title: An Initial Comparative Genomic Autopsy of Wasting Disease in Sea Stars

city: Merced

first: Lauren

last: Schiebelhut

state: CA

address: 5200 N. Lake Rd.

institute: University of California, Merced

summary: Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as ‘asteroid idiopathic wasting syndrome’ (AIWS) due to its elusive etiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. Here we take a forensic genomic approach to discover candidate genes that may help explain sea star wasting syndrome. We report the first genome and annotation for P. ochraceus, along with differential gene expression (DGE) analyses in four size classes, three tissue types, and in symptomatic and asymptomatic individuals. We integrate nucleotide polymorphisms associated with survivors of the wasting disease outbreak, DGE associated with temperature treatments in P. ochraceus, and DGE associated with wasting in another asteroid Pycnopodia helianthoides. In P. ochraceus, we find DGE across all tissues, among size classes, and between asymptomatic and symptomatic individuals; the strongest wasting-associated DGE signal is in pyloric caecum. We also find previously identified outlier loci co-occur with differentially expressed genes. In cross-species comparisons of symptomatic and asymptomatic individuals, consistent responses distinguish genes associated with invertebrate innate immunity and chemical defense, consistent with context-dependent stress responses, defensive apoptosis, and tissue degradation. Our analyses thus highlight genomic constituents that may link suspected environmental drivers (elevated temperature) with intrinsic differences among individuals (age/size, alleles associated with susceptibility) that elicit organismal responses (e.g. coelomocyte proliferation) and manifest as sea star wasting mass mortality.

overall_design: Tissue biopsies - of tube feet, pyloric caecum, and dermis - were taken from 17 individuals: 15 collected at McClures Beach and two from Lifeboat House in Point Reyes National Seashore (SI Appendix, Table S1) on the 19th and 21st August 2017, respectively, and preserved in RNAlater® in the field. A DGE analysis was first conducted to evaluate differential expression between tissue types. Subsequent analyses were conducted separately for each tissue type to assess differential expression between size classes and between symptomatic and asymptomatic individuals. Each size class (i.e. small, medium, large, or x-large) was compared to the mean of all other size classes. An additional analysis was conducted comparing just the small individuals directly to the x-large individuals to reveal potential DGE that might be masked by variation in intermediate size classes. Genes were filtered at a minimum threshold of mean 1 count per million (CPM). Significance was assessed at a false discovery rate (FDR) < 0.01 (unless otherwise noted).

first: Dannise

middle: V

last: Ruiz-Ramos

first: Katharina

last: Hoff

first: John

last: Wares

first: Michael

middle: N

last: Dawson


title: ChIP-seq of cholangiocytes treated with TGFbeta

status: Public on Feb 20 2020

city: Rochester

first: Shubham

last: Basu

state: Minnesota

address: 200 First St. SW

department: Division of Biomedical Statistics and Informatics

country: USA

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TGF beta has profound effects on global gene expression changes. To understand the epigenetic mechanisms associated with TGF beta stimulation, we performed ChIP-seq of cholangiocytes to understand the changes in histone modifications associated with TGF beta. We choose H3K27ac and H3K9ac, histone modification associated with gene expression. These histone modifications were correlated with SMAD3 occupancy, which is a canonical downstream mediator of TGF beta signaling.

overall_design: Cholangiocyte cell line, H69, were treated with Vehicle or TGF beta for 16 hours to evaluate H3K27ac, H3K9ac and SMAD3 chromatin occupancy following TGF beta.

first: Sayed

middle: O

last: Aseem

first: Robert

middle: C

last: Huebert


title: Transcriptional responses to TNF-alpha in germline A20 haploinsufficiency

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

country: United Kingdom

institute: Newcastle University

type: Expression profiling by high throughput sequencing

summary: Early-onset complex autoimmunity can arise from monogenic activating mutations in inflammatory signalling pathways or loss of function mutations of immunoregulatory molecules. We sought to define the molecular basis of severe early-onset autoimmunity, characterised by autoimmune diabetes, cytopenias, hepatitis, enteropathy and interstitial lung disease, in a child without pathogenic variants in STAT3 and FOXP3. We employed whole exome sequencing, together with in vitro assays of tumor necrosis factor-alpha (TNF-α) signalling and response, including RNA sequencing, in patient fibroblasts. We identified a novel de novo heterozygous variant in TNFAIP3, which encodes A20 - a key negative regulator of the NF-κB transcriptional induction pathway. The p.V489Afs*7 variant reduced A20 protein expression and resulted in hyperresponsiveness of TNF-α signal transduction. This was accompanied by significant enhancement of TNF-α induced NF-κB target gene expression. There was an excellent clinical response to matched unrelated haematopoietic stem cell transplantation (HSCT), with resolution of all pathological features except diabetes. This case reveals a novel association between a previously unreported heterozygous TNFAIP3 mutation and the development of early-onset complex autoimmunity, validating existing evidence from both genome-wide association studies and conditional murine knockout models that implicates TNFAIP3 in autoimmune pathogenesis. This case also expands the clinical spectrum of germline A20 haploinsufficiency, recently identified in a cohort of patients with Behçet’s-like autoinflammatory disease, and shows that correction of the molecular defect within the haematopoietic cell compartment may be a viable treatment option for severe clinical manifestations.

overall_design: The study consists of 12 samples; 6 control and 6 patient. 50% of patient and control samples were treated with TNF-alpha stimulation, whereas the remaining 50% were unstimulated. This experiment is in triplicate replication.

first: Christopher

middle: J

last: Duncan

first: Sophie

last: Hambleton


title: Chemotherapy neurotoxicity is codependent on cancer

status: Public on Feb 19 2020

city: Atlanta

first: Stephen

middle: Nicholas

last: Housley

state: GA

address: 555 14th Street

institute: Georgia Institute of Technology

summary:
Neurological disorders induced by chemotherapy, including pain and other debilitating sensory conditions correlate with alterations in diverse systemic, cellular, and molecular processes.  Chemotherapeutic agents variously induce inflammatory responses, metabolic disorders and associated gene expression changes, all of which have the capacity to impact sensory function .  Early evidence of independent effects by cancer alone on some of these same processes led us to hypothesize that neurological symptoms may emerge from cooperativity in the effects of chemotherapy and cancer.  We tested this hypothesis in a rodent model of human colon cancer after a full course of human-scaled treatment with the commonly used chemotherapeutic agent oxaliplatin.  Transcriptional profiling of dorsal root ganglia demonstrated that cancer and chemotherapy in combination produced changes that were unpredictable or undetectable from those observed with either alone. Unique combinatorial effects of chemotherapy and cancer were conserved as dysregulation of select ion-channel proteins and associated reduction in excitability of sensory neurons responsible for proprioception. Recognition of the non-additive interactions between chemotherapy and cancer may lead to the development of more effective strategies for the prevention and/or treatment of chronic neurological disorders commonly associated with cancer therapy.
We used microarrays to detail the global programme of gene expression underlying neurologic dysfunction following chemotherapy treatment in animals bearing and not bearing cancer.

overall_design: In total, 13 (three groups with biologic triplicates per group and 4 biologic replicates from a final combinatorial group) global transcriptional expression data sets were generated in this study

first: Paul

last: Nardelli

first: Dario

last: Carrasco

first: Lilya

last: Matyunina

first: Mengnan

last: Zhang

middle: F

last: McDonald

first: Tim

last: Cope


title: H3K27Ac mapping in isogenic CREBBP-WT, CREBBP-KO and  EP300-KO SUDHL4 cell lines

