title: CRISPR/Cas9 mediated intersectional knockout of GSK3b in D2 receptor expressing mPFC neurons reveals contributions to emotional regulation

city: Toronto

first: Martin

last: Beaulieu

address: 1 king's college circle room 4336

department: Pharmacology and Toxicology

summary: Comparison of ribosome associated RNA between mPFC D2 neurons that lack Gsk3β with Controls

overall_design: Gsk3β was knockout  in mPFC D2 neurons using CRISPR/Cas9, than ribosome associated RNA was isolated from Control and knockout cells using RiboTag immunoprecipitation and subjected to RNAseq

first: Jivan

last: Khlghatyan

first: Jean-Martin


title: The Influenza non-structural protein 1 (NS1) operates targeted mechanisms to suppress immune gene expression.

status: Public on Aug 13 2020

city: Hong Kong

first: Honglin

last: Chen

address: Rm 5-19, 5/F, Lab block, 21 Sassoon Road, Pokfulam

department: Department of Microbiology

country: Hong Kong

institute: The University of Hong Kong

type: Expression profiling by high throughput sequencing

summary: Influenza non-structural protein 1 (NS1) has been well cited to ellicit an inhibitory effect of immune gene expression thus resulting in the curtailment of efficient antiviral immunity. However the mechanisms and gene networks subjected to this immuno-suppression are unclear. We designed an RNA-Seq study to explore this viral trait and characterize the induced gene expression in response to wildtype (native) Influenza A infection. We have also developed an Influenza mutant virus that is deficient in its ability to expression NS1 (WSNdelNS1), thus our study incorporates a virus that will enable induced transcriptomic comparison between wildtype and mutant viral infections.

overall_design: We infected 293T cells with wildtype (native) influenza A/WSN/1933 (H1N1) or with a mutant virus deficient in encoding fully-functional NS1 (WSNdelNS1). These infection experiements were used to perform RNA-Seq analysis to assess for significant changes in the transcriptome of infected cells in response wildtype/mutant influenza infection.

first: Bobo

middle: W

last: Mok

first: Conor

last: Cremin


title: Transcriptome-Wide Analysis of PGC-1α-Binding RNAs Identifies Genes Linked to Glucagon Metabolic Action

status: Public on Aug 14 2020

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

summary: PGC-1α is a transcriptional coactivator that controls expression of metabolic/energetic genes programming cellular responses to nutrient and environmental adaptations such as fasting, cold or exercise.  Unlike most other coactivators, PGC-1α contains protein domains involved in RNA binding and processing such as serine/arginine (SR) and RNA Recognition (RRM) motifs.  However, little is known regarding the specific RNAs that bind PGC-1α to possibly control specific metabolic and energetic functions.  To address this, we have performed single-end enhanced crosslinking and immunoprecipitation (seCLIP)-based transcriptome-wide analysis to identify specific RNA sequences that bind to PGC-1α.  Primary hepatocytes were used to perform seCLIP experiments with glucagon-induced endogenous PGC-1α.  RNA sequencing reveals that a large fraction of the RNAs bound to PGC-1α were intronic sequences related to genes involved in transcriptional, signaling or metabolic function linked to glucagon and fasting responses, but were not the canonical direct transcriptional targets of PGC-1α, such as OXPHOS or gluconeogenic genes.  Validation of this analysis confirmed that among the top scoring RNA sequences bound to PGC-1α were Sik1, Camk1d, Ppard, Klf15, Gfra1 and Slc25a25.  PGC-1α depletion decreased a fraction of mRNA transcript levels of these glucagon-induced genes.  Importantly, knock-down of these genes affected glucagon-dependent glucose production, a PGC-1α-regulated metabolic pathway.  These studies show that PGC-1α largely binds to intronic RNA sequences, some of them controlling transcript levels associated with glucagon action.

first: Clint

middle: D

last: Tavares

first: Stefan

last: Aigner

first: Kfir

last: Sharabi

first: Sathe

last: Shashank

first: Pere

last: Puigserver


title: Bioinformatics Analysis of Degenerative Meniscus Tissue in Knee Osteoarthritis of Wuzhishan Pig

city: Haikou

first: Hui

last: Huang

address: 19 Xiuhua Road, Xiuying District

country: China

institute: Hainan Provincial People's Hospital

summary: Meniscus degeneration is one of the manifestations of knee osteoarthritis, but its specific molecular mechanism is still not very clear. We used Wuzhishan pig's anterior cruciate ligament resection to prepare meniscus degeneration models, and applied gene chip technology to detect the expression of differential genes in the degenerated meniscus tissue. The study detected a total of 893 differentially expressed genes, mainly related to hormones, apoptosis, inflammation and other mechanisms, and analyzed that TRP channels may play a key role. All in all, we have established a reliable animal model of meniscus degeneration and found that meniscus degeneration involves several possible molecular mechanisms, which provide molecular targets for future treatment of the disease.

overall_design: A total of 14 healthy adult male Hainan Wuzhishan pigs (Institute of animal husbandry and veterinary medicine, Hainan Academy of Agricultural Sciences, China), weighing 15-18kg, aged from 6 to 7 months, were not raised in single cage, and the environmental temperature was 20-28℃. The experimental animals were randomly divided into control group (sham group) and experimental group (OA group), normal light and diet.

first: Jianping

last: Lin


title: Microbiota–modulated CART+ enteric neurons autonomously regulate blood glucose

city: New York

first: Paul

middle: Andrew

last: Muller

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Microbial density and diversity increase in distal intestinal segments, affecting tissue physiology, metabolism, and function of both the immune and nervous systems. We characterized the influence of the microbiota on murine intrinsic enteric-associated neurons (iEAN). We found that iEAN are functionally adapted to the intestinal segment they occupy, with a stronger microbiota influence on ileal and colonic neurons. Chemogenetic characterization of microbiota-influenced iEAN identified a subset of viscerofugal CART+ neurons, enriched in the ileum and colon, able to modulate feeding and glucose metabolism. Retro- and anterograde tracing revealed that CART+ viscerofugal neurons send axons to the prevertebral ganglia and are poly-synaptically connected to the liver and pancreas. Microbiota depletion led to NLRP6 and Caspase 11-dependent loss of CART+ neurons, and impaired liver-mediated gluconeogenesis. Our results demonstrate a region-specific adaptation of enteric neurons and indicate that iEAN subsets are capable of regulating blood glucose levels independently from the central nervous system.

overall_design: Actively translated mRNA profiles from immunoprecipitated ribosome-bound mRNA from the duodenum, ileum, and colon of germ-free or specific pathogen free Snap25:RiboTag mice were prepared by deep sequencing on an Illumina NextSeq.

middle: A

first: Marc

last: Schneeberger

first: Fanny

last: Matheis

first: Zachary

middle: J

last: Kerner

first: Veronica

middle: Y

last: Jové

first: Daniel

last: Mucida


title: Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity

city: Bruxelles

first: Anthony

last: Piron

address: Route de Lennik 808 CP618

department: Faculté de Medecine

country: Belgium

institute: Université Libre de Bruxelles

summary:
Background: Prolonged exposure to elevated free fatty acids induces β-cell failure (lipotoxicity) and contributes to the pathogenesis of type 2 diabetes. In vitro exposure of β-cells to the saturated free fatty acid palmitate is a valuable model of lipotoxicity, reproducing features of β-cell failure observed in type 2 diabetes. In order to map the β-cell response to lipotoxicity, we combined RNA-sequencing of palmitate-treated human islets with iTRAQ proteomics of insulin-secreting INS-1E cells following a time course exposure to palmitate.
Results: Crossing transcriptome and proteome of palmitate-treated β-cells revealed 85 upregulated and 122 downregulated genes at both transcript and protein level. Pathway analysis identified lipid metabolism, oxidative stress, amino-acid metabolism and cell cycle pathways among the most enriched palmitate-modified pathways. Palmitate induced gene expression changes compatible with increased free fatty acid mitochondrial import and β-oxidation, decreased lipogenesis and modified cholesterol transport. Palmitate modified genes regulating endoplasmic reticulum (ER) function, ER-to-Golgi transport and ER stress pathways. Furthermore, palmitate modulated cAMP/protein kinase A (PKA) signaling, inhibiting expression of PKA anchoring proteins and downregulating the GLP-1 receptor. SLC7 family amino-acid transporters were upregulated in response to palmitate but this induction did not contribute to β-cell demise. To unravel critical mediators of lipotoxicity upstream of the palmitate-modified genes, we identified overrepresented transcription factor binding sites and performed network inference analysis. These identified LXR, PPARα, FOXO1 and BACH1 as key transcription factors orchestrating the metabolic and oxidative stress responses to palmitate.
Conclusions: This is the first study to combine transcriptomic and sensitive time course proteomic profiling of palmitate-exposed β-cells. Our results provide comprehensive insight into gene and protein expression changes, corroborating and expanding beyond previous findings. The identification of critical drivers and pathways of the β-cell lipotoxic response points to novel therapeutic targets for type 2 diabetes.

overall_design: We analyzed 6 human islet of Langerhans preparations examined under 2 conditions (control and palmitate treatment). 5 of those where previously made available under the serie number GSE53949. The preparations were sequenced with a Illumina Genome Analyzer II. The reads were mapped with Tophat. The transcripts quantification and RPKM normalization was done with flux-capacitor. We run the bioconductor R package Deseq2 to generate a paired palmitate vs control differential analysis.

first: Maria

last: Lytrivi

first: Kassem

last: Ghaddar

first: Miguel

last: Lopes

first: Victoria

last: Rosengren

first: Xiaoyan

last: Yi

first: Henrik

last: Johansson

first: Janne

last: Lehtiö

first: Mariana

last: Igoillo-Esteve

last: Cunha

first: Lorella

last: Marselli

first: Piero

last: Marchetti

last: Ortsäter

first: Decio

middle: L

last: Eizirik

first: Miriam

last: Cnop


title: Febrile temperature change modulates CD4 T cell differentiation via a TRPV channel-regulated Notch-dependent pathway

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

summary: Here we report the transcriptomic differences between ex vivo CD4+ T cells (naïve CD4+ T Cells), CD4+ T cells activated with a mixture of anti-CD3 and anti-CD28 for 3 hours in vitro at 37ºC and 39ºC. At the higher temperature, we report the upregulation of protein folding machinery while downregulation of genes associated with mitochondrial oxidative phosphorylation and cytoplasmic proteiin synthesis.

overall_design: CD4+ T cells were isolated from B6 mice spleen and subjected to activation at either 37ºC or 39ºC for three hours in presence of anti-CD3 and anti-CD28. Unactivated (naïve) cells as well as the activated cells were harvested and RNA was isolated using Trizol method. Total RNA was subjected to RNAseq analysis.

