lixia district

country: China

institute: Qilu Hospital of Shandong University

summary: Estrogen is proven to promote the malignant behaviors of many cancers via its receptors. Estrogen receptor alfa 36(ER-α36) is a newly identified isoform of estrogen receptor alfa （ERα）, which is different from the 66 kDa estrogen receptor alpha (ER-α66).However, the role of ER-α36 in regulating the effects of estrogen and its potential impact on human cervical cancer is poorly understood. In this study, we found that ER-α36 was over-expressed in cervical cancer tissues and elevated ER-α36 expression was associated with poor prognosis in cervical cancer patients. High expression of ER-α36 promotes the proliferation, invasion and metastasis of cervical cancer cells mediated by estrogen, while silencing ER-α36 had the opposite effects. Further research showed that high mobility group A2 (HMGA2) identified as a down-target of ER-α36 in cervical cancer cells. The oncogenic effect of ER-α36 was attenuated after HMGA2 knockdown. In conclusion, high expression of ER-α36 was correlated with a poor prognosis and metastasis in cervical cancer by regulating HMGA2.ER-α36 might serve as a prognostic biomarker and a target for cervical cancer treatment.

overall_design: The assay was performed on three biological triplicates as well as three experimental triplictes of ER-α36 knockdown and control cells.

first: Xingsheng

last: Yang


title: The effect of Atlantic salmon smolts quality, robustness and welfare on resistance towards a challenge with Piscirickettsia salmonis

first: Aleksei

last: Krasnov

summary: Mortalities due to infectious diseases is a long-term issue causing important economic losses to the Atlantic salmon industry worldwide. Producing better quality and more robust smolts before transfer to seawater cages may be an important measure to reduce mortalities and improve welfare. Exercise training fish while in fresh water tanks has proven to improve not just the cardiorespiratory capacity of fish, but also their growth potential and to stimulate the immune system thus increasing the survival rate when faced to an infection. In this study, we evaluated how subjecting the fish to exercising conditions by swimming in the tanks at water speeds considered optimal could improve their robustness and welfare, as well as their resistance to a P. salmonis controlled challenge. Compared to the control (untrained group), trained fish showed a better growth and better fin quality among other production-relevant parameters. Transcriptomic analyses indicated that training promoted an over-expression of genes involved in the cellular arm of the immune system. Furthermore, there was a massive effect of training on the cardiac muscle transcriptome, including genes that could be grouped into functional mechanisms such as metabolism, cellular and immune processes. Exercise training also promoted healthier liver and gills as shown by histopathological observations. Finally, the exercise regime did not improve resistance on the disease challenge with P. salmonis.

overall_design: Two groups of Atlantic salmon pre-smolts were subjected to different swimming speeds: 0.4 or 1.0 body-lengths per second for eleven weeks, after which fish from both groups were marked and set on a common tank for the disease challenge with P. salmonis infected shedders (cohabitation model). The challenge lasted for 60 days. During the training and challenge phases, samples were collected for transcriptomic and histological analyses.

first: Vicente

last: Castro


title: Comparison of good and poor swimmers (Atlantic Salmon parr) after a maximum swimming effort

summary: Swimming performance correlates with fitness of Atlantic salmon in the wild and farm conditions. Variation of this trait in salmon populations is high. The study assessed relationship between two parameters of swimming performance: the ability to cope with moderate and maximum swimming efforts.

overall_design: Atlantic salmon parr (average weight 25g) were classified as good or poor swimmers (best and worst performers) in a swim tunnel by an ramp-up program. After a recovery period of two weeks, individual fish were placed in a respiration swim tunnel, swam until exhaustion and the respiration rate was measured. The fish were either sampled right after exhaustion (E_crit) or after a recovery time of two hours (respiration). RNA from individuals (Cy3) were hybridized in a two-color setup together with an equalized mix of all test fish (Cy5).

first: Gerrit

last: Timmerhaus


title: JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells (RNA-seq)

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: SARS-CoV-2 infection of human airway epithelium activates genetic programs leading to progressive hyperinflammation in COVID-19 patients. Here, we report on transcriptomes activated in primary airway cells by interferons and their suppression by Janus kinase (JAK) inhibitors. Deciphering the regulation of the angiotensin-converting enzyme 2 (ACE2), the receptor for SARS-CoV-2, is paramount for understanding the cell tropism of SARS-CoV-2 infection. ChIP-seq for activating histone marks and Pol II loading identified candidate enhancer elements controlling the ACE2 locus, including the intronic dACE2 promoter. Employing RNA-seq, we demonstrate that interferons activate expression of dACE and, to a lesser extent, the genuine ACE2 gene. Interferon-induced gene expression was mitigated by the JAK inhibitors baricitinib and ruxolitinib used therapeutically in COVID-19 patients. Through integrating RNA-seq and ChIP-seq data we provide an in-depth understanding of genetic programs activated by interferons, and our study highlights JAK inhibitors as suitable tools to suppress these in bronchial cells.

overall_design: RNA-seq was used to characterize chromatin structures and gene expression profiles in cytokine stimulation.

first: Hye


title: Single-cell RNA-seq of sorted CD8+ T cells from B16 melanoma tumors

city: CAMBRIDGE

first: Aviv

last: Regev

state: MASSACHUSETTS

address: 415 MAIN ST

institute: Broad Institute

summary: The response of naive CD8 T cells to acute infections results in the generation of defined yet heterogeneous pools of effector and memory cells. In contrast, the complexity of tumor infiltrating CD8 T cell states is still not fully elucidated. To delineate the landscape of tumor infiltrating CD8 T cells in an unbiased manner, we performed single-cell (full-length) RNA-Seq of CD8 T cells infiltrating mouse B16 melanomas. Our analysis of cell heterogeneity revealed the presence of multiple distinct CD8 T cell subtypes including exhausted, terminal effector, naive and memory-like CD8 T cells, as well as novel intermediate states. TCR reconstruction and pseudotime ordering enabled us to follow differentiation of single clones and suggested distinct trajectories towards T-cell exhaustion.

overall_design:
single-cell (full-length) RNA-Seq of CD8 T cells infiltrating mouse B16 melanomas
Please note that [1] there are 192 samples included in the study, and the processed data was generated from  the 135 quality filtered samples (filetering parameters are provided in the data processing steps) [2] The cell subtype information for each sample is described and provided in the associated publication.

first: Meromit

last: Singer


title: The immune landscapes of primary central nervous system diffuse large B cell lymphoma

city: Montpellier

first: Jacques

last: Colinge

address: 208, avenue des Apothicaires

institute: Inserm

summary: Purpose: RNA-sequencing data was used to characterize the tumoral microenvironnement subtypes and its associated signaling networks.

overall_design: mRNA profiles were generated on NextSeq500 using single reads 75pb cycles.

first: Melissa

last: Alame

first: Emmanuel

last: Cornillot

first: Valère

last: Cacheux

first: Valérie

last: Rigau

last: Costes-Martineau

first: Vanessa

last: Lacheretz-Szablewski


title: Differential DNA methylation in gingival tissues in periodontal health and disease [Array]

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: We investigated differential DNA methylation in gingival tissues in states of periodontal health, gingivitis and periodontitis.