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

summary: Inactivating mutations of the CREBBP acetyltransferase and, at lower frequencies, its paralogue EP300 are among the most common genetic alterations in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), the two most frequent B cell malignancies. Here we uncover unexpected distinct functions for CREBBP and EP300 in the germinal center (GC), i.e. the target structure for most human B cell lymphomas. We show that these proteins modulate non-overlapping transcriptional programs that are preferentially enriched in biological functions associated with the separate anatomic compartments of the GC. Consistently, deletion of CREBBP or EP300 have opposing effects on GC formation in vivo. Nonetheless, these proteins partially compensate for each other to maintain a minimal threshold of acetyltransferase activity and guarantee homeostatic control of the GC, which is completely abrogated by their combined loss. This synthetic lethal interaction is retained in DLBCL cells, identifying an Achille’s heel in CREBBP-mutant lymphomas that could be pharmacologically targeted by using a novel, selective small molecule inhibitor of the CREBBP/EP300 bromodomain. These data shed light on the unique roles of CREBBP and EP300 in the physiology and pathology of GC B cells, and provide a proof-of-principle for the development and testing of EP300 inhibition as a therapeutic strategy in these diseases.

overall_design: CHIP-Seq analysis fo H3K27Ac in isogenic DLBCL cell lines lacking CREBBP or EP300 vs control CREBBP/EP300 WT cells.

first: Antony

middle: B

last: Holmes


title: Autophagic turnover of NBR1 restricts metastatic colonization during mammary tumor progression

city: San Francisco

first: Timothy

last: Marsh

state: California

address: 513 Parnassus Ave, Box 0502, HSW475

department: Pathology

institute: University of California, San Francisco

summary: Autophagy is implicated in promoting the metastatic potential of tumor cells. Utilizing a mouse model of mammary cancer to temporally delete essential autophagy regulators, ATG12 or ATG5, in tumor cells during distinct stages of carcinoma progression, we determine a stage-specific role for autophagy in suppressing metastatic colonization. In stark contrast to the tumor-promoting role of autophagy in primary mammary tumors, autophagy restricts colonization of disseminated tumor cells (DTCs) and prevents the acquisition of basal epithelial characteristics, effects that are dependent on turnover of the autophagy-specific substrate, Neighbor to BRCA1 (NBR1). Analysis of human breast cancer samples corroborates the importance of NBR1 in overall survival and metastasis, highlighting NBR1 as a potential therapeutic target in preventing DTCs from developing into overt, clinical disease.

overall_design: We inoculated primary GFP+ PyMT mammary tumor cells via lateral tail vein into naïve, 6-week old female C57BL/6 hosts and allowed them to seed the lung for 1 week. We then inducibly deleted the essential autophagy gene, ATG12, exclusively in metastatic tumor cells and allowed overt metastases to develop for an additional 3 weeks. Lungs were dissociated and resulting metastatic ATG12-knockout (ATG12 KO) and ATG12-floxed (control, ATG12 F/F) PyMT tumor cells were sorted by FACS (GFP+/MHC-I+/CD45-/CD31-/Ter119-) and RNA sequencing libraries prepared. Replicates: ATG12-knockout (n=5), ATG12 floxed (Control, n=6)

first: Hugo

last: Gonzalez

first: Zena

last: Werb

first: Jayanta

last: Debnath


title: A stem cell-driven lymphoangiogenic switch (scRNA-seq)

first: Hanseul

last: Yang

address: 1230 York Avenue

institute: Rockefeller University

summary: Tissues rely on stem cells (SCs) for homeostasis and wound-repair. SCs reside in specialized microenvironments (niches) whose complexities and roles in orchestrating tissue growth are still unfolding. Here, we identify lymphatic capillaries as critical SC niche components. In skin, lymphatics form intimate networks around the SCs of each hair follicle (HF) during their non-regenerative phase, and remodel upon regeneration. Seeking understanding, we unravel a secretome switch within SCs that controls lymphatic behavior. Resting SCs express Angiopoietin-like 7 (Angptl7), promoting lymphatic drainage. Upon activation, SCs trigger an anti-lympho-angiogenic program, transiently sparking lymphatic dilation and dampened drainage. In mammals, this dynamic aria between SCs and lymphatics is essential for coordinating HFSC behavior and hair regeneration: Upon either depleting lymphatics, silencing Angptl7 or super-activating anti-lympho-angiogenesis, SCs precociously proliferate and HF regeneration becomes asynchronous. In unearthing lymphatic capillaries as a hitherto under-appreciated SC-niche element, we’ve learned how SCs coordinate their activity across a tissue.

overall_design:
Mouse bulge hair follicle stem cells at the early hair cycle were FACS-purified for single cell RNA-seq analysis.

Mouse lymphatic endothelial cells at the telogen and early anagen were FACS-purified for single cell RNA-seq analysis.

first: Shiri

last: Gur-Cohen

first: Elaine

last: Fuchs


title: Increased intron retention is a post-transcriptional signature associated with progressive ageing and Alzheimer’s disease

city: Singapore

first: Swarnaseetha

last: Adusumalli

address: 1 Research Link,  National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: Intron retention (IR) may affect gene expression and protein functions during development and age-onset diseases. However, it remains unclear if IR undergoes spatial or temporal changes during different stages of ageing or neurodegenerative disorders like Alzheimer’s disease (AD). By profiling mRNA species across different ages of Drosophila heads, we observed significant increase in the level of IR of many conserved genes as animals aged. Interestingly, distinct sets of genes are affected at different stages of adult fly life with IR occurring at several AD-associated genes in old adult. This suggests that alteration of proper protein functions by IR during ageing may lead to AD pathogenesis.  Consistent with this notion, analyses of healthy human ageing brains and different AD datasets revealed similar increased aberrant IR activities in many AD-curated genes. Taken together, our data suggest that increase IR during ageing may be the driver for late-onset sporadic AD.

overall_design: Examination the transcriptome (by RNA-sequencing) of Drosophila heads isolated at day 10, 20, 30 and 50 of adult life.

first: Chin-Tong

last: Ong


title: High-throughput RNAi screening for genes essential for senecent cell viability

status: Public on Feb 18 2020

city: Minato-ku

first: Yoshikazu

last: Johmura

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

summary: We carried out the analysis using human skin fibroblast HCA2 (MJ90) cells. Cells were induced to be senescent cells by treatment with nutlin3a + RO3306. The cells were infected with lentiviruses enocoding shRNA against human genes (DECIPHER Human Modules 1-3). As a result, we found some gene candidates involved in senecent cell viability.

overall_design: shRNA library sceening of senescent HCA2 cells induced by nutlin3a + RO3306.

first: Makoto

last: Nakanishi


title: Intergrated epigenetics, transcriptomics and metabolomics to analyze the mechanism of Benzo[a]pyrene neurotoxicity in hippocampus

status: Public on Feb 21 2020

city: Chongqing

first: Jing

last: Wang

address: Yuzhong District Petroleum Road on the 1st

country: China

institute: Chongqing Medical University

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The aim of the study was to investigate the global effect of B[a]P on DNA methylation, non-coding RNAs (ncRNAs) and coding RNAs expression in the rat hippocampus.
Methods: High-throughput sequencing was applied to assess hippocampus DNA methylation, ncRNAs and coding RNAs expression.
Results: Exposure to B[a]P could influence the levels of DNA methylation, and the expression profiles of ncRNAs and mRNAs in rats.
Conclusions: B[a]P could bring on the epigenetics changes as well as the transcriptomics changes and further affected gene expression.

overall_design: B[a]P was dissolved in corn oil. The B[a]P-treated rat was administered by oral gavage each day in a dose of 2.0mg/kg B[a]P and the control rat was also administered by oral gavage but with equivalent volume of corn oil. Then high-throughput sequencing was performed for B[a]P-treated and  control rat hippocampal.

first: Chunlin

last: Li


title: Circular RNA expression profiles in human abdominal aortic aneurysm

city: Shanghai

first: Weiguo

last: Fu

address: 180 Fenglin Road

department: Department of Vascular Surgery

institute: Zhongshan Hospital Fudan University

summary: We have employed circRNA microarray expression profiling as a discovery platform to identify the dysregulated circRNAs in human abdominal aortic aneurysm.