first: G

first: Satyajit

last: Rath

first: Danish

last: Umar


title: Temporal analysis of Brd4 displacement in the role of B cell survival, proliferation and differentiation

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: JQ1 is a BET-bromodomain inhibitor that has immunomodulatory effects. However, the precise molecular mechanism that JQ1 targets to elicit changes in antibody production is not understood. Our results show that JQ1 induces apoptosis, reduces cell proliferation, and as a consequence, inhibits antibody secreting cell differentiation. ChIP-sequencing reveals a selective displacement of Brd4 in response to acute JQ1 treatment (<2 hours), resulting in specific transcriptional repression. After 8 hours, subsequent alterations in gene expression arose as a result of global loss of Brd4 occupancy. We demonstrate that apoptosis induced by JQ1 was solely attributed to the pro-apoptotic protein Bim (Bcl2l11). Conversely, cell cycle regulation by JQ1 was associated with multiple Myc-associated gene targets. Our results demonstrate that JQ1 drives temporal changes in Brd4 displacement that results in a specific transcriptional profile that directly affects B cell survival and proliferation to modulate the humoral immune response.

overall_design: Purified follicular B cells were isolated from C57Bl/6 mice. Cells were stimulated with LPS with or without JQ1 (250nM) for 2hr, 8hr and 48hr. Samples were collected for 3'RNA-Sequencing.Samples that were stimulated with LPS and were treated for 2hr and 8hr were also harvested for Brd4 ChIP-sequencing. H3K27ac ChIP-sequencing was also performed on 2hr samples.

first: Edwin

last: Hawkins

first: Stephin

last: Vervoort


title: Analysis of cerebrovascular dysfunction caused by chronic social defeat in mice

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: sychological stress and affective disorders are clinically associated with hypertension and vascular disease, but the biological links between the conditions have not been fully explored. To examine this relationship, we used chronic social defeat (CSD) stress, which produces anxiety-like and depressive-like behavioral declines in susceptible mice. In such mice, CSD also produces cerebrovascular microbleeds in scattered locations. Here, we showed further evidence of vascular pathology and blood–brain barrier breakdown by visualizing plasma immunoglobulins and erythrocytes within the parenchyma and perivascular spaces of CSD brains. To further characterize the impact of stress on the cerebrovasculature, brain endothelial cells (bECs) were isolated, and global gene expression profiles were generated. Bioinformatic analysis of CSD-induced transcriptional changes in bECs showed enrichment in pathways that delineate the vascular response to injury. These pathways followed a temporal sequence of inflammation, oxidative stress, growth factor signaling, and wound healing (i.e., platelet aggregation, hemostasis, fibrinogen deposition, and angiogenesis). Immunohistochemical staining for markers of fibrinogen deposition and angiogenesis confirmed the existence of the markers at the sites of vascular disruptions. Recovery after CSD cessation was marked by recruitment of leukocytes perhaps participating in vascular repair. The data suggest that co-morbidity of affective disorders and vascular diseases may be attributed in part to a common link in altered endothelial cell function

overall_design: wild-type mice were exposed to stressor for 10 min every day  for 1 day, 7 days and 14 days. Three to Four animals per group were studied, for a total of 19 animals.

first: Michael

last: Lehmann

first: Abdel

first: Miles

last: Herkenham


title: LARP7, a new ROS sensor,  protects against heart failure by enhancing  mitochondrial biogenesis

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary:
LARP7 controls the SIRT1 activity and homeostasis, which is essential for mitochondrial biogenesis, energy production and cardiac function.  The deprivation of LARP7 resulted from the activation ATM pathway attenuates the mitochondrial function and biogenesis and leads to the cardiomyopathy and heart failure.
Method: Heart morphology and functions were assessed by gross anatomy, serial echocardiography and histology on sections; Mitochondrial morphology and activity were evaluated by TEM and seahorse assays. The therapeutic potential of LARP7 in heart failure was evaluated in mouse myocardial infarction model either with AAV9 infection or pharmacological inhibitor.

overall_design: We used RNA-seq to profile and compare the transcriptome in the hearts of wildtype and  LARP7 conventional knockout mouse (LARP7-/-) and conditional knockout mouse (LARP7 LoxP).

first: Huijing

last: Yu

first: Fang

last: Zhang

first: Pengyi

last: Yan

first: Shasha

first: Yingmei

last: Lou

first: Zilong

last: Geng

first: Zixuan

last: Li

first: Yan

first: Chen

last: Chen

first: Yuejuan

last: Xu

first: Yanan

last: Lu

first: Junling

last: Liu

first: Daowen

last: Wang

first: Wei

last: Zhu

first: Yuzhen

first: Gengze

last: Wu

first: Chunyu

last: Zeng

first: William

middle: T

last: Pu

first: Kun

last: Sun

first: Bing


title: Analysis of transcriptome changes of human epidermal stem cells treated by EGF

city: Beijing

first: Sun

last: Jiachen

address: 51 Fucheng Road, Haidian District

department: Burns

institute: The Fourth Medical Center of PLA General Hospital

summary: We report the application of transcriptome sequencing technology in the analysis of transcriptome changes in human epidermal stem cells after EGF incubation. We found that EGF can significantly change the gene transcription of human epidermal stem cells. There are 3,759 differential genes, which are highly related to wound healing and the proliferation and differentiation of epidermal stem cells. This study provides a basis for comprehensive analysis of the effect of EGF/EGFR pathway on epidermal stem cells.

overall_design: Examination of function of EGF/EGFR pathway in epidermal stem cells

first: Jiachen

first: Chuanan

last: Shen


title: Transcriptome-wide m6A methylome of intestinal porcine epithelial cells (IPEC-J2) induced by deoxynivalenol

city: yangzhou

first: zhengchang

last: wu

address: southdaxueroad

institute: yangzhoudaxue

type: Methylation profiling by high throughput sequencing

summary: Deoxynivalenol (DON) frequently detected in a wide range of foods and feeds, inducing cytotoxicity to animals and humans. N6-methyladenosine (m6A) is an important epitranscriptomic marker with high abundance in eukaryotic mammals mRNAs. However, the role of the m6A methylomes in DON damage is still poorly understood. Here, we investigated the m6A transcriptome-wide profile in intestinal porcine epithelial cells (IPEC-J2) with and without 1000 ng/mL DON treatment via m6A sequencing and RNA sequencing. In total, 5406 new m6A peaks appeared with the disappearance of 2615 peaks in DON-induced IPEC-J2. The unique m6A-modified genes in DON-induced IPEC-J2 were associated with TNF signaling pathway. We identified 733 differentially expressed mRNA transcripts with hyper-methylated or hypo-methylated m6A peaks between DON-induced IPEC-J2 and normal IPEC-J2. Protein interaction network analysis and qPCR validation suggested that CSF2 probably acts as a promising new target for combating DON damage in IPEC-J2. Our first report of m6A transcriptome-wide map of IPEC-J2 cells presented here provides a starting roadmap for uncovering m6A functions that may affect DON infection.

overall_design: DON-treated IPEC-J2 (DON, n=3) and normal IPEC-J2 (Control, n=3) samples

first: Zhengchang

first: Fang

first: Haifei

first: Shenglong

first: Wenbin

last: Bao


title: Dual RNA-seq of symbiont and host during establishment of coral-algal symbiosis

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

summary:
Background: The molecular machinery underpinning the establishment of this relationship is not well understood. This is especially true of the symbiont side, as previous attempts to understand the interaction between coral larvae and Symbiodiniaceae have focused nearly exclusively on the host
Results: In the current study, we utilised dual RNA-seq approach to study both symbiont and coral transcriptomes during symbiosis establishment.  The transcriptomic response of C. goreaui to the symbiotic state was complex, the most obvious feature of which was extensive and generalized downregulation of gene expression. Included in this “symbiosis-derived transcriptional repression” were a range of stress response and immune-related genes. In contrast, a range of genes implicated in metabolism were upregulated in the symbiotic state. Consistent with previous ecological studies, this transcriptomic response of C. goreaui suggests that active translocation of metabolites to the host may begin early in the colonization process, and thus that the mutualistic relationship is established at the larval stage. The coral data imply the involvement of some SCRiP family members in the colonisation process and support the hypothesis that immune-suppression and arrest of phagosome maturation play important roles during the establishment of compatible symbioses.
Conclusions: This study provides novel insights into the transcriptomic remodelling that occurs in C. goreaui during transition to a symbiotic lifestyle, with important implications for understanding the establishment of symbiosis between corals and their dinoflagellate partners.

sample_organism:
Acropora tenuis
Cladocopium goreaui

platform_organism:
Acropora tenuis
Cladocopium goreaui

overall_design: mRNA profiles from colonised larvae after 3, 12, 48, and 72 h were generated by deep sequencing, in triplicate, using Illumina HiSeq platform

middle: R

first: Natalia

last: Andrade

first: Aurelie

last: Moya

first: Ali

last: Ali

first: Andrew

middle: P

last: Negri

first: David

last: Bourne

first: Eldon

middle: E

last: Ball

last: Miller


title: TREM2 blockade modifies the tumor myeloid landscape enhancing anti-PD-1 immunotherapy

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Checkpoint immunotherapy unleashes T cell effector functions that control tumor growth, but can be undermined by myeloid cells that induce immunosuppression. TREM2 is a myeloid surface receptor that binds lipids and transmits intracellular signals through protein-tyrosine phosphorylation known to sustain microglial responses during Alzheimer’s disease. Intriguingly, TREM2 expression has recently been noted in tumor-infiltrating macrophages. We found that Trem2–/– mice are more resistant to growth of sarcoma, colorectal and mammary cancer cells than wild-type mice and are more responsive to anti-PD-1 immunotherapy. Furthermore, treatment with anti-TREM2 mAb curbed tumor growth and led to complete tumor regression when combined with anti-PD-1. scRNA-seq revealed that both constitutive TREM2 deficiency and anti-TREM2 are  associated with relatively scant representation of MRC1+ and CX3CR1+ subsets in the macrophage tumor infiltrate, paralleled by expansion of subsets expressing immunostimulatory molecules. These changes were associated with improved T cell responses. TREM2 expression was evident in tumor macrophages in over 200 human cancer cases examined and inversely correlated with prolonged survival for two types of cancer. Thus, TREM2 is a promising target to modify tumor-infiltrating myeloid cells and effectively augment checkpoint immunotherapy.

overall_design: Immune cells from mice with transplanted MCA38 sarcoma tumor under various treatments were analyzed with 10x single-cell RNA sequencing.