overall_design: methylation profiles from 12 periodontitis, 12 gingivitis, and 12 healthy patients

first: Panos

last: Papapanou

first: Hyunjin

last: Kim

first: Fatemeh

last: Momen-Heravi

first: Steven

last: Chen

first: Per

last: Hoffman

first: Moritz

last: Kebschull


title: RNAseq of human brain cell lines

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: In the murine brain, perivascular fibroblasts were recently identified as a novel potential constituent of the BBB. Here we present the existence of human cells, that could be the equivalent to the murine brain perivascular fibroblasts. Using RNA sequencing, we here show a similar transcriptomic profile of cultured human brain cells and murine perivascular fibroblasts. These data open up for new hypotheses on cell types involved in human CNS diseases.

overall_design: we performed bulk-RNA sequencing of 18 human cell lines and compared their transcriptional profiles with our previously published adult murine brain vascular cells

first: Jianping

last: Liu

first: Liqun

first: Michael

last: Vanlandewijck

first: Khayrun

last: Nahar

first: Christer

last: Betsholtz

first: Bengt

last: Westermark

first: Johanna

last: Andrae


title: Estimation of peptide elongation times from ribosome profiling spectra

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

summary: We develop a model for ribosome-protected fragment (RPF) spectra that accounts for the local codon context-dependent variation of peptide elongation times and fragment processing biases. We use a Marquardt algorithm for non-linear regression with maximum likelihood (ML) like statistics to fit the RPF sequencing data. Taking advantage of the factorial character of the present model, we reconstruct the parameters adhering to an ideal, unbiased RPF spectrum.

overall_design: Ribosome profiling of E. coli MG1655 cultured in rich medium

last: Pavlov

first: Gustaf

last: Ullman

first: Mans

last: Eherenberg


title: JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells (ChIP-seq)

first: Hye Kyung

last: Lee

overall_design: ChIP-seq was used to characterize chromatin structures and gene expression profiles in cytokine stimulation.

first: Hye


title: Genome-wide DNA methylation maps of Decitabine and/or Cisplatin treated bladder cancer cells.

city: Los Angeles

first: Jiong

last: Li

state: CA - California

department: School of Dentistry

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: It is well established that low-dose Decitabine treatment can sustain long-term antitumor effects by targeting DNA methylation and altering gene expression32. We performed methylated DNA immunoprecipitation (MEDIP) followed by next-generation sequencing in 5637 cells. Daily Decitabine treatment with 100 nM for 72 hr (with or without 100ng/ml cisplatin treatment) reduced the methylation level at CpG-islands in the genome of 5637 cells . However, this low-dose DEC treatment did not cause a significant reduction of DNA methylation in non-CpG islands regions.Our study represents the first detailed analysis of DNA methylome generated by RNA-seq technology in bladder cancer cells treated with low-dose decitabine. This study help to reveal the direct target genes of decitabine in bladder cancer treatement.

overall_design: Examination of DNA methylation level of  bladder cancer cells treated with lose-dose decitabine.

first: Yang


title: Differential DNA methylation & mRNA expression in gingival tissues in periodontal health and disease

first: Shannon

last: McKinney-Freeman

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

overall_design: Refer to individual Series


title: Differential mRNA transcription in gingival tissues in periodontal health and disease [RNA-seq]

summary: We investigated differential mRNA expression in gingival tissues in states of periodontal health, gingivitis and periodontitis.

overall_design: mRNA profiles from 12 periodontitis, 12 gingivitis, and 12 healthy patients

first: Panos

last: Papapanou

first: Hyunjin

last: Kim

first: Fatemeh

last: Momen-Heravi

first: Steven

last: Chen

first: Per

first: Moritz


title: Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

institute: Center for Genomic Regulation

summary: A broad diversity of modifications decorate RNA molecules. Originally conceived as static components, evidence is accumulating that some RNA modifications may be dynamic, contributing to cellular responses to external signals and environmental circumstances. A major difficulty in studying these modifications, however, is the need of tailored protocols to map each modification type individually. Here, we present a new approach that uses direct RNA nanopore sequencing to identify diverse RNA modification types present in native RNA molecules. First, we show that each RNA modification type results in a distinct and characteristic base-calling ‘error’ signature, which we validate using a battery of genetic strains lacking either pseudouridine (Ѱ) or 2’-O-methylation (Nm) modifications at known sites. We then demonstrate the value of these signatures for de novo transcriptome-wide prediction of Ѱ modifications, confirming known Ѱ-modified sites in rRNAs, snRNAs and mRNAs, as well as uncovering novel Ѱ sites including a previously unreported Pus4-dependent Ѱ modification in yeast mitochondrial rRNA, which we validate using orthogonal methods. To explore the dynamics of pseudouridylation across environmental stresses, we treat the cells with oxidative, cold and heat stresses, finding that yeast ribosomal rRNA modifications do not change upon environmental exposures. By contrast, our method reveals over a dozen novel heat-sensitive Ѱ-modified sites in snRNAs and snoRNAs, in addition to recovering previously reported sites. Finally, we develop a novel software, nanoRMS, which we show can estimate per-site modification stoichiometries from individual RNA molecules by identifying the reads with altered current intensity profiles, and quantify the RNA modification stoichiometry changes between two conditions. Our work demonstrates that Ѱ RNA modifications can be predicted de novo and in a quantitative manner using native RNA nanopore sequencing.

overall_design: Nanopore Direct RNA Sequencing of total RNA and mRNA from different strains and different sucrose gradient fractions

first: Eva

first: Oguzhan

last: Begik

first: Morghan

last: Lucas

first: Ivan

last: Milenkovic


title: Full-length dystrophin restoration via targeted genomic integration by AAV-CRISPR in a humanized mouse model of Duchenne muscular dystrophy

city: Durham

first: Adrian

last: Oliver

state: North Carolina

address: 101 Science Drive, CIEMAS Rm. 2323

institute: Duke University

summary: This study applies targeted Cas9-based gene insertion strategies for the correction of full-length dystrophin in a pre-clinical humanized mouse model of Duchenne muscular dystrophy. Following intramuscular or intravenous delivery, full-length dystrophin is restored in skeletal and cardiac muscle.

overall_design: High-throughput unbiased sequencing to characterize and quantify gene-editing outcomes in genomic DNA and cDNA transcripts of treated mice.

last: Pickar-Oliver

first: Veronica

last: Gough

first: Joel

last: Bohning

first: Siyan

last: Liu

first: Jacqueline

last: Robinson-Hamm

first: Heather

last: Daniels

first: William

last: Majoros

first: Garth

last: Devlin

first: Aravind

last: Asokan

first: Charles

last: Gersbach


title: Hematopoietic origin of most CD45–  bone marrow cells

city: Utrecht

first: Judith

middle: Anne

last: Vivié

state: Utrecht

address: Uppsalalaan 8

department: Single Cell Sequencing Facility

country: Netherlands

institute: Hubrecht Institute

summary: The non-hematopoietic cell fraction of the bone marrow (BM) is classically identified as CD45– Ter119– CD31– (herein referred to as triple-negative cells or TNCs). Although TNCs are believed to contain heterogeneous stromal cell populations, they remain poorly defined. Here we show, unexpectedly, that the vast majority of TNCs (~85%) have a hematopoietic rather than mesenchymal origin. Single cell RNA-sequencing reveals erythroid and lymphoid progenitor signatures among CD51– TNCs. When cultured with BM-derived stromal cells, Ly6D+ CD44+ CD51–TNCs give rise to B-lymphoid cells, whereas Ly6D–CD44+ CD51–TNCs generate erythroid cells. In addition, CD44+ CD51– TNCs contribute to repopulate B-lymphoid and erythroid cells after transplantation in mice. The CD44+ CD51– TNC population also expands during phenylhydrazine-induced acute hemolysis or in a model of sickle cell anemia. These findings thus uncover physiologically relevant, yet unappreciated, classes of stromal-associated CD45– hematopoietic progenitors.