overall_design: In this study, full thickness abdominal aortic aneurysm (AAA) specimens were collected from 4 patients with AAA. Over the same period, abdominal aortic samples just below the aortic trunk from 4 heart-beating brain-dead organ donors were used as the controls.

first: Zhenyu

last: Shi


title: Distinct peripheral blood molecular signature emerges with successful tacrolimus withdraw in kidney transplant recipients

first: Miguel

last: Fribourg

address: 1 Gustave Levy Pl

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Tacrolimus (Tac) is an effective anti-rejection agent in kidney transplantation, but its off-target effects make withdrawal desirable. While studies indicate that Tac can be safely withdrawn in a subset of kidney transplant recipients, immune mechanisms that underlie successful vs. unsuccessful Tac removal are unknown. We performed microarray analyses of PBMC RNA from subjects enrolled in the Clinical Trials in Organ Transplantation-09 study in which stable kidney transplant recipients were randomized to Tac withdrawal or maintenance of standard immunosuppression beginning 6-mo post-transplant. Eight of 14 subjects attempted but failed withdrawal, while six developed stable graft function for ≥2 years on mycophenolate mofetil plus prednisone. Whereas failed withdrawal upregulated immune activation genes, successful Tac withdrawal was associated with a distinct, T cell-specific, downregulatory, and pro-apoptotic gene program. Functional analyses suggested stronger donor-reactive immunity in subjects who failed withdrawal without evidence of regulatory T cell dysfunction. Together, our data suggest that successful Tac withdrawal can unleash an active, protective pro-apoptotic T cell program, and provide the foundation for developing strategies to promote this protective immunological phenotype in kidney transplant recipients.

overall_design: Samples of PBMCs obtained from patients 6 months post kidney transplant randomized to no withdrawal (N=4) and Tac withdrawal (N=14), and 3 months post Tac withdrawal when tapering was completed. See PMID: 25925687 for more references.

first: Paolo

last: Cravedi

first: Peter

middle: S

last: Heeger


title: Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [RNA-seq]

first: Yilong

last: Zhang

address: No.800 Xiangying road, Yangpu Dirtrict, Shanghai, China.

department: Department of Tropical diseases,

institute: Second Military Medical University, Shanghai, China.

summary: We performed RNA-Seq analysis with synchronized 0-6h ring stage parasites of three P.falciparum lines within their third life cycle, to study the change of expression profiling when knocking down PfSWIB. The comparison analysis on screening of differentially expressed genes was done in parasite lines including 3D7(wild type: blank control), PfSWIB (wild type: self-control) and PfSWIB∆ (PfSWIB knockdown). Approximately 10.8% of the transcripts showed up-regulation between the PfSWIB-KD and two WT parasite, whereas 11.9% showed down-regulation (Fold change>1.5, P<0.05). Hierarchical clustering of differentially expressed genes uncovered several transcription factors such as PfApiAP2 family and PfSir2B, as well as certain histone modification enzymes, which proved to be involved in regulating on var gene transcription. We further screened out a number of var genes which exhibited differential expression among different lines, and performed qPCR on 44 diﬀerentially expressed vars in the PfSWIB vs PfSWIB∆ comparison group based on the RNA-seq results, to study the transcription patterns of upsA-, upsB- and upsC-subtype var genes. We found that most upsA- and upsC- type vars were significant down-regulated in PfSWIB∆ line. In contrast, the expression pattern of partial upsB vars presented a distinct change in PfSWIB∆ line. The RNA-seq and qPCR analysis provide a better understanding of the mechanism and function of PfSWIB on regulating the expression switching and clonal variation of var gene family contributing to the pathogenesis in malaria parasites.

overall_design: Examination of gene expression changes in 3 P.falciparum parasite lines including 3D7(wide type), PfSWIB(self-control) and PfSWIB∆(knock down).

first: Weifeng


title: RNAseq of mitral valves from Fbn1 mutant and control mice at 5 months

status: Public on Feb 27 2020

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

summary: Gene expression profiling of mitral valves of the Marfan Syndrome Fibrillin1 C1039G heterozygous mice compared to wildtype controls

overall_design: Cardiac mitral valves were dissected from Fbn1C1039G heterozygous mice and WT mice at 5 months of age.  Eight valves per group were pooled for RNA extraction.

first: Andrew

last: Kim

first: Alexia

last: Hulin


title: Identification of differentially-expressed circular RNAs in early osteogenic and chondrogenic differentiation of human bone marrow-mesenchymal stromal cells (hMSCs)

city: Davos Platz

first: Martin

last: Stoddart

address: Clavadelerstrasse 8

country: Switzerland

institute: AO Research Institute Davos

summary: The aim of this study was to identify non-coding RNA that were differentially expressed 7 days after induction of osteogenic or chondrogenic differentiation in human bone marrow-mesenchymal stromal cells (MSCs).

overall_design: Human MSCs were induced to osteogenic differentiation in monolayer (DMEM-LG, 10%FBS, 1%P/S, 50 µg/mL ascorbic acid 2-phosphate, 5 mM β-glycerol phosphate and 10 nM dexamethasone). Chondrogenic differentiation was induced in pellet culture using DMEM-HG, 1%P/S, 1% ITS+, 1% NEAA, 50 µg/mL ascorbic acid 2-phosphate, 100 nM dexamethasone, and 10 ng/ml TGF-β1. Media were refreshed every second day. At day 7, samples were collected in triplicate for each donor (n=3 donors) for RNA extraction. 2 samples for each condition and each donor were selected for microarray analysis.

first: Elena

last: Della Bella


title: Screening of differentially expressed genes in three Plasmodium falciparum parasite lines

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

overall_design: Refer to individual Series


title: Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [expression]

summary: We performed Agilent chip analysis with synchronized 0-6h ring stage parasites of three P.falciparum lines within their third life cycle, to study the change of expression profiling when knocking down PfSWIB .

overall_design: Examination of gene expression changes in 3 P.falciparum parasite lines including 307G7(wide type), ACT(self-control) and ACTsh(knock down).


title: Bookmarking by “non-pioneer” transcription factors during liver development establishes competence for future gene activation

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

summary: Transcription factor binding to enhancer and promoter regions is critical for gene activation. To understand how cell-specific gene expression patterns are generated, we studied the developmental timing of association of two prominent hepatic transcription factors with gene regulatory regions. We found that most individual binding events displayed extraordinarily high temporal variations during liver development. Early and persistent binding is necessary but not sufficient for gene activation. Stable gene expression patterns are mainly generated by the combinatorial activity of multiple transcription factors, which mark regulatory regions long before activation and promote progressive broadening of active chromatin domains. Both, temporally stable and dynamic binding events contribute to the developmental maturation of active promoter configurations. The results reveal a developmental “bookmarking” function of transcription factors, and illuminate remarkable parallels between the principles employed for gene activation during development, evolution and upon mitotic exit.

overall_design: Chromatin immunoprecipitation assays were performed in formaldehyde-crosslinked mouse liver extracts using antibodies recognizing C/ABPa or HNF4a or RNA-Polymerase-II. The extracts were prepared from mouse embryonic day 15.5, 18.5, newborn, postnatal day 14 and postnatal day 60. Each ChIP-seq assay were performed with 2 biological replicates. mRNAs for RNA-seq analyses were prepared from E18.5 livers of wild type (WT) or CEBPalox/lox-Alfp-Cre or HNF4lox/lox-Alfp-Cre mice.

first: Panagiota

last: Karagianni

first: Panagiotis

last: Moulos

first: Dominique

last: Schmidt

first: Duncan

last: Odom


title: A specific prelimbic-nucleus accumbens pathway controls resilience versus vulnerability to develop food addiction.

city: Mainz

first: Prof. Beat

last: Lutz

state: Rheinland

address: Duesbergweg 6

department: Institute of Physiological Chemistry

country: Germany

institute: University Medical Center of the Johannes Gutenberg University Mainz

summary: The aim of this study was to analyse the whole transcriptome profile of medial prefrontal cortex of food addicted and non-addicted Glu-CB1-WT and Glu-CB1-KO mice using total RNA-seq.