first: Martina

last: Molgora

first: Ekaterina

last: Esaulova

first: William

last: Vermi

first: Jinchao

last: Hou

first: Yun

last: Chen

first: Luo

last: Jingqin

first: Simone

last: Brioschi

first: Mattia

last: Bugatti

first: Andrea

middle: S

last: Omodei

first: Biancamaria

last: Ricci

first: Catrina

last: Fronick

first: Santosh

last: Panda

first: Yoshiko

last: Takeuchi

first: Matthew

middle: M

last: Gubin

first: Roberta

last: Faccio

first: Marina

last: Cella

first: Susan

last: Gilfillan

first: Emil

last: Unanue

middle: N

first: Robert

last: Schreiber

first: Marco

last: Colonna


title: small RNA sequencing of goat mamamary gland cells samples from different treatment groups

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

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

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

first: Dongxue

last: Ma

first: Lingjiang

last: Min


title: Transcriptome of Human Primary Corneal Endothelial Cells with SLC4A11 deficiency

city: Los Angeles

first: Wenlin

last: Zhang

address: 200 Stein Plaza, Dserc 3-143

institute: UCLA, Jules Stein Eye Institute

summary: Mutations in the solute-linked carrier family 4 member 11 (SLC4A11) gene are associated with several corneal endothelial dystrophies, in all of which visually significant cornea edema may require corneal transplantation. To elucidate the pathogenesis of SLC4A11 associated corneal endothelial dystrophies, we analyzed the transcriptome of SLC4A11 knock-down primary human corneal endothelium (SLC4A11 KD pHCEnC) and scrambled RNA treated pHCEnC as controls.

overall_design: 3 KD vs 3 CTRL

first: Ricardo

last: Frausto

first: Anthony

last: Aldave


title: Transcriptome of Immortalized Mouse Corneal Endothelial Cells with SLC4A11 deficiency

summary: Mutations in the solute-linked carrier family 4 member 11 (SLC4A11) gene are associated with several corneal endothelial dystrophies, in all of which visually significant cornea edema may require corneal transplantation. To elucidate the pathogenesis of SLC4A11 associated corneal endothelial dystrophies, we analyzed the transcriptome of immortalized mouse corneal endothelial cells (Slc4a11-/- MCEnC) and Slc4a11+/+ MCEnC as controls.

overall_design: Slc4a11-/- MCEnC P7 (n=3) vs Slc4a11+/+ MCEnC P6 (n=3);  Slc4a11-/- MCEnC P40 (n=3) vs Slc4a11+/+ MCEnC P39 (n=3).


title: Peripheral blood transcriptomic analysis of genetic regulation mechanism of salmonella infection in mice

city: jingzhou

first: xia

middle: li

last: huang

state: hubei

address: Yangtze university

institute: Yangtze university

summary: Analysis of gene expression profiles of 12 normal mice infected with Salmonella using deep sequencing technology.

overall_design: Peripheral blood transcriptomics analysis of the changes in gene expression caused by mice before and after Salmonella infection and the genetic regulation mechanism of Salmonella

first: Xiali

last: Huang

first: Tinghua


title: Influenza non-structural protein 1 (NS1) localization plays a key role in the anatagonism of host antiviral processes.

status: Public on Aug 12 2020

first: Honglin

last: Chen

summary: The influenza virus is opportunistic by nature and is capable of subverting cellular signalling pathways for the benefit of viral replication.  The function of non-structural protein 1 (NS1) as a core component for the influenza virus to interfere with host antiviral activity has been well cited in literature.  However, the mechanism as to how NS1 is capble of subverting the host's innate immune system is unknown. NS1 has a unique capability to migrate between both the cytoplasm and nucleus of infected cells.  To assess if NS1 interference operates a stratagy pertaining to a mechanism involved with nuclear-located signalling processes we designed two mutant virsus; WSNdelNS1 which encodes a deletion to prevent complete NS1 expression and WSN3M  which encodes a NS1-variant that is defective in NS1 nuclear-translocation, thus preventing NS1 from entering the nuclus of infected cells.

overall_design: We infected A549 cells with wildtype (native) influenza A/WSN/1933 (H1N1) or with a mutant virus deficient in encoding fully-functional NS1 (WSNdelNS1 or WSN3M). These infection experiements were used to perform RNA-Seq analysis to assess for significant changes in the transcriptome of infected cells in response wildtype/mutant influenza infection. We complemented this analysis with PolII/PolII-s2p/PolII-s5p ChIP-Seq in order to observe if changes in PolII densities and their variants reflect the transcriptomic profiles generated from our RNA-Seq analysis. Intergration of both RNA-Seq and ChIP-Seq datasets presented a unique profile of gene expression and  PolII transcription initiation and elongation dynamics during the early stages of influenza infection.

first: Conor

last: Cremin

first: Bobo

middle: W

last: Mok

first: Michi

last: Miura


title: The gene expression profiles associated with worsening left ventricle function after mitral valve repair

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
Background:To assess left ventricular (LV) transcriptome determinants of worsening LV function after mitral valve (MV) repair.
Results:Upregulated protein ubiquitination-related genes associated with worsening-LVF after MV repair may likely exert its adverse effect in left ventricle through increased apoptosis and contractile protein degradation.

overall_design: A total of 13 patients were divided into two groups for study: preserved LV function (preserved-LVF, N=8) and worsening LV function (worsening-LVF, N=5) after MV repair for severe, isolated chronic mitral regurgitation. Specimens of left ventricle from the patients were used for gene microarray study.

first: Feng-Chun

last: Tsai

first: Gwo-Jyh

last: Chang

first: Ying-Ju

last: Lai

first: Shang-Hung

first: Wei-Jan

first: Yung-Hsin

last: Yeh


title: Ribo-Pop: Simple, cost-effective, and widely applicable ribosomal RNA depletion

city: Oxford

first: Ilan

last: Davis

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: The measurement of RNA abundance derived from massively parallel sequencing experiments is an essential technique. Methods that reduce ribosomal RNA levels are usually required prior to sequencing library construction because ribosomal RNA typically comprises >90% of the total RNA molecules in a sample. For some experiments, ribosomal RNA depletion is favored over poly(A) selection because it offers a more inclusive representation of the transcriptome. However, methods to deplete ribosomal RNA are generally proprietary, complex, inefficient, applicable to only specific species, or compatible with only a narrow range of  RNA input levels. Here, we describe Ribo-Pop (ribosomal RNA depletion for popular use), a simple workflow and antisense oligo design strategy that we demonstrate works over a wide input range and can be easily adapted to any organism with a sequenced genome. We provide a computational pipeline for probe selection, a streamlined 20-minute protocol, and ready-to-use oligo sequences for several organisms. We anticipate that our simple and generalizable “open source” design strategy would enable virtually any lab to pursue full transcriptome sequencing in their organism of interest with minimal time and resources.

overall_design: We designed a simple ribosomal RNA depletion protocol and antisense oligonucleotide design strategy which we named Ribo-Pop. RNA sequencing was performed on Ribo-Pop depleted RNA samples (Drosophila melanogaster wandering third instar larval RNA) or matched input samples to assess the efficiency and specificity of depletion. Sequencing libraries were constructed with either a random priming approach or a poly(A) priming approach. Three biological replicates (using RNA extracted from different pools of larvae) were performed for each experiment.

first: Mary Kay

last: Thompson

first: Maria

last: Kiourlappou


title: Transcriptome-wide analysis of differential response to drought and heat stress in Moricandia suffruticosa and Brassica napus

city: WuHan

first: Hongfang

last: Liu

address: Tuanjie Road

institute: OCRI

summary: C3-C4 intermediate Moricandia suffruticosa showed tolerance to drought and heat stresses, and high photosynthetic capacity under these abiotic stresses as comparing with C3 relative crop rapeseed (Brassica napus). In our study, systematic analysis was conducted to reveal photosynthetic difference between C3-C4 Moricandia suffruticosa and its relative C3 rapeseed from the same Brassiceae tribe. It was found that Moricandia leaf photosynthesis and anatomy were significantly changed compared to rapeseed under drought and heat stress conditions. De novo transcriptome of Moricandia was assembled by next generation sequencing, and unigenes were mapped to respective rapeseed gene locus. Then comparative transcriptome analysis was conducted in leaf tissues of Moricandia and rapeseed under both drought and heat stresses. Main pathways and candidate genes were revealed from this analysis, which may be associated with the stress induced change in Moricandia.

sample_organism:
Brassica napus
Moricandia suffruticosa

platform_organism:
Brassica napus
Moricandia suffruticosa

overall_design: Examination of differential response of transcriptome in Moricandia suffruticosa and Brassica napus under drought and heat conditions.

first: Xiaoyi

last: Zhu

first: Wei

last: Hua


title: Paraburkholderia phymatum σ54 controls utilization of dicarboxylates, motility and interbacterial competition

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

summary: Paraburkholderia phymatum is a beta-proteobacterium, which lives in the soil and is able to enter nitrogen-fixing symbiosis with different legumes. The biological nitrogen fixation (BNF) process is of great ecological and agronomic importance. We previously showed that the expression of the key P. phymatum BNF enzyme – the nitrogenase –is regulated by the sigma factor σ54 (or RpoN) inside root nodules. This study focused on identifying the σ54 regulon of P. phymatum grown in nitrogen limited conditions using RNA-Sequencing. Among the genes significantly down-regulated in absence of σ54 we found those coding for a C4-dicarboxylate transport system (Bphy_0225-27), a flagellar biosynthesis cluster (Bphy_2926-64) and one of the two type 6 secretion system (T6SS-b) present in P. phymatum genome (Bphy_5978-97). Indeed, the σ54 mutant was unable to grow on C4 dicarboxylates (fumarate, malate and succinate) as the sole carbon source and was less motile compared to the wild-type strain. Both defects were complemented by adding rpoN in trans. Additionally, using reporter fusions we confirmed that T6SS-b expression is regulated by σ54. Finally, a σ54  mutant was less competitive than its parental strain against P. diazotrophica, suggesting a role of σ54 in controlling interbacterial competition.

overall_design: Unraveling the role of the master regulator RpoN in P. phymatum in free-living conditions.

first: Martina

last: Lardi

first: Yilei

first: Sebastian

last: Hug

first: Samanta

last: Bolzan de Campos

first: Leo

last: Eberl


title: Pancreatic Ductal Adenocarcinoma methylome analysis identifies differentially methylated genes in the Calcium signaling pathway and early methylation alterations.

city: Rio de Janeiro

first: Sheila

middle: Coelho

last: Soares-Lima

state: Rio de Janeiro

address: Rua André Cavalcanti 37

department: Molecular Carcinogenesis Program

country: Brazil

institute: Brazilian National Cancer Institute

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of pancreatic ductal adenocarcinoma (PDAC) and non-tumoral pancreatic samples (PT). The Illumina Infinium450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles in tissue samples. Samples included 6 PDAC and 9 PT.

overall_design: 6 pancreatic ductal adenocarcinoma (PDAC) vs 9  non-tumoral pancreatic samples (PT).