overall_design: Single CD44+ CD51- and CD44- CD51- TNCs were sorted and sequenced on an Illumina Nextseq500

first: Philip

last: Boulais

first: Paul

last: Frenette


title: ATAC-seq from inflammation-experienced regulatory T-cells (ENCSR993QKC)

status: Public on Apr 22 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from left cardiac atrium (ENCSR731ODJ)

summary:
ATAC-seq on human left cardiac atrium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from regulatory T cell (ENCSR724UJS)


title: DNase-seq from liver (ENCSR982PCS)

summary:
DNase-seq for liver of C57BL/6J mice after 66 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from liver (ENCSR130IPN)

summary:
DNase-seq for liver of C57BL/6J mice after 54 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from heart right ventricle (ENCSR212LYK)

summary:
ATAC-seq on human heart right ventricle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from activated regulatory T-cells (ENCSR826JKN)


title: Responses to infectious pancreatic necrosis virus (IPNV) in the liver of Atlantic salmon

first: Aleksei

last: Krasnov

summary: IPNV is a viral pathogen causing losses in commercial aquaculture of Atlantic salmon. This study was performed to examine transcriptomic responses to IPNV and to compare them with changes caused with other viruses.

overall_design: Salmon was smoltified with manipulation of photoperiod and challenged two weeks after seawater transfer. The i.p. injected shedders (20%) were placed in the tank. Liver was sampled before challenge and at 4, 6, 8 and 10 days post infection.

first: Nina

last: Santi

first: Thomas

last: Moen


title: ATAC-seq from lung (ENCSR647AOY)

summary:
ATAC-seq on human lung

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from heart left ventricle (ENCSR846VPV)

summary:
ATAC-seq on human heart left ventricle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from thoracic aorta (ENCSR344ZTM)

summary:
ATAC-seq on human thoracic aorta

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from HK-2 (ENCSR634YVQ)


title: DNase-seq from S2 (ENCSR834VXA)


title: DNase-seq from liver (ENCSR498GAH)

summary:
DNase-seq for liver of C57BL/6J mice after 50 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from liver (ENCSR297YSC)

summary:
DNase-seq for liver of C57BL/6J mice after 58 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Regulation of adipocyte differentiation by IRF3

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

institute: Cancer Science Institute of Singapore

summary: The hypothesis tested is that IRF3 regulates adipogenesis and adipocyte function. Global gene expression of IRF3 wildtype (WT) and knockout (KO) adipocytes at different days during differentiation was compared. The results provide evidence on how IRF3 controls PPARg -regulated adipogenic program thereby regulate adipocyte differentiation.

overall_design: IRF3 WT and KO preadipocytes were isolated from white adipose tissue for differentation. Cells were harvested at day 3, 5, 7 and 9 during differentiation to isolate RNA for microarray analysis.

first: Yongliang

last: Zhang

first: Peng

last: Tang


title: DNase-seq from liver (ENCSR765TON)

summary:
DNase-seq for liver of C57BL/6J mice after 62 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from Right ventricle myocardium superior (ENCSR074WMH)

summary:
ATAC-seq on human right ventricle myocardium superior

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: KRAS and MEK activation promote antisense oligonucleotide uptake and activity by limiting collagen production

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

department: Functional Genomics

institute: Ionis Pharmaceuticals

summary: Using RNAseq we describe transcriptional changes downstream of MEK1 affecting RNA kncokdown following free uptake RNaseH1 gapmer antisense oligonucleotides

overall_design: We perform RNAseq on cell lines with a stimulated MAPK pathway via inducible expression of KRAS(G12D), inducible expression of MEK1(S218/S222DD) and by stimulation with the PKC activator, PMA

first: Michael

last: Tanowitz

first: Brendan

middle: T

last: Finicle

first: Punit

middle: P

last: Seth

first: Aimee

middle: L

last: Edinger


title: Effect of cabozantinib on transcriptome and signaling pathways in leukemic cell line Kasumi-1

city: Taipei

first: Yu-Hsuan

last: Fu

address: No.1, Chang-Te St

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary: To identify molecular effects of the tyrosine kinase inhibitor cabozantinib (XL184), we applied gene expression profiling on human acute leukemic cell lines Kasumi-1, which harbors t(8;21) coupled with KIT mutation, by Whole Transcriptome Shotgun Sequencing (RNA-seq). After Kasumi-1 cells were treated with 100nM cabozantinib for 4h or 24h, differentially expressed genes (DEGs) of  124 genes upregulated and 416 were downregulated in 4h, and 184 genes upregulated and 69 genes were downregulated in 24h treatment, compared with vehicle group.

overall_design: Gene expression in Kasumi-1 was measured after exposure for 4h or 24 h to 100nM cabozantinib (XL184) or to the vehicle control (DMSO).

first: Liang-In

last: Lin

first: Kuan-Wei

last: Su


title: AGO104 is an RdDM effector of paramutation at the maize b1 locus

first: Daniel

last: Grimanelli

address: 911 Av Agropolis

institute: IRD

type: Non-coding RNA profiling by high throughput sequencing

summary: Paramutation is an exception among eukaryotes, in which epigenetic information is conserved through mitosis and meiosis. It has been studied for over 70 years in maize, but the mechanisms involved are largely unknown. All previously described actors of paramutation encoding components of the RNA-dependent DNA-methylation pathway (RdDM) are involved in the biogenesis of 24nt small RNAs. However, no actors of paramutation have been identified in the effector complex of RdDM. Through a combination of reverse genetics, immunolocalization and immunoprecipitation (siRNA-IP) we found that ARGONAUTE104 (AGO104), AGO105 and AGO119 are members of the RdDM effector complex in maize and bind siRNAs produced from the tandem repeats required for paramutation at the b1 locus. We also showed that AGO104 is an effector of the b1 paramutation in maize.

overall_design: siRNA for immature ears

first: Juliette

last: Aubert


title: Lsr2 and its novel paralogue mediate the adjustment of Mycobacterium smegmatis to unfavorable environmental conditions

city: Wrocław

first: Marta

last: Kołodziej

address: Joliot-Curie 14a

department: Faculty of Biotechnology

country: Poland

institute: University of Wroclaw

summary: In the present study, we sought to explore the role of Lsr2 as a regulator of transcription in the saprophytic species, M. smegmatis. We used RNA-seq to compare the global transcription profiles of Δlsr2 and wild-type M. smegmatis strains in an attempt to decode Lsr2 regulatory network under optimal conditions or during hypoxia. We show that Lsr2 binds AT-rich regions and mainly acts as a gene repressor, either directly by binding promoter regions or indirectly through DNA-loop formation.

overall_design: Total RNA transcriptomic profiles, following ribodepletion with Ribo-Zero kit(Illumina) of M. smegmatis WT nad Δlsr2 strains in two conditions (optimal growth and hypoxia), RNA/cDNA libraries prepared with KAPA stranded RNA preparation kit, True Seq v2 single indexing used for multiplexing.

first: Tomasz

last: Łebkowski

first: Przemysław

last: Płociński

first: Joanna

last: Hołówka

first: Mariola

last: Paściak

first: Bartosz

last: Wojtaś

first: Katarzyna

last: Bury

first: Igor

last: Konieczny

first: Jarosław

last: Dziadek

first: Jolanta

last: Zakrzewska-Czerwińska


title: eATP-responsive synthetic yeast ameliorate TNBS-induced colitis

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: By combining directed evolution and synthetic biology, we engineered novel synthetic yeasts probiotics for the dynamic modulation of intestinal inflammation. In this experiment we treated TNBS-colitis induced mice with these probiotics and test the amelioration of immune response in the transcriptional level in the colon.