overall_design: mPFC RNA was isolated of food addicted and non-addicted Glu-CB1-WT and Glu-CB1-KO mice, total RNA was rRNA depleted, and RNA sequencing was done on a Illumina NextSeq 500 sequencer.

first: L

last: Domingo-Rodriguez

first: I

last: Ruiz de Azua

first: E

last: Dominguez

last: Senabre

last: Serra

first: S

last: Kummer

first: M

last: Navandar

last: Baddenhausen

first: C

last: Hofmann

first: R

last: Andero

last: Gerber

last: Navarrete

last: Dierssen

first: B

last: Martín-García

last: Maldonado


title: Transcriptomics de novo analysis of Chinese Narcissus tazetta var. chinensis cv Jinzhanyintai for its floral scent

city: Zhangzhou

first: Yansen

last: He

state: Fujian

address: No.1499 Jiulong Avenue

summary: Chinese narcissus is well-known monocot plants with beautiful color, fresh and sweet floral scent. A lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms of narcissus floral scent volatiles biosynthesis. Hence, we hypothesized the functions of the significant differentially expressed genes (DEGs) identified using Illumina RNA-Seq technology, according to public protein annotation databases in this study.

overall_design: Species Jinzhanyintai of narcissus were grown in the experimental plantation of Institute of Subtropical Agriculture, Fujian Academy of Agricultural Sciences, China. Narcissus petal and corolla tissues of samples were collected at the first day of the early flowering stage (Day1) and the seventh day of the full-bloom stage (Day7) . Two petal samples (Day 1 and Day 7 stage, also short for P1 and P7) and two corolla samples (Day 1 and Day 7 stage, also short for C1 and C7) were used for transcriptional sequencing. Each sample contained two biological repeats. After collected from the plantation, sample tissues were frozen with liquid nitrogen and stored at -80°C for using. Subsequently, the eight sample tissues were entrusted to Beijing Biomarker Company (Beijing, China) for RNA extraction, cDNA libraries construction, transcriptome de novo assembly and sequencing using an Illumina HiSeq system. We named the samples as following - T01: Corolla of the early flowering stage on the first day- repeat sample 1; T02: Corolla of the early flowering stage on the first day- repeat sample 2; T05: Corolla of the full-bloom stage on the seventh day- repeat sample 1; T06: Corolla of the full-bloom stage on the seventh day- repeat sample 2; T03: Petal of the early flowering stage on the first day- repeat sample 1; T04: Petal of the early flowering stage on the first day- repeat sample 2; T07: Petal of the full-bloom stage on the seventh day- repeat sample 1; T08: Petal of the full-bloom stage on the seventh day- repeat sample 2. In this article, we mainly analyzed the genes expressed in corolla at the first day versus the seventh day (T01_02 VS T05_T06), and the genes in petal at the first day versus the seventh day (T03_04 VS T07_T08).

first: Min

last: Xu

first: Xiaojing

last: Chen


title: Identification of differentially-expressed miRNAs in early osteogenic and chondrogenic differentiation of human bone marrow-mesenchymal stromal cells (hMSCs)

first: Martin

last: Stoddart

overall_design: Human MSCs were induced to osteogenic differentiation in monolayer (DMEM-LG, 10%FBS, 1%P/S, 50 µg/mL ascorbic acid 2-phosphate, 5 mM β-glycerol phosphate and 10 nM dexamethasone). Chondrogenic differentiation was induced in pellet culture using DMEM-HG, 1%P/S, 1% ITS+, 1% NEAA, 50 µg/mL ascorbic acid 2-phosphate, 100 nM dexamethasone, and 10 ng/ml TGF-β1. Media were refreshed every second day. At day 7, samples were collected in triplicate for each donor (n=3 donors) for RNA extraction. 2 samples for each condition and each donor were selected for RNAseq analysis.

first: Elena

last: Della Bella


title: Simple differentiation method using FBS identifies DUSP6 as a marker for fine-tuning of FGF-ERK signaling activity in human pluripotent stem cells

city: Cheongju

first: Yong-Ou

last: Kim

state: Chungchung buk do

address: Osongsangmyeong 2ro

country: South Korea

institute: Korea National Institute of Health

summary: Assessment of differentiation potential is a basic requirement to obtain qualified human pluripotent stem cells (hPSCs). Here, we report a simple differentiation method using fetal bovine serum (FBS) to estimate differentiation potential and propensity of hPSCs. PluriTest using RNA-sequencing showed that cells differentiated after treatment with 5% FBS. Expression patterns of three germ layer markers revealed that cells cultured in Knockout Serum Replacement-containing medium (KSR) with mouse feeder cells had higher differentiation potential than cells cultured in a chemically defined medium (E8) with recombinant matrix proteins, especially into the mesoderm and endoderm lineages. Analysis of differentially expressed genes between KSR and E8 identified DUSP6 as a marker for where cells had been cultured. Expression of DUSP6 correlated with FGF-ERK signaling activity. Fine-tuning of FGF-ERK signaling activity to a range that can shut down DUSP6 transcription but sustain NANOG transcription partially increased the differentiation potential. Our data suggest that differentiation with 5% FBS is good to estimate differentiation potential and propensity at the early stage, and that DUSP6 is an excellent marker to monitor ERK signaling activity.

overall_design: Two biological replicates were analyzed for each point of differentiation of human pluripotent stem cells cultured in two widely used media. For differentiation with 5% FBS, hFSiPS1 cells were cultured KSR and E8 media for 3 weeks and differentiated with 5% FBS. Cells were harvested after 1, 2, 3 weeks. For culture media, hPSCs, hFSiPS1, hFmiPS2, SNUhES31, H9, were cultured for 13 weeks and harvested at 3 weeks and 13 weeks.

first: DaeHoon

last: Yoo

first: YoungSam

last: Im

first: EunHee

last: Jo

first: BoYoung

first: HyeYoung

first: Mi-Hyun

last: Park

first: SooKyung

last: Koo


title: Identification of differentially-expressed piRNAs in early osteogenic and chondrogenic differentiation of human bone marrow-mesenchymal stromal cells (hMSCs)


title: Expression data from mouse bladder tissues

city: Los Angeles

first: Hideki

last: Furuya

address: 110 N. George Burns Road, Davis 2025

department: Surgery

institute: Cedars Sinai Medical Center

summary:
PAI-1 is considered as an oncogenic protein. However, PAI-1 deficiency didn’t stop tumor development in animal cancer models. Thus, it is suggested that there may be compensatory pathway that support tumor growth in the absence of PAI-1.
We used microarrays to detail the global  gene expression  and identified differentially genes between genotypes and treatment.

overall_design: We selected mouse bladder tissues isolated from mouse at week 20. There are four groups in this study, including wild type mice treated with/without BBN (bladder carcinogen) and PAI-1 KO mice with/without BBN.

first: Charles

last: Rosser


title: DNMT3B has oncogenic activity but evidence suggests that it does not promote CIMP nor cooperate with activated BRAFV600E in human intestinal cancer. (RNA-Seq)