first: Cleandra

last: Gregório

first: Bárbara

last: Alemar

first: Mariana

last: Recamonde-Mendoza

first: Diego

last: Camuzi

first: Raquel

last: Rivero

first: Simone

last: Machado

first: Alessandro

last: Osvaldt

first: Patricia

last: Ashton-Prolla

first: Luis

last: Pinto


title: Single cell RNA-seq data for control and epicardial-specific Prmt1-deletion hearts at E12.5

status: Public on Aug 18 2020

first: Jian

last: Xu

address: 2250 Alcazar Street, CSA 106

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

summary: To study the role of PRMT1 in epicardial fate decision during development using Single cell RNA-seq analysis

overall_design: single cell isolated from E12.5 Tbx18-Cre; YFP/+ or Tbx18-Cre; Prmt1 fl/fl;YFP/+ hearts followed by RNA-seq and analysis

first: Nicha

last: Ungvijanpanya


title: The bacterial lifestyle that disguises stressful adaptations

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

summary: The stringent stress response, mediated by the signalling molecule guanosine penta(tetra)-phosphate (p)ppGpp, has recently gained more attraction as a potential new therapeutic target. However, interference of a global mediator could lead to unwanted side effects, therefore warrants detailed mechanistic understanding. We used RNA-Seq to investigate the transcriptional landscape of a Pseudomonas aeruginosa ppGpp-deficient strain under non-stressful conditions. In exponential growth phase in nutrient-rich broth, the lack of ppGpp led to >1600 transcriptional changes, which provided a novel aspect of the importance of ppGpp in general rather than having the traditional stress/starvation induced changes. Intracellular protein tracking indicated that RelA was bound to the ribosome while SpoT localized at the cell poles. Commonly dysregulated functional systems were divided into 34 clusters and revealed individual genes that might belong to the same pathway as other known adjacent regulon members. The regulatory network of ppGpp included global transcriptional regulators AlgR, OxyR, LasR, and AmrZ that further indirectly linked the stress response to secretion systems and polysaccharide production. The stress response directly influenced the expression of quorum sensing and other downstream effectors including AMB toxin production, the ECF-sigma factor PvdS, the transcriptional regulator PtxS, the two-component response regulator PprB, and various proteases such as ImpA, PA0572, ClpP2, and AprA.

overall_design: Studying the stringent response in Pseudomonas aeruginosa PAO1 by comparing a relA-spoT double-mutant to wild type, all grown in planktonic, non-stressful conditions

first: Daniel

last: Pletzer

first: Travis

last: Blimkie

first: Reza

last: Falsafi

first: Robert

last: Hancock


title: ERbeta modulation of NFkB pathway in colon cancer cell lines SW480 and HT29

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

country: Sweden

institute: KTH Royal Institute of Technology

summary: Analysis of differentially expressed genes in colon cancer cell lines SW480 and HT29 with and without stably expressed ERbeta gene, with and without 10ng/mL TNFa treatment for 2 and 24 hours.

overall_design: Total RNA obtained from colon cancer cell lines SW480 and HT29 with and without stably expressed ERbeta gene, with and without 10ng/mL TNFa treatment for 2 and 24 hours.


title: Expression data from murine glioma stem cells treated with or without doranidazole under normoxic or hypoxic conditions

city: Tokyo

first: Oltea

last: Sampetrean

address: 35 Shinanomachi Shinjuku-ku

department: Division of Gene Regulation

country: Japan

institute: Keio University School of Medicine

summary: Under hypoxic conditions, nitroimidazole compounds accumulate in cells in their reduced form and have oxygen-mimetic effects, serving as markers of hypoxia and radiosensitizers. The full potential of their bioreductive metabolism, including cytotoxicity for cancer stem cells, has not been sufficiently explored, however. Here we investigated the changes in gene expression induced by treatment with 2-nitroimidazole doranidazole in murine glioma stem cells, under normoxic or hypoxic conditions.

overall_design: Murine glioma stem cells (GSCs) were treated with PBS (control) or 3 mM doranidazole under normoxic conditions (21%O2) or hypoxic (1%O2) conditions for 24 h. Three independent replicates were analyzed for each goup. Gene expression was measured with Clariom S Mouse Arrays.

first: Koike

last: Naoyoshi

first: Sampetrean

last: Oltea


title: Galangin suppress H19 expression inducedpromotes cell apoptosis in hepatocellular carcinoma cells through suppression of H19 expression

city: ChangChun

first: Xiaowei

last: Zhong

address: Xi'an Road

institute: Jilin University

summary: Galangin, a natural flavonoid, derived from honey and Alpinia officinarum Hance (Zingiberaceae) has excellent was anti-tumor and anti-inflammatory properties. w It has been extensively studied as a novel therapeutic agent forhich was widely used in the treatment of various cancers. However, the effect of galangin in HCC remains elusive. Using RNA sequencing, the differential expression of LncRNA in MHCC97H cells treated with galangin was investigated in the present study. Furthermore, the expression of H19 was also determined in MHCC97H cells following treatment with galangin. And the effect of knockdown and overexpression of H19 on cell apoptosis, cell cycle, migration and invasion of HCC cells was also evaluated. Moreover, the in vivo effect of galangin on tumor development was also determined in nude mice. This study identified aT total of 50 LncRNAs were to be significantly differentially expressed by RNA-seq analysis in MHCC97H cells treated with galangin. It has been demostreated that noncoding RNA H19 are abnormally expressed in different cancers. Our results showed that Besides, the expression of H19 was markedly reduced after following treatment with galangin treatment in MHCC97H cells. In addition, galangin could increase the occurrence of cell apoptosis. Moreover, compared to the Control group, the galangin-treated group inhibited cell migration and invasion in MHCC97H cells.To further investigated if H19 expression pattern affect cell apoptosis, migration and invasion, knock down and overexpression of H19 vector were constructed.  The results of the knockdown of H19 expression showed knock down of H19 expression increased cell apoptosis and decreasedinhibited invasion. In addition, RNA-seq data showed also identified 161 mRNA which were was significantly differentially expressed after following treatment withof galangin. To further determine the underlying mechanism,confirmed cell apoptosis, p53 protein and its related proteins were was analyzed through micor RNA 675-3p (miR675-3p) which was in the H19 locus. Notably, Tthe results indicatedshowed that reduced knockdown of H19 and miR675 induced the protein expression of p53, eventually promoting cell apoptosis expression of H19 and miR675-3p increased p53 expression in MHCC97H cells. These results indicated that galangin promoted cell apoptosis through the regulation of H19 and miR675 expression in MHCC97H cells. Furthermorely, galangin was used to treated in nude mice. Tthe in vivo result showed that compared to the Control group, inhibited tumor growth was remarkably suppressed and reduced expression of H19 in galangin-treated  group. Taken together, these results indicated that galangin regulated cell apoptosis which associate with p53 protein through H19 and miR675 expression in MHCC97H cells.Collectively, our data suggested that galangin plays a role in hepatocarcinogenesis through regulation of H19 expression pattern.

overall_design: The long noncoding RNA profiles of MHCC97H cells treated with 100μM Galangin and MHCC97H cells treated with 0.1% DMSO were generated by deep sequencing, in triplicate, using Illumina HiSeqXten

first: Dongxu

last: Wang


title: tRNAArg-derived fragments mediate protein arginylation [tRNA]

city: Philadelphia

first: Dawei

last: Dong

state: Pennsylvania

address: 3620 Hamilton Walk

department: Biomedical Sciences

institute: University of Pennsylvania

summary: Arginyltransferase ATE1 mediates posttranslational arginylation that plays key roles in mammalian embryogenesis, cell migration, and normal brain function. The molecular mechanisms of arginylation remain elusive. ATE1 utilizes arginyl-tRNAArg as the donor of Arg, putting this reaction into a direct competition with the protein synthesis machinery. Here, we addressed these questions of ATE1- arginyl-tRNAArg specificity as a potential mechanism enabling this competition in vivo. Using in vitro arginylation assays and ATE1 knockout models, we find that while arginylation is specific to tRNAArg, it is able to utilize short tRNAArg derivatives that bear structural resemblance to tRNA-derived fragments (tRF), a new class of small regulatory non-coding RNAs with poorly characterized but critical functions in vivo. Arginyl-tRFArg can be generated in vitro directly from pre-charged -tRNAArg, and ATE1 is able to utilize these arginyl-tRFArg fragments with similar efficiency as arginyl-tRNAArg. Lack of arginylation in ATE1 knockout cells leads to a decrease in tRFArg generation and a significant increase in the ratio of tRNAArg to tRFArg compared to wild type, suggesting a functional link between tRFArg and arginylation in vivo. We propose that generation of physiologically important tRFs can play a critical role as a switch between protein translation and arginylation in vivo.

overall_design: Comparison between wild-type and Ate1-knockout cells

first: Irem

last: Avcilar-Kucukgoze

first: Howard

last: Gamper Jr

first: Christine

last: Polte

first: Zoya

last: Ignatova

first: Ralph

last: Kraetzner

first: Michael

last: Shtutman

first: Ya-Ming

last: Hou

first: Anna

last: Kashina


title: Aggregation adaptive routes revealed by transcriptomic and ultrastructural signatures in Phytophthora parasitica

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Within oomycetes, Phytophthora is a genus of eukaryotic microorganisms encompassing some of the most damaging plant pathogens. It spreads by airborne sporangia or waterborne zoospores. Zoospores perceive plant signals through chemotaxis and electrotaxis, and produce signals to attract other zoospores (autotaxis), resulting in auto-aggregation or biofilm formation on the plant surface. The mechanisms underlying intercellular communication and consequent attraction, adhesion and aggregation are largely unknown. Recent studies demonstrated that in Phytophthora parasitica the perception of K+ gradient induced coordinated motion and rapid aggregation. Based on this model, we combined data mining and ultrastructural microscopy analyses to propose a first definition of molecular events leading to oomycete aggregation. Results indicate that the transcriptome repertoire required for aggregation is fully functional already at this single zoospore stage, before aggregation or encystment. Freely swimming zoospores secrete or harbor proteins implied in aggregation through adhesion and extracellular matrix elaboration. They secrete vesicular and fibrillary material, including fibronectin-like proteins, resulting in intercellular structure formation. Consistently, the signature of transcriptome dynamics during transition from single-cell to aggregate is an upregulation of genes contributing to vesicular trafficking, possibly involved in adhesive proteins and extracellular matrix components mobilization. Moreover, the transcriptome signature suggests that pH homeostasis may contribute to aggregation by acting on both zoospore movement and adhesion.

overall_design: Samples were taken from control (not K+-treated cells; C) and K+-treated cells, at different time points (5, 10, 15 min; K5, K10, K15) after K+ application. The experiment was performed in triplicates (R1, R2 and R3).