overall_design: A colon piece was colected from each mouse at the peak of the diesease for transcriptional analysis. Control groups were included.

first: Cristina

last: Gutierrez-Vazquez

first: Francisco

last: Quintana


title: DNase-seq from liver (ENCSR802MKV)

first: ENCODE

last: DCC

summary:
DNase-seq for liver of C57BL/6J mice after 70 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: RNA-seq analysis of mouse heart tissue ischemia/reperfusion (I/R)

city: guizhou

first: Hua

last: Fang

address: 83 Zhongshan East Road, Nanming District

institute: Guizhou university

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

overall_design: 4 Samples in total; 2 samples sham surgery and 2 ischemia/reperfusion (IR)


title: RNA-seq of postnatal day 0 (P0) wild-type and Fezf2-/- cortices

city: Santa Cruz

first: Bin

last: Chen

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

summary: The goal of the study was to compare gene expression of P0 wild-type and P0 Fezf2-/- cortices. Total RNAs were isolated from P0 cortices dissected from wild-type and Fezf2-/- mice (n=3 for each genotype), following Qiagen RNAeasy kit instruction.Sequence libraries were made following Illumina RNA TruSeq library preparation guide.The libaries were pair-end sequenced (50nt per end). Differentially expressed genes were identified by DESEQ.

overall_design: Total RNAs were isolated from P0 cortices (3 control and 3 mutants), and sequenced on Illumina Genome Analyzer

first: David

last: Tastad

first: Jeremiah

last: Tsyporin

first: Sol

last: Katzman


title: Systems analysis of human T helper17 cell differentiation uncovers distinct time-regulated transcriptional modules

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Th17 cells protect from infections and are pathogenic in autoimmunity. While human Th17 cell differentiation has been defined, the global and stepwise transcriptional changes accompanying this process remain uncharacterized. Herein, by performing transcriptome analysis of human Th17 cells we uncovered three time-regulated modules: early, involving exclusively ‘signalling pathways’ genes; late, characterized by response to infections; persistent, involving effector immune functions. To assign them an inflammatory or regulatory potential, we compared Th17 cells differentiated in presence or absence of IL-1β, respectively. Most inflammatory genes belong to the persistent module, while regulatory genes are lately or persistently induced. This study represents the first integrative analysis of the stepwise human Th17 differentiation program and offers new perspectives towards therapeutic targeting of Th17-related autoimmune diseases.

overall_design: Total RNA-sequencing analyses of naïve CD4+ T cells, either unpolarised (Th0) or differentiated under "inflammatory"(Th17) or "regulatory" (Th17 without IL1b) Th17 conditions, obtained from 5 independent healthy donors (HD), harvested at 48h and 5 days of differentiation.

first: Alessia

last: Capone

first: Chiara

last: Naro

first: Manuela

last: Bianco

first: Marco

last: De Bardi

first: Floriane

last: Noël

first: Paolo

last: Macchi

first: Luca

last: Battistini

first: Vassili

last: Soumelis

first: Elisabetta

last: Volpe

first: Claudio

last: Sette


title: Multi-omics analysis of small RNA, transcriptome and degradome of RSV-infected Nicotiana benthamiana - the regulatory networks of Nicothiana benthamiana genes in response to RSV infection

city: Ningbo

first: Cui

last: Weijun

address: Fenghua Road No. 818

institute: Ningbo University

summary: Rice stripe virus (RSV) causes the general chlorosis symptom and influences expression of numberous chloropalst-related genes at transcriotional level in Nicotiana benthamiana plants, but the mechanism are not well understood. Small RNAs (sRNAs), including virus-derived siRNA (vsiRNA) play roles in modulating genes expression post-transcriptionally. This present work presents multi-omics analysis of the transcriptome, sRNAome and degradome in RSV-infected N.benthamiana plants. Transcriptome-seq profiled 4127 N. benthamiana genes, with differentially expressed genes (DEGs) enriched in functional categories such as metabolic process, protein phosphorylation, regulation of transcription, carotenoid biosynthetic process. We identified 400863, 203874 and 244713 reads of vsiRNA from 3 sRNA libraries of RSV-infected N.benthamiana plants respectively. The degradome-seq report discovered a significant number of N.benthamiana genes that might be regulated by vsiRNAs post-transcriptionally. Based on integrated analysis of the three omics, we provide a substantial amount of novel information on the transcriptional and post-transcriptional networks in RSV-infected N.benthamiana, which will extends our horizon about the interactions between virus and their hosts.

sample_organism:
Nicotiana benthamiana
Tenuivirus oryzaclavatae

overall_design: Analysis of RSV-derived small RNA transcriptome and mRNA transcriptome in 6 libraries (2 treatments × 3 biological replicates); Analysis of mRNA degradome in 1 libraries (a pool of 3 biological replicates of RSV-infected Nicotiana benthamiana)

first: Fei

last: Yan

first: Jianping


title: Pharmacological Activation of Nrf2 Enhances Functional Liver Regeneration

city: Liverpool

first: Ian

last: Copple

address: Ashton Street

department: Department of Pharmacology and Therapeutics

country: United Kingdom

institute: University of Liverpool

summary: The transcription factor Nuclear factor erythroid 2-related factor 2 (Nrf2) regulates an array of cytoprotective genes, yet studies in transgenic mice have led to conflicting reports on its role in liver regeneration. We aimed to test the hypothesis that pharmacological activation of Nrf2 would enhance liver regeneration. Wild type (WT) and Nrf2 null mice were administered bardoxolone methyl (CDDO-Me), a potent activator of Nrf2 that has entered clinical development, and then subjected to partial hepatectomy (PHx). CDDO-Me enhanced the rate of restoration of liver volume and improved liver function (multispectral optoacoustic imaging in wild type, but not Nrf2 null, mice following two-thirds partial hepatectomy. These effects were associated with an increase in hepatocyte hypertrophy and proliferation, the suppression of immune and inflammatory signals, and metabolic remodeling in the remnant liver tissue.

overall_design: Liver tissues were resected from wild type (WT) mice treated with DMSO or 3 mg/kg CDDO-Me, untreated Nrf2 null (KO) mice, and KO mice treated with 3 mg/kg CDDO-Me (n=4 animals/group). Liver resections were performed 24 hours after the treatments. RNA was isolated and RNA-Seq was performed.

first: Benjamin

middle: K

last: Chan

first: Mohamed

last: Elmasry

first: Shiva

last: Forootan

first: Giusy

last: Russomanno

first: Tobias

last: Bunday

first: Fang

last: Zhang

first: Nathalie

last: Brillant

first: Philip

last: Starkey Lewis

first: Rhona

last: Aird

first: Emanuele

last: Ricci

first: Timothy

last: Andrews

first: Rowena

last: Sison-Young

first: Amy

last: Schofield

first: Yongxiang

last: Fang

first: Adam

last: Lister

first: Jack

middle: W

last: Sharkey

first: Harish

last: Poptani

first: Neil

middle: R

last: Kitteringham

first: Stuart

last: Forbes

first: Hassan

last: Malik

first: Stephen

last: Fenwick

first: B

last: Park

first: Christopher

middle: E

last: Goldring


title: RAD21 is a driver of chromosome 8 gain in Ewing sarcoma to mitigate replication stress