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

summary: Approximately 10% of human colorectal cancer (CRC) are associated with activated BRAFV600E mutation, typically in absence of APC mutation and often associated with a CpG Island Methylator Phenotype (CIMP) phenotype. To protect from cancer, normal intestinal epithelial cells are thought to respond to oncogenic BRAFV600E by activation of intrinsic p53 and p16-dependent tumor suppressor mechanisms, such as cellular senescence. Conversely, CIMP is thought to contribute to bypass of these tumor suppressor mechanisms, e.g. via epigenetic silencing of tumor suppressor genes, such as p16. It has been repeatedly proposed that DNMT3B is responsible for BRAFV600E-induced CIMP in human CRC. Here we set out to test this by multiple approaches. By analysis of human TCGA data, we confirmed that expression of DNMT3B is frequently upregulated in CRC and this is often linked to amplification of the DNMT3B gene. In vitro, we found that ectopic expression of DNMT3B antagonizes BRAFV600E-induced proliferation arrest and inflammatory gene expression, two hallmarks of the tumor suppressive senescence program triggered by oncogenes in primary cells. Moreover, DNMT3B over expression decreased survival in a mouse model of BRAFV600E-induced intestinal cancer. However, in primary human cells in vitro, activated BRAFV600E repressed expression of DNMT3B and failed to induce a CIMP phenotype. Finally, a closer analysis of human TCGA data revealed that BRAFV600E mutations and CIMP are both linked to a low expression of DNMT3B. We conclude that while both BRAFV600E and DNMT3B both harbor oncogenic potential in vitro and in vivo and show some evidence of cooperation in tumour promotion, they do not frequently cooperate to promote CIMP and human intestinal cancer.

overall_design: Expression profiling by high-throughput sequencing of BRAF oncogene induced senescent fibroblasts with/without ectopically expressed DNMT3B with relevant controls.

first: Douglas

last: MacKenzie

first: Catrin

last: Pritchard

first: Karen

last: Blyth

first: Peter

middle: D

last: Adams


title: Identification of differentially-expressed miRNA, piRNA and circRNA in early osteogenic and chondrogenic differentiation of human bone marrow-mesenchymal stromal cells (hMSCs)

first: Martin


title: Next Generation Sequencing unveils the difference between human TR3-56 cells from healthy and T1D subjects

city: Naples

first: Mario

last: Galgani

address: via S. Pansini, 5

country: Italy

institute: IEOS Istituto per l'endocrinologia e l'oncologia sperimentale

summary:
Purpose: The goal of this study was the transcriptome high-throughput data analysis of TR3-56 cells isolated from peripheral blood of healthy and T1D subjects
Methods:  total RNA profile of  human TR3-56 cells from healthy and T1D subjects (1. Healthy Subject, 2.Healthy Subject, 3.Healthy Subject; 4. T1D subject, 5. T1D subject, 6. T1D subject; deeep sequencing, using Ovation SoLo RNA-seq Library Preparation KIt (NuGen), Library were prepared for sequencing on NextSeq 500 (llumina technology)
Results: Principal component analysis and unsupervised clustering showed that TR3-56 cells from healthy donors are transcriptionally different from TR3-56 cells isolated from T1D subjects.
Conclusions: Several genes are differently regulated between TR3-56 cells from T1D and healthy donors.

overall_design: TR3-56 cell mRNA profiles of 3 healthy subjects and 3 T1D subjects were generated by deep sequencing, using Illumina platform.


title: Granulins Regulate Aging Kinetics in the Adult Zebrafish Telencephalon

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

state: Bayern

address: Großhaderner Straße 9

department: Department for Cell Biology

institute: LMU München

summary: Granulins (GRN) are secreted factors that promote neuronal survival and regulate inflammation in various pathological conditions. However, their roles in physiological conditions in the brain remain poorly understood. To address this knowledge gap, we analysed the telencephalon in Grn-deficient zebrafish and identified morphological and transcriptional changes in microglial cells, indicative of a pro-inflammatory phenotype in the absence of any insult. Unexpectedly, activated mutant microglia shared part of their transcriptional signature with aged human microglia. Furthermore, transcriptome profiles of the entire telencephali isolated from young Grn-deficient animals showed remarkable similarities with the profiles of the telencephali isolated from aged wildtype animals. Additionally, 50% of differentially regulated genes during aging were regulated in the telencephalon of young Grn-deficient animals compared to their wildtype littermates. Importantly, the telencephalon transcriptome in young Grn-deficent animals changed only mildly with aging, further suggesting premature aging of Grn-deficient brain. Indeed, Grn loss led to decreased neurogenesis and oligodendrogenesis, and to shortening of telomeres at young ages, to an extent comparable to that observed during aging. Altogether, our data demonstrate a role of Grn in regulating aging kinetics in the zebrafish telencephalon, thus providing a valuable tool for the development of new therapeutic approaches to treat age-associated pathologies.

overall_design: Telencephalic mRNA profiles from young (5 months) and old (18 months) wildtype and grna-/-;grnb-/- were generated by deep sequencing and 5 samples per conditions were analysed. Additionally, mRNA profiles from young wildtype and grna-/-;grnb-/- microglial and oligodendroglial cells, isolated through FACS, were also generated by deep sequencing and 3/4 samples per condition were analysed.

first: Alessandro

last: Zambusi


title: Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder

city: São Paulo

first: Karina

middle: Griesi

last: Oliveira

state: SP

address: Rua Brentano, 292, Ap. 61

country: Brazil

institute: Hospital Albert Einstein

summary: Evaluation of expression profile in autism spectrum disorder (ASD) patients is an important approach to understand possible similar functional consequences that may underlie disease pathophysiology regardless of its genetic heterogeneity. Induced pluripotent stem cell (iPSC)-derived neuronal models have been useful to explore this question. Using RNAseq, we examined the transcriptome of iPSC-derived Neuronal Progenitor Cells (NPC) and neurons from a normocephalic ASD cohort composed mostly of high functioning individuals and from non-ASD individuals. ASD patients presented expression dysregulation of a module of co-expressed genes involved in protein synthesis in NPC, and a module of genes related to synapse/neurotransmission and a module related to translation in neurons. Remarkably, the comparison of our results to a series of transcriptome studies revealed that the module related to synapse has been consistently found as upregulated in iPSC-derived neurons, while downregulated in brain samples. Therefore, the expression pattern of this network might be used as biomarker for ASD and should be experimentally explored as a therapeutic target.

overall_design: mRNA profiles obtained by RNAseq of 12 samples of iPSC-derived NPC (6 controls/6 ASD individuals; total of 29 clones) and 9 samples of iPSC-derived Neurons (4 controls/5 ASD individuals; total of 19 clones). Transcriptome analysis was performed using dream algorithm (from variationPartition package), to find the differentially expressed genes between controls and patients, and WGCNA, to find co-expressed networks of genes that were dysregulated in these cell types in ASD.

first: K

last: Griesi-Oliveira

first: B

middle: G

last: Pinto


title: CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq

city: Columbus

first: Pearlly

last: Yan

state: Ohio

department: Comprehensive Cancer Center

institute: The Ohio State University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq (mouse)

summary: Direct cDNA preamplification protocols developed for single-cell RNA-seq (scRNA-seq) have enabled transcriptome profiling of rare cells without having to pool multiple samples or to perform RNA extraction. We term this approach limiting-cell RNA-seq (lcRNA-seq). Unlike scRNA-seq, which focuses on ‘cell-atlasing’, lcRNA-seq focuses on identifying differentially expressed genes (DEGs) between experimental groups. This requires accounting for systems noise which can obscure biological differences. We present CLEAR, a workflow that identifies robust transcripts in lcRNA-seq data for between-group comparisons. To develop CLEAR, we compared DEGs from FACS-derived CD5+ and CD5- cells from a chronic lymphocytic leukemia patient at different input RNA levels. When using CLEAR transcripts vs. using all available transcripts, downstream analyses reveal more consistent DEGs, improved Principal Component Analysis separation by cell type, and consistency across input RNA amounts. CLEAR also performs well on external sc- and lcRNA-seq data and an internal murine neural cell lcRNA-seq data set.

overall_design: Dentate Gyrus (DG) regions of Nestin-GFP mice were dissociated and three cell types (Astrocyte, Progenitor, and Stem Cells) were sequenced using the Clontech SMARTer v4 kit.

first: P

first: L

last: Walker


title: DNMT3B has oncogenic activity but evidence suggests that it does not promote CIMP nor cooperate with activated BRAFV600E in human intestinal cancer.


title: DNMT3B has oncogenic activity but evidence suggests that it does not promote CIMP nor cooperate with activated BRAFV600E in human intestinal cancer. (WGBS)

overall_design: Epigenetic profiling by whole genome bisulfite sequencing of BRAF oncogene induced senescent fibroblasts with controls.