first: Virginie

last: Magnone

first: Ilaria

last: Bassani

first: Corinne

last: Rancurel

first: Eric

last: Galiana


title: Gene expression of a 3D-cultured human breast cancer cell line after radiation treatment

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: To understand the gene expression alteration of 3D-cultured MDA-MB-231 cell line after 2 Gy x 4 days radiation treatment.

overall_design: The gene expression of 3D-cultured MDA-MB-231 cells with or without 2 Gy x 4 days radiation were compared.

first: Jin-Min

last: Nam


title: tRNAArg-derived fragments mediate protein arginylation [tRF]


title: tRNAArg-derived fragments mediate protein arginylation

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

overall_design: Refer to individual Series


title: Effect of RAGE on macrophage transcriptome in regression of diabetic atherosclerosis

city: New York

first: Richard

middle: A

last: Friedman

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

summary:
Ldlr null (Ager+/+ Ldlr-/-) diabetic mice were raised on a Western diet.
Their aortas were transplanted to diabetic mice rasied on standard chow,
which were either WT (Ager+/+ Ldlr+/+) or Ager null (Ager-/- Ldlr+/+). The
gene expression profile of either the donor (CD45.2) or recipient (CD45.1)
sorted macrophages from both genotypes was studied.

overall_design:
Ldlr-/- Donor:  Macrophages from the aortas of  Ldlr null CD45.2 diabetic mice fed a Western Diet, and not transplanted (n=4)
WT Recipient: WT recipient macrophages, from the transplant: Aortas of Ldlr null CD45.2 diabetic mice fed a Western Diet, and transplanted into standard chow-fed WT CD45.1 diabetic mice (n=4).
Ldlr-/- Donor → WT: Ldlr null donor macrophages, from the transplant: Aortas of Ldlr null CD45.2 diabetic mice fed a Western Diet, and transplanted into standard chow-fed WT CD45.1 diabetic mice (n=4).
Ager-/- Recipient: Ager null recipient macrophages, from the transplant: Aortas of Ldlr null CD45.2 diabetic mice fed a Western Diet, and transplanted into standart chow-fed Ager null CD45.1 diabetic mice (n=6).
Ldlr-/- Donor → Ager-/-: Ldlr null donor macrophages, from the transplant: Aortas of Ldlr null CD45.2 diabetic mice fed a Western Diet, and transplanted into standard chow-fed Ager null CD45.1 diabetic mice (n=4).

first: Laura

last: Senatus

first: Raquel

last: López-Díez

first: Lander

last: Egaña-Gorroño

first: Jianhua

last: Liu

first: Huilin

last: Li

first: Gurdip

last: Daffu

first: Qing

first: Karishma

last: Rahman

first: Yuliya

last: Vengrenyuk

first: Tessa

last: Barrett

first: Zahidunnabi

last: Dewan

first: Edward

last: Fisher

first: Ravichandran

last: Ramasamy

first: Ann

last: Schmidt


title: Gene expression analysis in primary cells derived from patients with Autosomal-dominant hyper-IgE syndrome (AD-HIES)

city: Bethesda

first: Manfred

last: Boehm

state: MD

address: 9000 Rockbille Pike

institute: NHLBI


title: Analysis of gene expression in skin fibroblasts derived from patients with Autosomal-dominant hyper-IgE syndrome (AD-HIES)

summary:
Autosomal-dominant hyper-IgE syndrome (AD-HIES, Job’s syndrome) is a primary immunodeficiency caused by loss of function mutations in signal transducer and activator of transcription 3 (STAT3), a critical regulator of diverse cellular processes. In addition to immunological deficits, patients experience severe non-immunological features including skeletal, connective tissue and vascular abnormalities, poor post-infection healing, and subsequent pulmonary failure. The underlying mechanisms of these STAT3-dependent non-immunological features are not understood, preventing the development of targeted treatments.
In this study, global gene expression was analysed in the patients skin fibroblasts in order to identify signaling pathway affected by the disease-causing STAT3 mutations with ultimate goal to better understand the disease mechanism and identify promising therapeutic targets.

overall_design:
Cultured skin fibroblasts isolated from skin biopsies obtained from 3 AD-HIES patients and 3 healthy volunteers, were treated with or without TNFα for 8h and mRNA expression profiles were analyzed by RNA-Seq.

**RAW data not provided due to patient privacy concerns**

first: Natalia

middle: I

last: Dmitrieva


title: Gene expression analysis in endothelial cells derived from patients with Autosomal-dominant hyper-IgE syndrome (AD-HIES)

summary:
Autosomal-dominant hyper-IgE syndrome (AD-HIES, Job’s syndrome) is a primary immunodeficiency caused by loss of function mutations in signal transducer and activator of transcription 3 (STAT3), a critical regulator of diverse cellular processes. In addition to immunological deficits, patients experience severe non-immunological features including skeletal, connective tissue and vascular abnormalities, poor post-infection healing, and subsequent pulmonary failure. The underlying mechanisms of these STAT3-dependent non-immunological features are not understood, preventing the development of targeted treatments.
In this study, global gene expression was analysed in the patients umbilical vein endothelial cells in order to identify signaling pathway affected by the disease-causing STAT3 mutations with ultimate goal to better understand the disease mechanism and identify promising therapeutic targets.

overall_design:
Cultured endothelial cells isolated from umbilical cords of 3 babies with AD-HIES STAT3 mutations and from 3 control cords were treated with or without TNFα for 8h and mRNA expression profiles were analyzed by RNA-Seq.

**RAW data not provided due to patient privacy concerns**


title: Cellular diversity of the regenerating caudal fin

city: St. Louis

first: Ting

last: Wang

address: 4515 McKinley Avenue, Room 5121

department: Genetics

institute: Washington University St Louis

summary: single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell-type-specific genetic program during regeneration

overall_design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax (Innovative Cell Technologies), filtered through 40-μm cell strainers, and washed with 1× Dulbecco’s phosphate-buffered saline (DPBS)–0.04% bovine serum albumin to generate single-cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 3’ v2 (10x Genomics) and were subsequently sequenced on HiSeq2500 (Illumina) with read lengths of 26 + 75 (Read1 + Read2). Raw reads were processed by Cell Ranger (10x Genomics) with default parameters for read tagging, alignment to zebrafish reference genome (GRCz10), and feature counting based on Ensembl release 91 (cellranger count).

first: Yiran

last: Hou

first: Hyung Joo

last: Lee

first: Yujie

last: Chen

first: Jiaxin

last: Ge

first: Fujr Osman Ibrahim

last: Osman

first: Anthony

last: McAdow

first: Mayssa

middle: H

last: Mokalled

first: Stephen

middle: L

last: Johnson

first: Guoyan

last: Zhao


title: Rice plants treated with D-Tagatose

city: Miki

first: Kazuya

last: Akimitsu

state: Kagawa

address: Ikenobe 2393

department: Faculty of Agriculture

institute: Kagawa University

summary: Rare sugars are monosaccharides that are rarely present in nature. To reveal a effect of D-tagatose in plant and the responses to the D-Tagatose in rice at gene expression level, we performed a microarray analysis using the Agilent Rice Oligo Microarray (44K, custom-made; Agilent Technologies, Redwood City, CA, USA). As a result, there are no significant differences on the gene expression patterns between in mock- and D-tagatose-treated rice plants, and several PR-protein genes which had been reported to be induced by D-allulose or D-allose treatment, were compared by that with D-tagatose treatment in rice.

overall_design: An Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA) was used for the microarray analysis. By using RNeasy plant mini kit (Qiagen, Hilden, Germany), total RNA was extracted from shoots of two-leaf stage rice plants that had been treated with 0.5 mM D-tagatose or no sugar for 2 days. For each biological replicate, material from at least five rice plants was pooled to provide a single sample for RNA extraction. We performed 3 biological replicates for each treatment. All microarray procedures and data analyses were performed according to the manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (400 ng) was labeled with Cy-3 or Cy-5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, following wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2505B and software G2565BA; Agilent Technologies). Feature extraction software (version 9.1; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.

first: T

last: Fukumoto

first: K

last: Ohtani

first: S

last: Mochizuki

last: Ohara


title: Endocrine-exocrine signaling in obesity-driven pancreatic ductal adenocarcinoma

city: Somerville

first: Daniel

last: Burkhardt

state: MA

address: 101 South Street, 6th Floor

institute: Cellarity

summary: Obesity is a major modifiable risk factor for pancreatic ductal adenocarcinoma (PDAC), yet how and when obesity contributes to PDAC progression is not well understood. Leveraging an autochthonous mouse model, we demonstrate a causal and reversible role for obesity in early PDAC progression, showing that obesity markedly enhances tumorigenesis, while genetic or dietary induction of weight loss intercepts cancer development. Bulk and single cell molecular analyses of human and murine samples define microenvironmental consequences of obesity that promote tumor development rather than new driver gene mutations. We observe increased inflammation and fibrosis and also provide evidence for significant pancreatic islet cell adaptation in obesity-associated tumors. Specifically, we identify aberrant beta islet cell expression of the peptide hormone cholecystokinin (CCK) in tumors as an adaptive response to obesity. Furthermore, islet CCK expression promotes oncogenic Kras-driven pancreatic ductal tumorigenesis. Our studies argue that PDAC progression is driven by local obesity-associated changes in the tumor microenvironment – rather than systemic effects – and implicate endocrine-exocrine signaling beyond insulin in PDAC development. Furthermore, our demonstration that these obesity-associated adaptations are reversible supports the use of anti-obesity strategies to intercept PDAC early during progression.

overall_design: Islets from pancreata from ob/ob and wild-type (WT) mice

first: Katherine

last: Chung

first: Jaffarguriqbal

last: Singh

first: Lauren

last: Lawres

first: Kimberly

middle: J

last: Dorans

first: Cathy

last: Garcia

middle: B

first: Rebecca

last: Robbins

first: Arjun

last: Bhutkar

last: Cardone

first: Xiaojian

first: Ana

last: Babic

first: Sara

last: Vayrynen

first: Andressa

middle: D

last: Costa

first: Jonathan

last: Nowak

middle: T

last: Chang

first: Richard

middle: F

last: Dunne

first: Aram

last: Hezel

first: Albert

middle: C

last: Koong

first: Joshua

last: Wilhelm

first: Melena

last: Bellin

first: Vibe

last: Nylander

first: Anna

last: Gloyn

first: Mark

last: McCarthy

middle: G

last: Kibbey

first: Smita

last: Krishnaswamy

first: Brian

last: Wolpin

first: Tyler

last: Jacks

first: Charles

last: Fuchs

first: Mandar

last: Muzumdar


title: RNA-seq analysis of D-tagatose-treated Arabidopsis thaliana inoculated with Hyaloperonospora arabidopsidis isolate Noco-2

first: Kazuya

last: Akimitsu

summary: Rare sugars are monosaccharides that are rarely present in nature. To reveal a effect of D-tagatose in plant and the responses to the D-Tagatose in Arabidopsis inoculated with Hyaloperonospora arabidopsidis (Hpa) isolate Noco-2 at gene expression level, we performed a RNA-seq analysis using the Illumina NGS. As a result, there are no significant differences on the gene expression patterns between in mock- and D-tagatose-treated Arabidopsis plants and Hyaloperonospora arabidopsidis.