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Aneuploidy, defined as whole chromosome gain or loss, causes cellular stress but, paradoxically, is a frequent occurrence in cancers. Here, we investigate why around 50% of Ewing sarcomas, driven by the EWS-FLI1 fusion oncogene, harbor chromosome 8 gains. Expression of the EWS-FLI1 fusion in primary cells causes replication stress that can result in cellular senescence. Using an evolution approach, we show that trisomy 8 mitigates EWS-FLI1 induced replication stress through gain of a copy of RAD21. Low-level ectopic expression of RAD21 is sufficient to dampen replication stress and improve proliferation in EWS-FLI1 expressing cells. Conversely, deleting one copy in trisomy 8 cells largely neutralizes the fitness benefit of chromosome 8 gain and reduces tumorgenicity of an Ewing sarcoma cancer cell line in soft agar assays. We propose that RAD21 promotes tumorigenesis through single gene copy gain. Such genes may explain some recurrent aneuploidies in cancer.

overall_design: Human mesenchymal progenitor (hMPro cells) were infected with 26-ORF lentiviral expression constructs and/or lentiviral Tet-on doxycycline-controlled expression EWS-FLI oncogene construct (or Vector control).  The 26-ORF expression plasmid library was selected from the Precision LentiORF Collection acquired from Dharmacon. The backbone plasmid is pLOC with CMV promoter controlling expression of the target genes (Table S4 in the paper). After the drug selection for the infected cells, cells were continuously cultured in the presence of doxycycline. Cells were sampled for RNA-extraction at passages 1, 4, 8. The total RNA was sequenced by 3’-DGE NGS RNA sequencing method. Every time point in each experiment was sampled in 3-5 experimental replicates for RNAseq.

first: Xiaofeng

last: Su

first: Duanduan

last: Ma

first: James

middle: V

last: Parsons

first: John

middle: M

last: Replogle

last: Amatruda

first: Kimberly

last: Stegmaier

first: Angelika

last: Amon


title: RNA-seq in different hematopoietic stem and progenitor cell subpopulations of patients with chronic and progressed polycythemia vera and controls

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: Hematopoietic stem/multipotent progenitor cells (HSC/MPPs, referred to as HSCs) can differentiate into functionally divergent cell lineages including common myeloid progenitors (CMPs), megakaryocyte-erythrocyte progenitors (MEPs) or granulocyte-macrophage progenitors (GMPs). When this stem cell differentiation process is altered, abnormal (pre)leukemic stem cell subpopulations may form, eventually resulting in clonal hematopoiesis and in the onset of chronic or acute leukemias such as for example polycythemia vera (PV) or acute myeloid leukemia (AML). To understand the molecular and biochemical changes underlying trilineage hyperproliferation in PV and the process of progression to post-PV myelofibroses (post-PV MF) or post-PV acute myeloid leukemia (post-PV AML), highly refined analyses of PV stem and progenitor cells are required. We performed transcriptomics and proteomics analyses in hematopoietic stem and progenitor cells of patients with chronic and progressed PV as well as controls to identify key molecular changes in these cell subpopulations for disease manifestation and progression.

overall_design: Unbiased RNA-seq analysis was performed in HSC/MPPs, CMP/MEPs, CMP, MEPs and GMPs of 18 patients with chronic and progressed PV and 21 controls.

first: Fabienne

last: Meier-Abt


title: Role of Lsd1 in HOTAIR function

first: Marina

last: Pinskaya

address: rue d'Ulm

institute: Institut Curie

summary: HOTAIR is a scafold long non-coding RNA tethering PRC2 and Lsd1/REST/coREST complexes to gene promoters to repress transcription of genes involved in epithelial to mesenchymal transition (EMT). To decipher a role of the Lsd1 in HOTAIR function we generated epithelial cell lines expressing full length and truncated versions of HOTAIR missing first 5'-300 (Epi-HOTΔP) and last 3'-500 bp (Epi-HOTΔL) interacting with HOTAIR partners. These cell lines were further used to determine Lsd1 binding sites using chromatin immunoprecipitation approach.

overall_design: For all cell lines, crosslinked chromatin was purified from two independent biological duplicate cell cultures. For each replicate, an aliquot was kept as Input while the rest was used for Chromatin Immunoprecipitation using the antibody against Lsd1.

first: Julien

last: Jarroux

first: Violaine

last: Saint-André

first: Camille

last: Gautier

first: Antonin

last: Morillon


title: The CD33 short isoform is a gain-of-function variant that enhances Aß1-42 phagocytosis in microglia

status: Public on Apr 21 2021

city: Edmonton

first: Jason

middle: R.

last: Plemel

state: Alberta

address: 5-64 Heritage Medical Research Centre

department: Department of Medicine

country: Canada

institute: University of Alberta

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

overall_design: Refer to individual Series


title: The CD33 short isoform is a gain-of-function variant that enhances Aß1-42 phagocytosis in microglia II

summary:
Background: CD33 is genetically linked to Alzheimer’s disease (AD) susceptibility through differential expression of isoforms in microglia. The role of the human CD33 short isoform (hCD33m), preferentially encoded by an AD-protective CD33 allele (rs12459419T), is unknown. Here, we test whether hCD33m represents a loss-of-function or gain-of-function variant.    Results: In both primary microglia and U937 cells, we find that hCD33m enhances phagocytosis. This contrasts with the human CD33 long isoform (hCD33M) that represses phagocytosis, as previously demonstrated. As revealed by scRNAseq, hCD33m+ microglia are enriched in a cluster of cells defined by an upregulated expression and gene regulatory network of immediate early genes, which was further validated within microglia in situ. Using a new hCD33m-specific antibody enabled hCD33m expression to be examined, demonstrating a preference for an intracellular location. Moreover, this newly discovered gain-of-function role for hCD33m is dependent on its cytoplasmic signaling motifs, dominant over hCD33M, and not due to loss of glycan ligand binding.    Conclusions: These results provide strong support that hCD33m represents a gain-of-function isoform and offers insight into what it may take to therapeutically capture the AD-protective CD33 allele.
We have developed two models to test the role of hCD33m. The first is a new strain of transgenic mice expressing hCD33m in the microglial cell lineage. The second is U937 cells where the CD33 gene was disrupted by CRISPR/Cas9 and complemented with different variants of hCD33. Primary microglia and U937 cells were tested in phagocytosis assays and single cell RNA sequencing (scRNAseq) was carried out on the primary microglia. Furthermore, a new monoclonal antibody was developed to detect hCD33m more efficiently.

overall_design: single-cell RNA-seq of wildtype, hCD33M and hCD33m mouse brain. This is the data set referenced in the supplemental data of the associated paper.


title: DNA compaction by a novel viral-encoded protein globally dysregulates host gene expression.