title: CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq (human)

overall_design: Total RNA from human CLL B cells was quantified using the Invitrogen Qubit RNA HS Assay kit (Invitrogen, Carlsbad, CA) and serially diluted to masses characteristic of single- and low cell number RNA-Seq (10-, 100-, and 1000-pg). The Clontech SMARTer v4 kit (Takara Bio USA, Inc., Mountain View, CA) was used for global preamplification in serially diluted CD5+/CD5- RNA prior to library generation at triplicate with the Nextera XT DNA Library Prep kit (Illumina, Inc., San Diego, CA).


title: Next Generation Sequencing of WT and DM1 mutant muscle stem cell and its differentiated cells Transcriptomes

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

summary: In order to decipher the mechanisms of DM1 disease, we generated new DM1 mouse model and found the knockout MuSCs were defects in stem cell differentiation. The gene expression of the MuSCs and its diffferented cells were determined using RNA sequencing.

overall_design: MuSCs expanded in T cell medium and differentiated for one day or two days were collected and referred to RNA extraction.

first: Jinsong

first: Qi

last: Yin


title: Developmental Genome-Wide DNA Methylation Asymmetry Between  Mouse Placenta and Embryo

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

summary: In early embryos, DNA methylation is remodelled to initiate the developmental program. For mostly unknown reasons, methylation marks are acquired unequally between embryonic and placental cells. To better understand this, we generated high-resolution maps of DNA methylation in mouse mid-gestation (E10.5) embryo and placenta. We uncovered specific subtypes of differentially methylated regions (DMRs) that contribute directly to the developmental asymmetry existing between mid-gestation embryo and placenta. We show that the asymmetry between embryonic and placental DNA methylation patterns occurs rapidly during the acquisition of marks in the post-implanted conceptus (E3.5-E6.5), and that these patterns are long-lasting across subtypes of DMRs throughout prenatal development and in somatic tissues. We reveal that at the peri-implantation stages, the de novo methyltransferase activity of DNMT3B is the main driver of methylation marks on asymmetric DMRs, and that DNMT3B can largely compensate for lack of DNMT3A in the epiblast and extraembryonic ectoderm, whereas DNMT3A can only partially palliate for the absence of DNMT3B. However, as development progresses and as DNMT3A becomes the principal de novo methyltransferase, the compensatory DNA methylation mechanism on DMRs becomes less effective.

overall_design: RRBS analyses of whole E10.5 Embryo and whole E10.5 Placenta. Included are also unpublished RRBS data on two independent Trophoblast Stem (TS) celll lines before vs after differentiation.


title: HP1gamma/Cbx3 deficiency results in reduction of H3K27me3 in mouse neurosphere neuronal genes

status: Public on Feb 17 2020

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: HP1gamma/Cbx3 is one of the components of heterochromatin and strongly expressed in  neural stem cells and neurospheres. To evaluate the functions of HP1gamma, gene expressions in wild-type and HP1gamma KO neurospheres were compared.

overall_design: Neurospheres from one embryonic brain at E14.5 were cultured as one sample. Total RNAs from quaternary neurospheres were extracted for analyses. Two or Three replicates were performed for each experiment.

first: C

last: Naruse

last: Abe

first: T

last: Yoshihara

last: Kato

first: M

last: Asano


title: Fecal metatranscriptomics from healthy adults before and after supplementation with bovine milk oligosaccharides

city: Davis

first: Samuel

middle: Taler

last: Westreich

state: CA

address: 1 Shields Ave

department: Genome Center

institute: University of California, Davis

summary: Complex oligosaccharides found in human milk play a vital role in gut microbiome development for the human infant. Bovine milk oligosaccharides (BMO) have similar structures with those derived from human milk, but have not been well studied for their effects on the healthy adult human gut microbiome. Healthy human subjects consumed BMO over two-week periods at two different doses and provided fecal samples. Metatranscriptomics of fecal samples was conducted to determine microbial and host gene expression in response to the supplement. Fecal samples were also analyzed by mass spectrometry to determine levels of undigested BMO. No changes were observed in microbiome activity across all participants. Repeated sampling enabled subject-specific analyses: four of six participants had minor, yet statistically significant, changes in microbial activity. No significant change was observed in the gene expression of host cells in stool.  Levels of BMO excreted in feces after supplementation were not significantly different from placebo and were not correlated with dosage or expressed microbial enzyme levels. Collectively, these data suggest that BMO is fully digested in the human gastrointestinal tract prior to stool collection. Participants’ gut microbiomes remained stable but varied between individuals.  Additionally, the unaltered host transcriptome provides further evidence for the safety of BMO as a dietary supplement or food ingredient.

overall_design: 6 healthy adult participants provided four fecal samples: two samples prior to any exposure to BMO (samples T1-D0 and T2-DO), one sample (T2-D11) after eleven days of consumption of low dose (25% of dietary fiber recommendation) of BMO, and then one sample (T3-D11) after eleven days of consumption of a high dose (35% of dietary fiber recommendation) of BMO.

middle: T

first: Jennifer

last: Smilowitz

first: Ian

last: Korf

first: David

last: Mills

first: Daniella

last: Barile

first: Danielle

last: Lemay


title: EBF1-mutant bone marrow stroma confers long-term changes in hematopoietic stem cell potential [HSC]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: Crosstalk between mesenchymal stromal cells (MSCs) and hematopoietic stem and cells (HSCs) is essential for hematopoietic homeostasis and lineage output. Here, we investigate the role of Early B-cell factor 1 (EBF1) in MSCs to support hematopoiesis. Ebf1-/- MSCs have reduced mesenchymal lineage potential. Ebf1 deletion in Cxcl12-abundant reticular (CAR) cells and PDGFRα+Sca1+CD45-CD31-Lin- (PαS) cells in the bone marrow decreases the numbers of HSPCs and myeloid cells. Single cell and bulk transcriptome analysis, combined with analysis of chromatin accessibility in EBF1-deficient MSCs revealed an altered niche composition and MSCs identity. In HSCs that were exposed to the EBF1-deficient niche, we detected an altered chromatin accessibility and impaired occupancy by AP-1, ETS and IRF proteins. Notably, the effects of the EBF1-deficient niche on HSPCs are retained after transfer to a wild-type niche. Thus, genetic alterations in the bone marrow niche can result in long-term changes of the chromatin landscape in HSCs.

overall_design:
RNA-Seq analysis of endogenous, primary transplanted Ebf+/+ PrxCre and Ebffl/fl PrxCre LT HSCs; ATAC-Seq analysis of endogenous, primary and secondary transplanted Ebf+/+ PrxCre and Ebffl/fl PrxCre LT HSCs.

Please note that the processed data generated from multiple samples is linked to the corresponding rep1 sample records or to the Series records.

first: Derecka

last: Marta

first: Rudolf

last: Grosschedl


title: The effect of Chickpea on gene expression during a differentiation of 3T3-L1 cells to adipocyte

city: Otsu

first: Shigeo

last: Shinohara

state: Shiga

address: 3-31-13 Saigawa

department: Nutraceuticals Division

institute: Otsuka Pharmaceutical Co., Ltd.

summary:
Chickpea was extracted with ethanol and adjusted to 70% solid content. The extracts were used as CP in the present study and diluted to 0.5% in culture medium before use.
321 metabolic-syndrome-related genes and 13 control genes were tested using the Kurabo GeneSQUARE multiple assay DNA microarray. Gene that exhibited changes in gene expressions that were more than double during 8 days of differentiation from preadypocytes to adipocytes in the control group were 31 genes. However, the gene expressions induced for the control group were significantly inhibited compared to the G group in which CP coexisted during 8 days of differentiation.