overall_design: mRNA profiles of mock- and D-tagatose-treated Arabidopsis inoculated with Hpa were generated by deep sequencing using Illumina Hiseq.

first: T

last: Fukumoto

first: S

last: Mochizuki

last: Ohara

first: K


title: The role of stretch, tachycardia and sodium-calcium exchanger in induction of early cardiac remodeling

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary:
Accute stretch and tachycardia are capable of inducing pathological excitation transcription coupling - an early invent before structural cardiac remodeling which  transitions to heart failure. The sodium calcium exchanger is a key player in maintaining calcium homeostasis and is implicated in pathological signaling during heart failure.
Neonatal rat ventricular cardiomyocytes (NRVCM) were subjected to mechanical stress and high freqency elecrical stimulation to study genes regulated during the early phase of trigger induced cardiac remodeling. Inhibition of the sodium calcium exchanger was used in an attempt to supress the early remodeling process and gain insight into the pathological signaling pathway.

overall_design: Samples subjected to stretch, tachycardia, their respective controls and an NCX inhibitor - KB-R7934 treated samples under the mentioned conditions (4 groups, 3 biological replicates per group) were used for RNA extraction and microarray hybridisation on the Affymetrix gene chip. Tecnical replicates from the same isolation were pooled together on each chip.

first: Natasa

last: Djalinac

first: Birgit

last: Lohberger

first: Simon

last: Sedej

first: Akos

last: Heinemann

first: Dirk

last: van Lewinski

first: Egbert

last: Bisping


title: N1-methyladenosine methylome in messenger RNA in petunia

city: Guangzhou

first: Yixun

last: Yu

address: Wushan

department: College of Forestry and Landscape Architecture

institute: South China Agricultural University

summary: N1-methyladenosine is a unique base methylation because it blocks Watson-Crick base paring and introduces a positive charge. Previous studies showed that m1A is prevalent in yeast and mammals mRNA and has a functional role in promoting translation of methylated mRNA. However, little is known about its abundance, topology and dynamics in plant mRNA. In this study, dot blotting and LC–MS/MS analyses reveal a dynamic pattern of m1A mRNA modification in various tissues and at different developmental stages in petunia (Petunia hybrida). Transcriptome-wide profiling of mRNA m1A in petunia was reported by applying m1A mRNA immunoprecipitation followed by a deep-sequencing approach (m1A-seq). m1A-seq analysis identified 4993 m1A peaks in 3231 expressed genes in petunia corollas. Each methylated gene averagely carries 1.55 peaks. Among the identified m1A peaks, there are 251 m1A peaks in which the adenines was partly replaced by thymine (T) and/or the reverse transcription stops happened in adenine site, in 199 expressed genes. We found that m1A is enriched in coding sequences with one peaks located immediately after start codons, and a slight negative correlation between methylated genes and gene expression was observed. Totally, ethylene treatment reduced the m1A level of mRNA in petunia corollas. We show that a RNA m1A-methyltransferase, tRNA specific methyltransferase 61A (PhTRMT61A), is an m1A mRNA methyltransferase. PhTRMT61A silencing results in decreased m1A peaks in mRNA in leaves and abnormal leaf development. PhTRMT61A is located to the nucleus. Our results suggest that m1A in mRNA is an important epitranscriptome marker and plays a role in plant development.

overall_design: m1A modification in plant mRNA

first: Juanxu

last: Liu


title: Long noncoding RNA landscape in breast cancer [Mexico]

city: CDMX

first: Alberto

last: Cedro-Tanda

state: CMDX

address: Periferico sur #4809

country: Mexico

institute: INMEGEN

summary: Breast cancer (BC) is the most commonly diagnosed neoplasm in women worldwide and a well-recognized heterogeneous pathology classified into four molecular subtypes: Luminal A, Luminal B, HER2-enriched and Basal-like, each one with different biological and clinical characteristics. It is well recognize that clinical and molecular heterogeneity of BC is driven in part by mRNA and lncRNAs. We profiled mRNAs and lncRNA in 75 adjuvant tumors using an Affymetrix microarray platform.

overall_design: Breast cancer tumors were collected from the archives of the Fundacion de Cancer de Mama (FUCAM) after a carefully histopathological review by two training pathologist, according to the following criteria: adjuvant therapy and collection of the surgical sample without any treatment.  We obtain molecular subtype by PAM50 algorithm

first: Hidalgo-Miranda

last: Alfredo

first: Dominguez-Reyes

last: Carlos

first: Tenorio-Torres

last: Alberto

first: Bautista-Piña

last: Veronica

first: Cedro-Tanda


title: Genome-wide transcriptome analysis of human iPSC-derived healty control and schizophrenia cortical interneurons under inflammation conditions.

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: We report changes in gene expression in cortical interneurons under inflammation conditions by genome-wide transcriptome analysis, compared to the previous dataset generated without inflammation conditions (GSE118313).

overall_design: RNA sequencing analysis (bulk) of healthy control interneurons and schizophrenia interneurons. Four independent iPS lines per group (total 8 iPSC lines) with three independent differentiations

first: Sangmi

last: Chung

last: Xi


title: A long noncoding RNA landscape in breast cancer reveals a potential role for lncRNA AC009283.1  in proliferation and apoptosis in HER2-enriched molecular subtype

summary:
We silenced lncRNA AC009283.1 using shRNAs in cell line SKBR3, carried a ~75% silencing compared to thenegative control (NC).
We evaluated the role of lncRNA AC009283.1 on oncogenic phenotypes in the HER2-enriched SKBR3 breast cancer cell line model. The knockdown of lncRNA AC009283.1 was achieved with ~75% of silencing efficiency. A complete transcriptomic analysis after silencing of lncRNA AC009283.1 revealed an impact on the global expression.

overall_design: We analyzed expression profile of knockdown of lncRNA AC009283.1 in SKBR3 cell line using the Affymetrix Human Transcriptome Array 2.0 platform. Array data was processed by Affymetrix Exon Array Computational Tool.

first: Alfredo

last: Hidalgo-Miranda


title: Integrated genomic analysis of chromosomal alterations and mutations in B-cell acute lymphoblastic leukemia reveals distinct genetic profiles at relapse

city: Salamanca

first: Jesús

middle: Maria

last: Hernández-Rivas

state: Salamanca

address: Paseo San Vicente, 88-182

department: Hematology

country: Spain

institute: Hospital Universitario de Salamanca, Universidad de Salamanca-CSIC

type: Genome variation profiling by genome tiling array

summary: Background: The clonal basis of relapse in acute lymphoblastic leukemia (ALL) is complex and not fully understood. Methods: Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH), and multiplex-ligation-dependent probe amplification (MLPA) were carried out in matched diagnosis-relapse samples from 13 B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients to identify patterns of genetic evolution that could account for the phenotypic changes associated with disease relapse. Findings: The integrative genomic analysis of aCGH, MLPA and NGS revealed that 100% of BCP-ALL patients showed at least one genetic alteration at diagnosis and relapse. In addition, there was a significant increase in the frequency of chromosomal lesions at the time of relapse (median, 6 alterations per sample) relative to that at diagnosis (median, 47 alterations) (p = 0.019). The combination of MLPA and aCGH techniques showed that IKZF1 was the most frequently deleted gene. Notably, TP53 was the most frequently mutated gene at relapse (31%). Two TP53 mutations were detected only at relapse, whereas the three others showed an increase of their mutational burden at relapse. Interpretation: Clonal evolution patterns were heterogeneous, involving acquisition, loss and maintenance of lesions at relapse. Therefore, this study confirmed that BCP-ALL is a genetically dynamic disease with distinct genetic profiles at diagnosis and relapse. The combination of the NGS, aCGH, and MLPA approaches enables better molecular characterization of the genetic profile in ALL patients during the evolution from diagnosis to relapse.

overall_design: aCGH Nimblegen array performed on 13 paired samples of ALL at diagnosis and relapse

first: Maribel

last: Forero-Castro

first: Adrián

last: Montaño

first: Cristina

last: Robledo

first: Alfonso

last: de Coca

first: Jose

last: Fuster

first: Natalia

last: de las Heras

last: Queizán

first: María

last: Hernández-Sánchez

first: Luis

last: Corchete-Sánchez

first: Marta

last: Martín-Izquierdo

first: Jordi

last: Ribera

middle: M

first: Rocío

last: Benito

first: Jesus


title: In vivo probing of promoter overlapping between σ-factors in Escherichia coli (ChIP-Seq)

city: Daejeon

first: Byung-Kwan

last: Cho

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: An alternative sigma factor (σ32) recognizes the unique set of promoters upon heat shock. Here, we determined 54  σ32 promoters at nucleotide resolution using ChIP-exo, enabling us to compare those with housekeeping σ70 promoters. The results elucidated the overarching principles of promoter overlapping between the two σ-factors, which are sequence-specific non-, half-, and full-shared modes with a perfect sequence conservativeness of −35 element as a key determinant of full-shared mode.