city: Bethesda

first: Deborah

last: Hinton

address: 8 Center drive

institute: NIDDK

summary:
Purpose: We investigated the effect of the T4 MotB protein on E. coli gene expression
Method: TOP10F' E. coli containing either pNW129 or pNW129-MotB were grown to early log phase (OD600 ~ 0.3)  then induced with 0.2% arabinose for 20 minutes. T4 phage added to the culture at MOI10. Cells were then harvested at 0, 5, and 10 min time points and total RNA was isolated. The cDNA library was prepared using a modified RNATagSeq workflow as previously described (Shishkin, A.A. et al. 2015 Nat Methods). Optimum fragmentation of the total RNA samples in this library was determined to be 3 min at 94C in FastAP buffer (Thermo Fischer Scientific).  The cDNA Library was run on a Bioanalyzer using the Agilent High Sensitivity DNA Kit to evaluate the quality of the library.  The concentration of the cDNA library was determined by qPCR using the KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA, USA) and CFX96 Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA). Sequencing was performed by the NIDDK Genomics Core facility using a MiSeq system with the single-end 50 bp Sequencing Kit (Illumina, San Diego, CA, USA). RNA-seq data was processed as previously described using E. coli str. K-12 substr. MG1655 (NC_000913.3) as the reference genome.  Differential expression between conditions was represented as a fold change, and genes with both a fold change ≥2 or ≤ 0.5 and adjusted p value ≤ 0.05 were considered significant.
Results: RNA-seq data revealed that the expression of 542 E. coli genes were significantly changed after motB expression. The expression of 704 and 706 E. coli genes were changed T4 5 min and 10 min post infection after MotB expression, respectively. After 5 min T4 infection, 34 T4 genes were significantly changed.
Conclusion: T4 MotB is a DNA binding protein that compacts host DNA and disrupts H-NS dependent repression.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: To determine the effect of the T4 MotB protein on E. coli  gene expression, RNAseq was performed for TOP10F' E. coli infected by T4 after producing T4 MotB for 20 minutes .

first: Bokyung

last: Son

first: Jennifer

last: Patterson-West

first: Emilios

last: Dimitriadis

first: Revathy

last: Ramachandran

last: Iben

first: Leslie

last: Knipling

first: Jingen

last: Zhu

first: Venigalla

middle: B

last: Rao


title: Gene expression profiling of Trypanosoma cruzi in the presence of heme points to glycosomal metabolic adaptation of epimastigotes inside the vector

city: Nottingham

first: Fei

last: Sang

address: QMC

department: School of Life Sciences

institute: University of Nottingham

summary: Using the Deep Seq transcriptome sequencing we characterized the heme induced transcriptome of epimastigotes and determined that most of the upregulated genes were related to glucose metabolism inside the glycosomes.

overall_design: the RNA-Seq analysis should be a valuable screening tool strategy for identifying stage-regulated T. cruzi genes and metabolic pathways affected by heme

first: Marcia

middle: C

last: Paes

first: Marcos

last: Alcocer


title: The CD33 short isoform is a gain-of-function variant that enhances Aß1-42 phagocytosis in microglia I

overall_design: single-cell RNA-seq of wildtype, hCD33M and hCD33m mouse brain. This is the data set used in the associated paper.


title: MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in nematodes, mice and human cells

city: GuangZhou

first: Yongfei

last: Hu

state: GUangDong

address: Road LuJing

institute: Dermatology Hospital of Southern Medical University

type: Genome variation profiling by high throughput sequencing

summary: CRISPR-mediated gene activation (CRISPRa) is a promising therapeutic gene editing strategy without inducing DNA double-strand breaks (DSBs). However, in vivo implementation of these CRISPRa systems remains a challenge. Here, we report a compact and robust miniCas9 activator (termed miniCAFE) for in vivo activation of endogenous target genes. The system relies on recruitment of an engineered minimal nuclease-null Cas9 from Campylobacter jejuni and potent transcriptional activators to a target locus by a single guide RNA. It enables robust gene activation in human cells even with a single DNA copy and is able to promote lifespan of C. elegans through activation of longevity-regulating genes. As proof-of-concept, delivered within an all-in-one adeno-associated virus (AAV), miniCAFE can activate Fgf21 expression in the liver and regulate energy metabolism in adult mice. Thus, miniCAFE holds great therapeutic potential against human diseases.

overall_design: using RNA-seq, we tested the specificity of gene activation with S-D system. Compared with the control group transfected with all the plasmids except the sgRNA, the expression level of untargeted genes in the groups co-transfected with S-D system and sgRNA2 targeting MYOD promoter region was not broadly affected, and the expression of MYOD was significantly increased (FDR<0.05).  To check whether a truncated 15-nt sgRNA or WT CjCas9 could affect the specificity of gene activation, we profiled genome-wide gene expression by RNA-seq using IL1RN as the target gene in HEK293T cells. Similar to V-D co-transfected with a 22-nt sgRNA1, V-D or V-WT co-transfected with a 15-nt sgRNA1 showed comparable high specificity.  And we also noted that miniCAFE/sgRNA (F) system showed more potent capability to activate gene expression in mouse cells at each ratio. Again, RNA-seq revealed high specificity of the miniCAFE/sgRNA (F)system.

first: Xin

last: Zhang

first: Sihan

last: Lv

first: Zhenhuan

last: Luo


title: The synthetic opioid fentanyl elicited transcriptomic alterations related to viral replication, immune response, and inflammation in vitro.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: The US is in the midst of a major drug epidemic fueled in large part by the widespread recreational use of syntheticopioids such as fentanyl. we evaluated the impact of fentanyl using in cell lines that replicate infectious viruses. RNAseq identified a number of hepatocyte genes that were differentially regulated by fentanyl, including those related to apoptosis, the antiviral / interferon response, chemokine signaling, and NFkB signaling.

overall_design: Huh7.5 and HepG2 cell lines were exposed to fentanyl or left as untreated controls in duplicate.

last: Blackard


title: miR-33 silencing reprograms the immune cell landscape in atherosclerotic plaques

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

summary: We used single cell RNA-sequencing of aortic CD45+ cells, combined with immunohistologic, morphometric and flow cytometric analyses to define the changes in plaque immune cell composition, gene expression and function following miR-33 inhibition. We report that anti-miR-33 treatment of Ldlr–/– mice with advanced atherosclerosis reduced plaque burden and altered the plaque immune cell landscape by shifting the balance of pro- and anti-atherosclerotic macrophage and T cell subsets.  By quantifying the kinetic processes that determine plaque macrophage burden, we found that anti-miR-33 reduced levels of circulating monocytes and splenic myeloid progenitors, decreased macrophage proliferation and retention, and promoted macrophage attrition by apoptosis and efferocytotic clearance. scRNA-sequencing of aortic arch plaques showed that anti-miR-33 reduced the frequency of MHCIIhi “inflammatory” and Trem2hi “metabolic” macrophages, but not tissue resident macrophages. Furthermore, anti-miR-33  led to derepression of distinct miR-33 target genes in the different macrophage subsets: in resident and Trem2hi macrophages, anti-miR-33 relieved repression of miR-33 target genes involved in lipid metabolism (e.g., Abca1, Ncoa1, Ncoa2, Crot), whereas in MHCIIhi macrophages, anti-miR-33 upregulated target genes involved in chromatin remodeling and transcriptional regulation. Anti-miR-33 also reduced the accumulation of aortic CD8+ and CD4+ Th1 cells, and increased levels of FoxP3+ regulatory T cells in plaques, consistent with an immune-dampening effect on plaque inflammation.