overall_design: 3T3-L1 cells were induced to adipocytes in differentiation-inducing media containing either 0.5%CP or additive-free media for 8 days. Total RNA were extracted from 3T3-L1 cells of before induction of differentiation (day0) to gene expression of 2 days after start of the differentiation (day2), 4 days later (day4), and 8 days later (day8). 321 metabolic-syndrome-related genes and 13 control genes were tested using the Kurabo GeneSQUARE multiple assay DNA microarray.

first: Hiroshi

last: Kimura


title: RNA-seq analysis of Wildtype and Prdm16 cKO ventricular zone tissue during cortex development in mouse

status: Public on Feb 16 2020

city: New York

first: Qiangqiang

last: Zhang

address: 430 East 67th St

institute: Memorial Sloan-Kettering Cancer Center

summary: Purpose: To explore the mechanisms by which PRDM16 regulates reactive oxygen species levels and oxidative stress in radial glia progenitors during cortical development in mouse.

overall_design: Ventricular tissue were isolated from three pairs of wild-type (WT) and Prdm16 cKO (conditional knockout) mutant E11.5, E13.5, E15.5, and E17.5 embryos. RNA was isolated using Qiagen RNeasy Micro Kit (QIAGEN). After RiboGreen quantification and quality control by Agilent BioAnalyzer, 125-150ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102). Samples were barcoded and ran on the HiSeq 4000 platform, using the HiSeq 3000/4000 SBS Kit (Illumina).

first: Angela

last: Chui

first: Songhai

last: Shi


title: Genome-wide maps of chromatin state for LAG-1 in whole animals

city: St. Louis

first: Jian

last: Chen

state: MO

address: 4523 Clayton Ave.

department: Genetics

institute: Washington University School of Medicine

summary: We report the application of conventional ChIP-seq analysis for LAG-1 chromatin state in whole animals. We identified 76 genes putatively regulated by LAG-1 that's overlapped by two independent antibodies (FLAG ab and GFP ab). These genes including previously known targets lst-1, sygl-1, and mir-61/250, supporting the success of the assay.

overall_design: Two independent antibodies are used for ChIP (FLAG ab and GFP ab); total of three biological replicates (two from GFP ab and one from FLAG ab) are used to compare to input DNA; ChIP-seq peaks are called by MACS2.0 with fold enrichment (IP / input) greater than 2.0 and False discovery rate less than 0.05.

first: Chen

last: Jian

first: Schedl

last: Tim


title: Next Generation Sequencing for Transcriptomes Analysis in GLP-1 Notch receptor ON and OFF genetic background

summary:
Purpose: Ultilize the Next Generation Sequencing to determine the genes that are activated or repressed by GLP-1 Notch receptor in C. elegans germline. The list of genes generated from RNA-seq were intersected with the LAG-1 germline ChIP-seq data to identify direct transcriptional targets of the GLP-1/LAG-1 transcriptional complex in C. elegans germline stem cells.
Methods: RNA isolated from hand dissected C. elegans germline tumor (one day old adult animals) are used for RNA-seq library.
Results: 94 genes were identified as activated by GLP-1 Notch receptor from 5 biological replicates with the following criteria: gene counts per million greater than 2.0; fold of change greater than 2.0; false discovery rate (FDR) <0.05.
Conclusions: lst-1 and sygl-1, two previously reported genes, were identified as direct transcriptional target for GLP-1/LAG-1 in C. elegans germline stem cells.

overall_design: Ribo-depleted RNA-seq libraries are prepared with five biological replicates.


title: Next Generation Sequencing for Transcriptomes Analysis for LAG-1 time course by auxin treatment.

summary:
Purpose: Ultilize Next Generation Sequencing to identify genes that are activated or repressed by LAG-1 (following auxin treatment to specifically deplete LAG-1 in C. elegans germline). The list of genes generated from RNA-seq identify primary and secondary targets of LAG-1 in C. elegans germline stem cells.
Methods: RNA isolated from hand dissected C. elegans germline tumor (one day old adult animals) were used for RNA-seq library.
Results: two genes (lst-1 and sygl-1) were identified as primary target for LAG-1 (2 hours auxin treatment); five additional genes are identified as secondary targets of LAG-1 based on their RNA accumulation depend on primary targets lst-1 and sygl-1 activity (4 hours auxin treatment). 94 genes are identified to be activated by LAG-1 (48 hours auxin treatment) from 4 biological replicates with the following criteria: gene counts per million greater than 2.0; fold of change greater than 2.0; false discovery rate (FDR) <0.05.
Conclusions: lst-1 and sygl-1, two previously reported genes, are identified as primary transcriptional target for LAG-1 in C. elegans germline stem cells.

overall_design: Ribo-depleted RNA-seq libraries are prepared with four biological replicates


title: Comparative Transcriptome analysis of hESCs- and iPSCs-derived Corneal Endothelial Cells

city: Baltimore

first: S. Amer

last: Riazuddin

state: Maryland

address: 600 N. Wolfe St

institute: Johns Hopkins University School of Medicine

summary:
Purpose: We previously reported the generation of corneal endothelial cells (CECs) using the human peripheral blood mononuclear cells (PBMC)-originated induced pluripotent stem cells (iPSCs). Herein, we extend our analysis through RNA-Seq based transcriptome profiling of H9 human embryonic stem cells (hESCs)- and iPSCs-derived CECs.
Methods:  The PBMC obtained from a healthy donor were subjected to generate iPSCs using Sendai-virus delivery system Cytotune 2.0 whereas the H9 hESCs were obtained commercially. Both hESCs and iPSCs were subjected to the 20-day procedure according to our previously published CECs generation method. The differentiated CECs were characterized by immunocytochemistry.  Total RNA from hESCs- and iPSCs-derived CECs was used for the preparation of RNA-Seq libraries, which were sequenced on HiSeq 2500 system. The raw RNA-Seq reads were processed and analyzed using Lasergene Genomics Suite and the expression profiles were examined for differential expression using Spotfire DecisionSite with Functional Genomics.
Results: The hESCs and iPSCs were differentiated into CECs through multipotent neural crest cells (NCCs) using a 20-day procedure. The differentiating CECs on day 20 (D20) exhibited a tightly packed hexagonal/polygonal shape, which expressed CECs-associated markers, zona occludens-1 and N-cadherin at the cell boundaries. A total of 180.18, and 179.01 million reads were obtained for hESCs- and iPSCs-derived CECs, respectively. Of these, >97% reads aligned to the human reference genome resulting in >250x sequence coverage for both hESCs- and iPSCs-derived CECs. Additional analysis identified expression (≥ 0.659 RPKM) of 13,561 and 13,551 genes in hESCs- and iPSCs-derived CECs, respectively, representing ~68% of the total human protein-coding transcriptome expressed in these CECs. Finally, a comparative analysis of both hESCs- and iPSCs-derived CECs transcriptomes identified >95% similarity at the gene level.
Conclusion: These analyses reveal an overall similar transcriptional profile in both hESCs- and iPSCs-derived CECs.

overall_design: The hESCs and iPSCs were differentiated into CECs through multipotent neural crest cells (NCCs) using a 20-day procedure. Subsequently, RNA-Seq based whole transcriptome profiling was performed for a comparitive analysis of hESCs and iPSCs-derived CECs.

first: Muhammad

last: Ali

first: Shahid

middle: Y

last: Khan

first: C

last: Talbot

first: John

last: Gottsch

first: S


title: Determining genetic stability in Clostridium tetani vaccine strains

status: Public on Feb 15 2020

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

summary: To develop a method for improved assessment of the genetic stability of bacterial vaccine strains, we applied next-generation sequencing to a Clostridium tetani model strain (including inter- and intra-lab replicates) and other strains. Data were processed to determine (gain or loss of) gene copy numbers. Strains could easily be distiguished based on gain/loss of prophage-like and CRISPR/Cas genes. We found that the model strain has multiple copies of the plasmid carrying the gene coding for tetanus toxin as well as several other genes. Data were reproducible within and between laboratories. The limit of detection of our method is an order of magnitude better than that of the pulsed-field gel electrophoresis (PFGE) currently used during manufacturing. This approach may part of an approach to reduce animal testing during vaccine manufacturing.

overall_design: 14 samples,including the model A strain and three other strains, with inter- and intra-laboratory replicates for the model strain.


title: Single-cell RNA sequencing in human retinal degeneration reveals distinct glial cell populations.