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

overall_design: ChIP-seq profiles of sigH (30 ℃) and sigH (42 ℃) were generated by deep sequencing in duplicates using Illumina MiSeq.

first: Suhyung

first: Yoo-Bok

first: Eunju

last: Lee

first: YeonI

last: Woo

first: Sun

last: Kim


title: In vivo probing of promoter overlapping between ?-factors in Escherichia coli

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


title: In vivo probing of promoter overlapping between σ-factors in Escherichia coli (ChIP-exo)

overall_design: ChIP-exo profiles of sigH (30 ℃), sigH (42 ℃), RNAP beta (42 ℃) were generated by deep sequencing in duplicates using Illumina MiSeq.


title: Premature activation of immune transcription programs in autoimmune-predisposed mouse embryonic stem cells and blastocysts

status: Public on Aug 11 2020

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

country: Germany

institute: Medical Center - University of Freiburg

summary: To study the underlying mechanism of autoimmunity predisposition in autoimmune-proned mouse strains, we characterize embryonic stem cells derived from various mouse strains.

overall_design:
We performed mRNA-Seq analysis to determine the transcriptional differences between embryonic stem cells derived from auto-immune proned mouse strains.
NOD: autoimmune-prone

first: Eugene

last: Ke

first: Oktay

last: Kirak


summary: To study the underlying mechanism of autoimmunity predisposition in autoimmune-prone mouse strains, we characterize embryonic stem cells derived from various mouse strains.

overall_design:
We performed mRNA-Seq analysis to determine the transcriptional differences between embryonic stem cells derived from auto-immune prone mouse strains.
NOD: autoimmune-prone
NZB: autoimmune-prone


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

overall_design: Refer to individual Series


title: Effect of Maternal Separation (MatSep) on renal vasculature isolated from male neonates (Postnatal day 10) and adult (Postnatal day 180)

city: Lexinton

first: Analia

middle: S

last: Loria

state: KY

address: 900 S Limestone

department: Pharmacology

country: USA

institute: U of Kentucky

summary:
Optimal Ang II levels during postnatal life are required for a normal maturation of the rat kidney. This study investigated both short- and long-term effect of MatSep on: 1) the status of intrarenal renin-angiotensin system components, 2) the isolated renal vasculature genome-wide gene expression trajectory from neonatal to adult life, and 3) the renal vascular architecture and function.
In this dataset, gene expression changes by MatSep at P10 in renal vasculature isolated from neonates, modulate extracellular structure organization, vasculature development, inflammation and angiogenesis. The long -term effects of MatSep on renal vasculature gene expression is assessed at P180, which reveal clusters of genes with short, long, and downstream changes in expression.

overall_design: 20 total samples were analyzed in 4 experimental groups: un-stressed (control littermates) and stressed (MatSep) neonates (P10) and adult (P180) rats (n=5 per group). We performed pair-wise comparisons and defined Early-life genes as those with expression levels at P10 > at P180 in un-stressed controls and Adult-life genes as those with expression levels at P180 > at P10. Early life MatSep affected genes were identified by pair-comparison between P10 MatSep group and P10 controls. The long-term MatSep effects on expression of genes were identified by pair-comparison between P180 MatSep group and P180 controls.

first: Carolina

last: Dalmasso

first: Kuey

last: Chen


title: ALKBH5 impacts malignancy of hepatocellular carcinoma via m6A-mediated epigenetic modulation

city: Hangzhou

first: Yunhao

address: 79 Qingchun Road

country: China

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

summary: N6-methyladenosine (m6A) modification is implicated in the tumorigenicity of hepatocellular carcinoma (HCC). AlkB homolog 5 (ALKBH5) is one of the m6A demethylases, and it has not been well characterized in HCC. In our study we clarify the biological roles and potential mechanisms of ALKBH5 in HCC. We identify the expression profile of ALKBH5 in HCC and find that it serves as an independent prognostic factor of HCC survival. It impacts the proliferation and invasion capability of HCC cells in vitro and in vivo. ALKBH5-mediated m6A demethylation leads to a post-transcriptional modulation of LYPD1. In addition, we reveal the tumor-related behaviors of LYPD1.

overall_design: We employed MeRIP-seq analyses in ALKBH5-overexpressed (OE) and negative control (NC) HCCLM3 cells to explore the features and distribution dynamics of ALKBH5-mediated RNA m6A modification.


title: DDX5 targets tissue specific RNAs to promote intestine tumorigenesis

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Tumorigenesis in different segments of the intestinal tract involves tissue-specific oncogenic drivers. In the colon, complement component 3 (C3) activation is a major contributor to inflammation and malignancies. By contrast, tumorigenesis in the small intestine involves fatty acid-binding protein 1 (FABP1). However, little is known of the upstream mechanisms driving their expressions in different segments of the intestinal tract. Here, we report that an RNA binding protein DDX5 augments C3 and FABP1 expressions post-transcriptionally to promote tumorigenesis in the colon and small intestine, respectively. Mice with epithelial-specific knockout of DDX5 are protected from intestine tumorigenesis. The identification of DDX5 as the common upstream regulator of tissue-specific oncogenic molecules provides a new therapeutic target for intestine cancers.

overall_design:
Primary small intestine epithelial cells and Th17 cells were harvested, crosslinked with UV, lysed and immunoprecipitated to enrich for RNA fragments bound to DDX5-containing protein complexes.
Primary small intestine of 8wk adult female mice and colon epithelial cells from 120 days old Apcfl/+ CDX2Cre mice were harvested, crosslinked with UV, lysed and immunoprecipitated to enrich for RNA fragments bound to DDX5-containing protein complexes.

first: Nazia

last: Abbasi

first: Tianyun

last: Long

first: Yuxin

last: Li

first: Evelyn

last: Ma

first: Brian

last: Yee

first: Ibrahim

last: Sayed

first: Nissi

last: Varki

first: Soumita

last: Das

first: Pradipta

last: Ghosh

middle: W

first: Wendy

last: Huang


title: Long non-coding RNA Dlx6os1 serves as a potential treatment target for diabetic nephropathy via regulating multiple apoptosis and inflammation-related pathways derived from RNA-Seq

city: Shanghai

first: Shan

address: 1111 Xianxia Road

department: Department of Endocrinology

institute: Tongren Hospital, Shanghai Jiao Tong University School of Medicine

summary: We investigated the effect of long non-coding RNA (lncRNA) Dlx6os1 silencing on cell proliferation, apoptosis, fibrosis, and further explored its influence on mRNA expression profile in mouse mesangial cells (MMCs) of diabetic nephropathy (DN) cellular model. DN cellular model was constructed in SV40 MES13 cells (MMCs) under high glucose condition (under 30 mmol/L glucose culture).

overall_design: LncRNA Dlx6os1 ShRNA plasmids and negative control ShRNA plasmids were transfected into MMCs of DN cellular model as Sh-LncRNA group and Sh-NC group respectively. The mRNA expression profile was determined in Sh-LncRNA group and Sh-NC group.


title: Transcriptional response of mce3R induction and ctpD disruption in Mycobacterium tuberculosis CDC1551

city: Seattle

first: Shuyi

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

summary: We identified mce3R and ctpD as genes that could alter M tuberculosis (Mtb) response to isoniazid when perturbed using a regulatory network-based TRIP screen [see associated data at PRJNA483505]. To investigate the mechanisms underlying this response, we performed RNAseq on genetically perturbed mutant strains either in the presence or absence of isoniazid.

overall_design: RNAseq analysis was performed on two Mtb mutant strains in the CDC1551 background: 1) CDC1551 transformed with an episomal plasmid that could induce mce3R (Rv1963c) expression upon supplementation with anhydrotetracycline (ATc), and 2) a ctpD (Rv1469) transposon disruption strain in the CDC1551 background (CDC1551::1469tn) transformed with an episomal plasmid that could induce mce3R expression upon ATc supplementation. Bacteria were harvested at 1 day after being exposed to isoniazid (3.6μM) or no drug, as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.

first: Jessica

last: Farrow-Johnson

first: Tige

middle: R

last: Rustad

first: David

last: Sherman


title: Profiling of gene expression signatures for human corneal epithelial cell after transfection with microRNA-184 or NC.

city: Wenzhou

first: Qiongjie

last: CAO

state: Zhejiang

address: 270 Xueyuan Road

institute: Wenzhou Medical University

summary: Our previous study identified that microRNA-184 as one of the most highly expressed miRNAs in the corneal epithelium. To gain insight into the underlying mechanisms of miR-184 modulation of corneal epithelial cell proliferation and migration, we probed for its gene targets by microarray analysis . HCECs transfected with miR-184 or a NC for 48 h were harvested and a gene microarray evaluated transcriptome expression patterns. Ectopic miR-184 expression resulted in numerous genes undergoing either upregulation or downregulation. Since miRNAs mediate biological functions by impeding expression of their target genes in mammals, a total of 901 differentially downregulated genes (Foldchange ≤ 0.667) were firstly selected.

overall_design: Gene expression in human corneal epithelial cell was measured at 48 hours after transfection with either a 50 nM miR-184 mimic or negative control (NC)

last: Cao

first: Weiwei

last: Xu


title: Primary tumors and metastases from the NPK (Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+) prostate cancer mouse model

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

type: Genome variation profiling by high throughput sequencing


title: RNA-seq of iPSC-ECs treated e-cig liquids with and without nicotine

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: Two healthy iPSC lines (78 and 273) were differentiated into ECs. iPSC-ECs were then treated with e-cig liquids RY4 (RY) or Marcado (MAR) with 18mg/ml of nicotine (18) and without nicotine (0).

first: Won-Hee

last: Lee

first: Sang-Ging

last: Ong

first: Joseph

last: Wu


title: The miRNA-mRNA Interactome of murine iPSC-derived Chondrocytes in Response to Inflammatory Cytokines

city: Saint Louis

first: Alison

last: Ross

state: Missouri

address: Couch Biomedical Research Building

institute: Washington University in St. Louis

summary: The goal of this study was to understand the mechanisms of miRNA regulation of the transcriptome of tissue engineered cartilage in response to IL-1β and TNF-α using an in vitro murine induced pluripotent stem cell (miPSC) model system. miPSCs were chondrogenically differentiated for 21 days and then treated with 1 ng/mL of IL-1β, 20 ng/mL of TNF-α, or control media without cytokines for 0, 4, 12, 24, and 72 hours. We performed an integrative analysis of miRNA- and RNA-sequencing data to determine the temporal and dynamic responses of miRNAs and genes to specific inflammatory cytokines. Through integration of mRNA and miRNA sequencing data, we created networks of miRNA-mRNA interactions which may be controlling the response to inflammatory cytokines.

overall_design: miRNA and mRNA profiles of tissue-engineered cartilage; in triplicate, using a Illumina HiSeq3000

first: Farshid

last: Guilak


title: RUNX1 knockdown and BET protein proteolysis targeting chimera (PROTAC) exerts potent lethal activity against mtRUNX1 AML cells

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

summary: Bromodomain extraterminal protein (BETP) inhibitors transcriptionally repress oncoproteins which undermines the growth and survival of AML cells. However, BETi treatment causes accumulation of BETPs, associated with reversible binding and incomplete inhibition of BRD4, which potentially compromises the activity of BETi in AML cells. Unlike BETi, BET-PROTAC (proteolysis-targeting chimera) ARV-825 recruits and utilize an E3-ubiquitin ligase to effectively degrade BETPs in AML cells. BET-PROTACs induce more apoptosis than BETi of mtRUNX1 AML cells. BET-PROTAC treatment induced more perturbations in the mRNA and protein expressions than BETi. It was noted that treatment with BETi or BET-PROTAC caused significant and sustained depletion of RUNX1 in AML cells.  We also determined the effects of global depletion of RUNX1 in mtRUNX1 expressing AML OCI-AML5 cells. We observed an overlap in the signature of RUNX1 knockdown by shRNA with that of OTX015 and ARV-825 in OCI-AML5 cells.