overall_design: Anti-miR-33 treatment of Ldlr–/– mice

first: Milessa

last: Afonso

first: Monika

last: Sharma

first: Martin

last: Schlegel

first: Coen

last: van Solingen

first: Graeme

middle: J

last: Koelwyn

first: Lianne

last: Shanley

first: Lauren

last: Beckett

first: Daniel

last: Peled

first: Karishma

last: Rahman

first: Alireza

last: Khodadi-Jamayran

first: Edward

middle: A

last: Fisher

first: Kathryn

last: Moore


title: Direct RNA-RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention

city: Marseille

first: Anne-Marie

last: François-Bellan

address: 27 Bd Jean Moulin

department: Facute de Medecine

institute: CNRS-AMU

summary: The goal of this study was to determine if the lncRNA Neat1, in addition to its structural role, may also be directly involved in the binding by base pairing of RNAs and consequently in their retention in paraspeckles

overall_design: GH4C1 sommatolactotroph pituitary cells (ATCC_ CCL-82.2™,  Molsheim, France) were grown in HamF10 medium supplemented  with 15% horse serum and 2% fetal calf serum. Cells were crosslinked with psoralen which only fix the RNA-RNA interactions. We then perfomed an RNA pull-down and RNAseq to determine the RNAs direcltely linked to Neat1

first: Audrey

last: Jacq

first: Denis

last: Becquet

first: Severine

last: Guillen

first: Benedicte

last: Boyer

first: Maria-Montserrat

last: Goutierrez

first: Jean-Louis

last: Franc


title: Biophysically patterned glioblastoma model via rapid 3D bioprinting for investigation of tumorigenesis and angiogenesis

city: La Jolla

first: Rana

last: Tariq

state: California

address: 9500 Gilman Dr

department: Pedatrics

institute: University of California, San Diego

summary:
Purpose: Our goals of transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods in our study are to evaluate changes in specific genes and pathways in sphere culture, 3D soft and 3D stiff culture of GBM cells.
Conclusions: Our study represents the first detailed transcriptional analysis of GBM cells cultured in 3D systems with biophysical patterning. The results demonstrated that the stiff patterns promote the mesenchymal phenotype of cells, while the soft pattern enriches cells with the classical subtype. Thus the 3D biophysical patterning permits recapitulation of different molecular subtypes of GBM in vitro.

overall_design: Global transcriptome profiling on human patient derived glioblastoma cells (GBM, TS576) cultured as spheres and the tumor-only 3D soft and the tumor-only 3D stiff conditions.

first: Min

last: Tang

first: Shashi

last: Tiwari

first: Kriti

last: Agrawal

first: Trevor

last: Tam

first: Jing

last: Tian

first: Tariq

last: Rana

first: Shaochen

last: Chen


title: Exosomes from antler stem cells alleviates MSC senescence and osteoarthritis

city: Beijing

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

institute: institute of zoology, CAS

summary: The therapeutic functions of stem cells were mainly depending on paracrine effects rather than their own proliferation and differentiation on site. In advantage of easy to collected from conditioned medium, have contents of cytokines, growth factors, signaling lipids, mRNAs, and regulatory miRNAs, exosomes from stem cells were considered to be a promising material for stem cell-based cell-free therapies. In traditional Chinese medicine, antler extracts have been used to alleviates aging and aging related diseases. We have demonstrated that exosomes from antler stem cells (ASCs), the source of the annual full regeneration of deer antler, could alleviate cellular senescence and aging related diseases. With exosomes treatment, the senescent phenotype of primary MSCs and hMSCs at late passage were significantly mitigated. When injected into articular cavity, exosomes from ASCs markedly promote joint function recovery and bone and cartilage regeneration. By LC-MS/MS assay, we found that exosomes from ASCs contain various proteins which in the regulation of biological processes including cell proliferation and migration, immunoregulation, wound healing and angiogenesis. With the advantages of abundant sources, low risk of tumorigenicity and immunogenicity, exosomes from ASCs may consider as a promising bio-material for cell-free therapies in the future.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In mice, PBS-treated controls, osteoarthritis modeling, and exosomes-treated mice joint. Among hMSCs, PBS-treated control and exosome-treated cells. Among primary MSCs, PBS-treated control and exosome-treated cells.

first: Guanghui

last: Liu


title: Chronic social instability stress during adolescence does not change the acute stress response in adult male mice

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

department: D-HESZ

institute: ETH Zürich

summary: Chronic stress exposure in adolescence can lead to a lasting change in stress responsiveness later in life and is associated with increased mental health issues in adulthood. Here we investigate whether the Chronic Social Instability (CSI) paradigm in mice influences the molecular response to novel acute stressors

overall_design: Mice were either subjected to a chronic social instability (CSI) (random weekly chagemate changes for 7 weeks) paradigm, or kept as control animals (no cagemate changes). Then, a subset of both groups was subjected to a novel acute stressor in the form of restraint stress (30 min). 45min after onset of restraint stress animals were sacrificed and ventral hippocampi dissected and the transcriptome alanyzed with next generation sequecing

first: Oliver

last: Sturman

first: Johannes

last: Bohacek


title: Molecular and cellular design of ovotestis development

city: Wuhan

first: Xin

last: Wang

address: No.299 Bayi Road, Wuchang District

department: College of Life Sciences

institute: Wuhan University

summary: Ovotestis often occurs in intersex individuals under certain pathological and physiological conditions. However, how ovotestis is formed remains unknown. Here, we report the first comprehensive single-cell developmental atlas of the model fish ovotestis. We provide an overview of ovotestis cell identities and a roadmap of germline, niche, and stem cell development in ovotestis by cell lineage reconstruction and a uniform manifold approximation and projection. We identify common progenitors of germline stem cells with two states, which reveal their bipotential nature to differentiate into both spermatogonial stem cells and female germline stem cells. Moreover, we found that ovotestis infertility was caused by developmental defects in oogenesis owing to dynamic autophagic degradation in female germline cells, and in spermatogenesis due to deficiency of histone-to-protamine replacement in spermatid differentiation. Notably, signaling pathways in gonadal niche cells and their interaction with germline cells synergistically determined cell fates of both male and female germlines in ovotestis. Overall, we reveal a cellular fate map of germline and niche cell development that shapes cell differentiation directions of ovotestis, and provide novel insights into ovotestis development.

overall_design: Single cell transcriptome of ovotestis in Monopterus albus

first: Rongjia

last: Zhou


title: Maternally expressed imprinted gene SDC modulates circadian period and hypocotyl length

first: Lei

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

institute: insitute of botany, chinese academy of sciences

summary: As a time-keeping system, circadian clock times numerous key processes to the appropriate time of day. The proper phasing of the plant circadian clock, which is mainly determined by circadian period, can provide the growth fitness for plants by facilitating the endogenous rhythms to match the external day–night cycle. Here we provide the comprehensive evidences that genomic 5-methylcytosine is critical for regulating circadian period. We found that chemical inhibition of DNA methyltransferases could significantly lengthen circadian period in the seedlings of Arabidopsis. Dysfunction of methyltransferases met1-3 and drm1 drm2 cmt3 cmt2 for both hypo-CG and hypo-non-CG texts can dramatically lengthen circadian period. To find the target genes of 5mC for modulating the circadian period, we conducted RNAseq experiments of Aza vs Mock at ZT1 h or ZT13 h time window and ddcc vs Col-0 at LL 24 h or LL36 time window. Each sample has two biological replicates.

overall_design: To explore the different expressed circadian genes infected by 5mC. Aza vs Mock seedlings were collected at ZT1 h and ZT13 time window, ddcc vs Col-0 seedlings were collected at LL 24 h and LL36 time window, each sample has two biological repeats.

first: Wenwen


title: Differential regulation of apoptotic and key canonical pathways in psoriasis by therapeutic wavelengths of ultraviolet B radiation