overall_design: Fifteen samples in biologic triplicates

middle: N


title: Effect of microgravity on HUVECs (Human Umbilical vein Endothelial cells) cells and its transcriptome analysis.

city: Cochin

first: Ravi

last: Gupta

state: Kerala

address: Plot no: 43A,SDF, 3rd floor, A Block,CSEZ, Kakkanad

department: Bioinformatics

country: India

institute: SciGenom Labs Pvt. Ltd.

summary: The scope of this study is to understand effect of microgravity on HUVECs (Human Umbilical vein Endothelial cells) and comparative analysis with respect to control group.

overall_design: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform.The sequence reads were aligned with Homo sapiens genome downloaded from Ensembl release 75 database. Alignment of sequence were performed using STAR (version 2.4.2a ) program with Homo sapiens gene model. Expression estimation carried out using cufflinks program (version 2.2.1). Differential expression analysis carried using the cuffdiff program in cufflinks(version 2.2.1)

first: Dharanibalan

last: kasiviswanathan

first: Suvro

last: Chatterjee


first: Manching

last: Ku

overall_design:
We performed ChIP-Seq analysis to determine the transcriptional differences between embryonic stem cells derived from auto-immune prone mouse strains.
NOD:autoimmune-prone

first: Eugene

last: Ke


title: Neutrophil extracellular traps mediate articular cartilage damage and enhance the immunogenicity of cartilage components in rheumatoid arthritis

status: Public on Aug 10 2020

city: Bethesda

first: Stephen

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: This study invesigates the effects of neutrophil extracellular traps (NETs) on articular cartilage degredation and resulting autoimmune responses in rheumatoid arthritis.

overall_design: This dataset includes bulk RNA sequencing of fibroblast-like synoviocytes (FLS) that were treated with NETs for 48 hours.

first: C

last: Carmona-Rivera

first: P

last: Carlucci

first: R

last: Goel

first: E

last: James

first: S

last: Rims

first: V

last: Hoffman

first: D

middle: A

last: Fox

first: J

last: Buckner

first: M

last: Kaplan


title: Whole-exome sequencing analysis of primary tumors and metastases from the NPK (Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+) prostate cancer mouse model

first: Antonina

last: Mitrofanova

summary: Whole-exome sequencing analysis of lineage-marked prostate primary tumors and metastases from the NPK mouse model (Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+)

overall_design: Male mice of a a predominantly C57BL/6 background were induced to form tumors at 2-3 months of age by administration of tamoxifen using 100 mg/kg (in corn oil) once daily for 4 consecutive days. Following tamoxifen-induction, mice were monitored daily and euthanized when their body condition score was <1.5, or when they experienced body weight loss  >20% or signs of distress, such as difficulty breathing or bladder obstruction. Whole exome sequencing was done on matched trios of primary tumors, lung metastases, and bone metastases, as well as tails (as a control) from five independent mice.

first: Juan

last: Arriaga

first: Cory

last: Abate-Shen


title: Addressing the essential role of cohesin STAG2 in embryos and adult mice

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

institute: CNIO

summary: STAG2 is commonly mutated in cancer and germline mutations have been identified in cohesinopathy patients. To better understand the underlying pathogenic mechanisms, we here report the consequences of Stag2 ablation in mice. STAG2 is largely dispensable in adults and its tissue-wide inactivation does not lead to tumors but reduces fitness and affects both hematopoiesis and intestinal homeostasis. STAG2 is also dispensable for murine embryonic fibroblasts in vitro. In contrast, Stag2 null embryos die by mid gestation showing global developmental delay and defective heart morphogenesis, most prominently in structures derived from secondary heart field progenitors. Our analyses suggest that both decreased proliferation and altered transcription of tissue-specific genes contribute to these defects. These results provide compelling evidence on cell- and tissue-specific roles of the two cohesin complexes and how their dysfunction contributes to disease.

overall_design: RNA-Seq for STAG2 KO and WT embryos at E9.5 (21-23 pairs of somites)

first: Magali

last: De Koninck

first: Elenonora

last: Dapi

first: Claudio

last: Badia-Careaga

first: Itziar

last: Cossío

last: Giménez-Llorente

first: Miriam

last: Rodríguez-Corsino

first: Elena

last: del Pilar Andrada

first: Andrés

last: Hidalgo

first: Miguel

last: Manzanares

first: Francisco

middle: X

last: Real

first: Ana

last: Losada


title: Single-cell RNA seq analysis of primary tumors and metastases from the NPK (Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+) prostate cancer mouse model

summary: Single-cell transcriptome analysis of lineage-marked prostate primary tumors and metastases from the NPK mouse model (Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+)

overall_design: Male mice of a a predominantly C57BL/6 background were induced to form tumors at 2-3 months of age by administration of tamoxifen using 100 mg/kg (in corn oil) once daily for 4 consecutive days. Following tamoxifen-induction, mice were monitored daily and euthanized when their body condition score was <1.5, or when they experienced body weight loss  >20% or signs of distress, such as difficulty breathing or bladder obstruction. Single-cell transcriptomic analysis of bulk tissues was done on two matched primary tumors and macrodissected bone metastases  from 2 independent mice.


title: RNA seq analysis of primary tumors and metastases from the NPK (Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+) prostate cancer mouse model

summary: Transcriptome analysis of lineage-marked prostate primary tumors and metastases from the NPK mouse model (Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+)

overall_design: Male mice of a a predominantly C57BL/6 background were induced to form tumors at 2-3 months of age by administration of tamoxifen using 100 mg/kg (in corn oil) once daily for 4 consecutive days. Following tamoxifen-induction, mice were monitored daily and euthanized when their body condition score was <1.5, or when they experienced body weight loss  >20% or signs of distress, such as difficulty breathing or bladder obstruction. Transcriptomic analysis of bulk tissues was done on primary tumors (n=19) and matched macrodissected metastases from lung (n=11), liver (n=5), lymph nodes (n=4), or bone (n=12) from 11 independent mice. RNA was prepared from snap-frozen tissues the using MagMAX-96 total RNA isolation kit and only RNA samples having between >200 ng and 1 ug and with an RNA integrity number (RIN) > 8 were used.


title: RNA-sequencing (transcriptome analysis) of Desulfovibrio ferrophilus IS5 conducting electron uptake from electrodes at different potentials

city: Tsukuba

first: Xiao

last: Deng

state: Ibaraki

address: 1-1 Namiki

institute: National Institute for Materials Science

summary: Desulfovibrio ferrophilus IS5 was incubated on indium-tin oxide (ITO) electrodes poised at −0.4 V and −0.5 V (versus standard hydrogen electrode) in H-type reactors for 10 days. Total RNA was extracted from cells after incubation, and RNA fragments were purified and transcribed into cDNA. cDNA was sequenced by NovaSeq 6000 System.

overall_design: Gene expression profile of Desulfovibrio ferrophilus IS5 incubated for 10 days on ITO electrodes poised at −0.4 V [sample name 1_2] and −0.5 V [Sample name 3_4] (vs. SHE).

first: Akihiro

last: Okamoto


title: Nalm 6 WT; Nalm6 BKO; Nalm 6 A hets

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

summary: Four replicas of cells with and without TOP2B and cells heterozygous for TOP2A

overall_design:
Four replicas each sample type:
WT Nalm6 - a B cell precursor
TOP2B-/- Nalm 6 - a B cell precursor
TOP2A+/- Nalm 6 - a B cell precusor

first: Caroline

last: Austin


title: Limited Cell Fluorescence Activated Cell-sort Sequencing (LC-FACSeq) is a method for detecting rare clones in leukemia

city: Columbus

first: Eileen

middle: Yifan

last: Hu

state: OH

address: Rm 449, 410 West 12th Ave

institute: The Ohio State University

summary: Detecting and monitoring tumor clonal evolution in the setting of measurable residual disease is technically difficult due to 1) high sequencing background due to limited numbers of disease cells, 2) loss of tumor genetic material due to the need for high quality purified DNA, and 3) resource and bioinformatics intensive requirements of traditional next generation sequencing techniques. Limited Cell Fluorescence Activated Cell-sort Sequencing (LC-FACSeq), is a fast, reproducible, and cost effective amplicon based sequencing technique that does not require genomic material isolation. It can be used in the context of just a few hundred tumor cells and is easily generalization for monitoring clonal evolution in various different malignancies.

overall_design:
Using the LC-FACSeq method to examine clonal evolution in 20 patients treated with ibrutinib for over 4 years (baseline and varying on treatment samples are included for each patient). We validated the reproducibility of LC-FACSeq using different cell titrations (50, 100, 300, 500 cells) of five sorted chronic lymphocytic leukemia (CLL) and 8 sorted acute myeloid leukemia (AML) samples and their corresponding bulk cell samples (100000 cells).
The accompanying manuscript is using these samples to test of novel sequencing technique and the variations identified are from drug treatment studies in patients (already found using alternative methods).

middle: Y

last: Byrd

first: Gerard

last: Lozanski

first: Natarajan

last: Muthusamy


title: Transcriptional changes upon Jagn1 loss in LPS-stimulated plasmablasts.

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

institute: IMP/IMBA

summary: We report that Jagn1-deficiency is associated with alterations in the ER of antibody-producing cells and decreased immunoglobulin levels. By doing QuantSeq of FACS-sorted CD22-CD138+ plasmablasts, we found several differentially expressed genes in Jagn1DB knock-out mice.

overall_design: Examination of consequences of B-cell specific knock-out of Jagn1 in LPS-stimulated splenic B cells (from 4 mice per genotype), which were FACS-sorted for CD22-CD138+ plasmablasts after 4 days of LPS stimulation.

first: Astrid

last: Hagelkruys


title: The molecular response of Aspergillus niger to guar gum

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: Guar gum consists mainly of galactomannan, and constitutes the endosperm of guar seeds that acts as a reserve polysaccharide for germination. Due to its molecular structure and physical properties, this biopolymer has been considered as one of the most important and widely used gums in industry. However, for many of these applications this (hemi-)cellulosic structure needs to be modified or (partially) depolymerized in order to customize and improve its physicochemical properties. In this study, transcriptome was employed to decipher the complete enzymatic arsenal for guar gum depolymerization by Aspergillus niger.

overall_design: In this study, we aimed to gain a comprehensive insight into the transcriptome of A. niger during guar gum degradation (after 8, 24 and 48 hours of incubation) and compare this to the transcriptome on the main guar gum components D-mannose, D-galactose and mannan, as well as D-glucose and guar gum that was used as a control after 2 hour incubation.

first: Nancy

last: Linares

first: Marcos

last: Di Falco

first: Isabelle

last: Benoit

first: Birgit

last: Gruben

first: Mao

last: Peng

first: Adrian

last: Tsang

first: Miia

last: Mäkelä

middle: P