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary: Phototherapy is an effective therapy and may induce remission of psoriasis.  Previous studies have established the action spectrum of clearance and that apoptosis is differentially induced in psoriasis plaques by clinically effective wavelengths of ultraviolet B (UVB).  The aim of this study was to investigate the molecular mechanisms regulating psoriasis plaque resolution by studying the transcriptomic response to clinically effective (311nm, narrow band) UVB compared to a clinically ineffective (290nm) wavelength.  We irradiated lesional psoriatic skin in vivo with a single 3 MED (minimal erythemal dose) of 311nm or 290nm wavelength of UVB and performed skin biopsies at 4h or 18h post irradiation and from un-irradiated lesional skin.  Forty-eight micro-dissected epidermal samples were analysed using the Illumina DASL array platform from 20 psoriatic patients.  Bioinformatic analysis identified differentially expressed genes (DEGs) associated with 311nm but not 290nm irradiation; these DEGs were subject to Ingenuity pathway and upstream regulator analysis.        The number of differentially regulated epidermal genes was greatest at 18h following UVB, after irradiation with clinically effective (311nm) UVB. The main pathways differentially affected by 311nm UVB only were apoptosis, necrosis, acute phase signalling, p53 signalling and chemotaxis. The greatest fold change observed was a 7.5 fold increase in expression of CDKN1A (WAF1/ p21), the p53 target gene, following irradiation with 311nm UVB but not 290nm (clinically ineffective UVB).  Acute phase, LXR and PTEN signalling, dendritic cell maturation, granulocyte adhesion and atherosclerotic pathways were also differentially regulated by 311nm compared to 290nm UVB.      This work provides insight into the molecular mechanisms regulating psoriatic remodelling in response to UV phototherapy, supports a key role for apoptosis and cell death in psoriasis plaque clearance, and identifies a number of novel therapeutic pathways.  Further studies may lead to development of potential biomarkers to assess which patients are more likely to respond to UVB.

overall_design: Gene expression profiling by Illumina DASL BeadArray of human skin biopsies. Samples taken from consenting human donors and fall into one of the following groups: i) psoriatic skin irradiated with UVB (311nm) after 6h; ii) as (i) but after 18h; iii) as (i) but irradiation with 290nm; iv) as (ii) but with 290nm; v) un-irradiated psoriatic skin; vi) un-irradiated non-lesional skin. Each subject had a maximum of 4 biopsies. 20 individuals in total, 48 samples in total.

first: Rachel

last: Addison

first: Nick

last: Reynolds


title: Single cell dual-omics reveals the transcriptomic and epigenomic diversity of cardiac non-myocytes

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University


title: Complementary capability of cell division and photosynthesis triggers growth vigor in Arabidopsis hybrids

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: Mechanism behind heterosis has remained a mystery for a very long time despite its agricultural importance. Here, we report an integrated analysis of the phenotypes and transcriptomes of early shoot and true leaf during seedling growth at high-temporal-resolution in two Arabidopsis ecotypes and their F1 hybrid. We identify the core gene co-expression networks underlying the dynamic regulations of transcriptomes and their sophisticated differences between hybrid and parents. We provide the first evidence of spatiotemporally transcriptional dominant complementation in hybrid between the network hub genes involved in cell division and photosynthesis, respectively. Our findings highlight the pivotal roles of functionally dominant allelic action and expression complementation of fundamental biological pathways in growth heterosis.

overall_design: mRNA profiles of early seedling shoot at 3-8 days after sowing (DAS) and the first true leaf at 7-21 DAS in Arabidopsis ecotypes Col-0, Per-1 and their F1 hybrid (Col-0 × Per-1), including three biological replicates

first: Guangming

last: He

first: Wang

middle: X

last: Deng


title: NAD+-capped RNAs are preferentially produced from inducible genes in response to growth conditions in E. coli

city: HONG KONG

first: Huan

last: ZHONG

state: HONG KONG

address: T1012 CHA CHI-MING SCIENCE TOWER

department: BIOLOGY

country: Hong Kong

institute: HKBU

summary: Recent findings regarding NAD+-capped RNAs (NAD-RNAs) indicate that prokaryotes and eukaryotes employ non-canonical RNA capping to regulate genes, a previously unrecognized mechanism. Two methods for transcriptome-wide analysis of NAD-RNAs, NAD captureSeq and NAD tagSeq, are based on copper-catalyzed azide-alkyne cycloaddition click chemistry reaction to label NAD-RNAs. However, copper can fragment RNA, interfering with the analyses. Here we report development of NAD tagSeq II, which uses copper-free, strain-promoted azide-alkyne cycloaddition for labeling NAD-RNAs, followed by identification of tagged RNA by direct RNA sequencing. Using this method, we compared NAD-RNA and total transcript profiles of E. coli cells in the exponential and stationary phases and identified hundreds of NAD-RNA species. For some genes, the majority of their transcripts were found as NAD-RNAs. Our study indicates that NAD-RNAs are preferentially produced from inducible genes in response to different growth conditions.

overall_design: Four groups of Samples, exponential and stationary plus and minus

first: Hailei

last: Zhang

last: Zhong

first: Yiji

last: Xia


title: Time of day prioritizes the pool of translating mRNAs in response to heat stress

city: Riverside

first: Dawn

last: Nagel

address: 900 University Avenue

country: USA

institute: UC Riverside Department of Botany and Plant Sciences

summary: The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under growth limiting temperatures, time of day modulates the accumulation of polyadenylated mRNAs. In response to heat stress, plants will conserve energy and selectively translate mRNAs. How the clock and/or time of day regulates polyadenylated mRNAs bound by ribosomes in response to heat stress is unknown. In-depth analysis of Arabidopsis thaliana translating mRNAs found that time of day gates the response of approximately one-third of the circadian regulated heat responsive translatome. Specifically, time of day and heat stress interact to prioritize the pool of mRNAs in cue to be translated. For a subset of mRNAs, we observed a stronger gated response during the day, and preferentially before the peak of expression. We propose previously overlooked transcription factors (TFs) as regulatory nodes and show that the clock plays a role in the temperature response for select TFs. When the stress was removed, the redefined priorities for translation recovered within one-hour, though slower recovery was observed for abiotic stress regulators. Through hierarchical network connections between clock genes and prioritized TFs, our work provides a framework to target key nodes underlying heat stress tolerance throughout the day.

overall_design: Analysis of the Arabidopsis transcriptome and translatome response to heat stress  (37°C vs 22°C) at eight different times of day during a 24 h time course, and recovery post heat stress.

first: Titouan

last: Bonnot

middle: H


title: ChIP-seq in Oikopleura dioica

city: Bergen

first: Pavla

last: Navratilova

address: Thorm hlensgt. 55

department: Sars International Centre for Marine Molecular Biology

institute: University of Bergen

summary: ChIP-seq was used to generate chromatin state maps, profile binding patterns of key architectural proteins and locate putative enhancer regions in the early development (TB stage) and developing gonads of the marine chrodate Oikopleura dioica.

overall_design: Histone modification enrichments by ChIP-seq in three different tissues of Oikopleura dioica

first: Gemma

last: Danks

first: Gunnar

last: Schulze

first: Eric

last: Thompson


title: Trancriptome profiling of OAW42-R human ovarian carcinoma cell line after transfection with siRNAs directed against UCA1

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary:
Inhibition of UCA1 by siRNAs sensitizes the chemoresistant ovarian cancer cell line OAW42-R to the effect of cisplatin
We therefore studied the transcriptomic consequences of UCA1 downregulaiton in order to asses the mechanisms and pathways by which regulation the downregulaiton of UCA1 affects cell's response to cisplatin

overall_design: Comparison of transcriptomic profiles after control siRNA transfection or UCA1-directed siRNAs transfection

first: M

last: Meryet-Figuiere

first: Marie

last: Villedieu