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

summary:
Purpose: The goals of this study were to identify cell specific expression patterns from a donor with a presumed diagnosis of autoimmune retinopathy (AIR). A particular focus of this study was to identify expression signatures of Müller glia and astrocytes in AIR.
Methods: Independent libraries were prepared for foveal and peripheral retina from five human donors in two experiments. Foveal and peripheral samples in donors 1-3 were acquired, analyzed, and uploaded in a previous experiment (GSE130636). In donors 4-5, new reads were acquired from a 2-mm fovea-centered punch and an 8-mm peripheral punch from the inferotemporal region in each donor. Donor 4 had no documented history of retinal disease. Donor 5 was followed for 19 years at the University of Iowa Hospitals and Clinics for progressive visual field loss and pigmentary changes and was given a presumptive diagnosis of autoimmune retinopathy. Foveal and peripheral retinal tissue were gently dissociated in papain for 1.25 hours before cryopreservation. In both experiments, libraries were sequenced on a HiSeq4000. Sequenced reads were mapped to the human genome build hg19 with CellRanger(v3.0.1) and filtered to remove cells likely to be doublets or cells with a high proportion of mitochondrial reads. Libraries from all five donors were aggregated to the same effective sequencing depth, and log-normalization of aggregated reads was performed with Seurat (v2.3.4) using a scale factor of 10,000.
Results: A total of 23,429 cells were recovered after filtering with 117,885,744 corresponding reads. A total of 9,801 cells were recovered from the fovea while 13,628 cells were recovered from the periphery. A total of 7,189 cells were recovered from the donor with presumed AIR. In total, 23 clusters were identified and corresponded to all retinal cell types. The proportion of recovered cells was compared between the control (donors 1-4) and AIR (donor 5) patients. In addition, differential expression analysis identified genes enriched in each population of cells originating from the AIR donor. Particular emphasis was given to the expression profiles of glial cells (Müller cells and astrocytes) that originated from the AIR donor.
Conclusions: This study provides a complementary clinical and molecular interrogation of the retina in a blinding inflammatory condition. Glial cells from the AIR donor were enriched in genes implicated in reactive gliosis, including ANXA1. Clinical, histologic, and transcriptomic evidence identify the loss of cone and rod photoreceptor cells with relative preservation of inner retinal cell types.

overall_design: mRNA profiles for thousands of cells from foveal and peripheral retinal isolates were generated from five human donor eyes using 10X Genomics Chromium single-cell system followed by sequencing on an Illumina HiSeq 4000.

first: Robert

last: Mullins

first: Edwin

middle: M

last: Stone


title: Histone methylation profiles of H3K4me3, H3K27me3, H3K9me3, and H3R8me2a in WT and mdig/mina53 KO BEAS-2B cells

city: Detroit

first: Fei

state: Michigan

address: 259 Mack Ave.

department: Pharmaceutical Sciences

institute: Wayne State University

summary: The mineral dust-induced gene (mdig) is overexpressed in a number of human cancers, suggesting critical roles of this gene played on the pathogenesis of cancers. Unlike several other JmjC-domain containing proteins that exhibit histone demethylase activity, it remains enigmatic whether mdig is involved in the demethylation processes of the histone proteins. To provide direct evidence suggesting contribution of mdig to the demethylation of histone proteins, we report the global histone methylation profile of H3K4me3, H3K27me3, H3K9me3, and H3R8me2a in human bronchial epithelial BEAS-2B cells with mina53/mdig knockout. ChIP-seq revealed a pronounced increase of the repressive histone trimethylation with mdig depletion, including H3K9me3 and H3K27me3. Data from both ChIP-seq and RNA-seq suggested that genetic disruption of mdig enriches repressive histone trimethylation and inhibits expression of target genes in the oncogenic pathways of cell growth, stemness of the cells, tissue fibrosis, and cell motility. Our study provides the first insight into the molecular effects of mdig as an antagonist for repressive histone methylation markers and suggests that targeting mdig may represent a new area to explore in cancer therapy.

overall_design: Examination of 4 different histone modifications in WT and mdig KO cells.

first: Qian


title: RNA-seq and DNA methylation and hydroxymethylation profiles in sensitive and treatment-resistant cancer cell lines

city: Leuven

first: Diether

last: Lambrechts

address: Herestraat 49

department: Human Genetics

country: Belgium

institute: KU Leuven

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

overall_design: Refer to individual Series


title: RNA sequencing after HOPX knockdown in human squamous cell carcinoma cell line SCC13

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

institute: Swiss Institute of Bioinformatics

summary: Cutaneous squamous cell carcinomas (cSCC) are frequent heterogeneous tumours, arising from sun-exposed regions of the skin and characterized by complex pathogenesis. The goals of this study are to investigate the precise role of HOPX in cutaneous SCC development and progression using different approaches, including RNA sequencing analysis in order to find differently expressed genes and signaling pathways altered after HOPX knockdown in cancer cells.

overall_design: RNA sequencing was performed after HOPX-knockdown on control-, shRNA1-, and shRNA2- infected human squamous cell carcinoma cell line SCC13 to assess global expression patterns and identify genes differently expressed between knockdown et control conditions.

first: Olesya

last: Pavlova

first: Karine

last: Lefort

first: Marcel

last: Huber

first: Daniel

last: Hohl

first: Sandra

last: Calderon


title: MicroRNA-202 is a gatekeeper of meiosis initiation and regulates recombination in male germ line

city: Beijing

first: Xiwen

last: Lin

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology,CAS

summary: We preformed RNA sequencing to identify differentiatially expressed mRNAs after miR-202 knockout in isolated spermatogonia and spermatocytes, and cultured spermatogonial stem cells from male mice.

overall_design: Both wildtype and knockout in each cell type were used for RNA sequencing. At least two biological replicates were included in each group.

first: Jian

last: Chen

first: Chunsheng

last: Han


title: RNA sequencing data of paired parental and therapy resistant cancer cell lines transfected with negative control siRNA's or a pool of siRNA's targeting  DNMT1, DNMT3A and DNMT3B

summary: RNA sequencing data of paired parental and therapy resistant cancer cell lines. Parental cell lines are mostly established cell lines. Resistant cell lines were obtained through long term exposure of the parental cells to gradually increasing doses of cancer therapies. Samples include 7 parental and 10 derived resistant cell lines. Our aim was to assess whether the resistant cells had undergone Epithelial to Mesenchymal Transition upon resistance acquisition and whether EMT disappears upon knock down of the DNMTs

overall_design: RNA from in total 12 samples (3 parental cell lines, 3 derived resistant cell lines, each transfected with control siRNA's or siRNAs targeting the DNMTs) processed according to standard Illumina protocols.

first: Eva

last: Galle


title: ZGLP1 is a determinant for the oogenic fate in mice (RNA-seq)

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Mammalian sexual reproduction relies on the dichotomy of male and female germ cell development. However, the underlying mechanisms remain unclear. Here, we show that ZGLP1, a conserved transcriptional regulator with GATA-like zinc fingers, determines the oogenic fate in mice. ZGLP1 acts downstream of bone morphogenetic protein (BMP), but not retinoic acid (RA), and is essential for the oogenic program and meiotic entry. ZGLP1 overexpression induces differentiation of in vitro primordial germ cell-like cells (PGCLCs) into fetal oocytes by activating the oogenic programs repressed by Polycomb activities, whereas RA signaling contributes to the oogenic program maturation and PGC program repression. Our findings elucidate the mechanism for mammalian oogenic fate determination, providing a foundation for promoting in vitro gametogenesis and reproductive medicine.

overall_design: RNAseq analysis of PGCs, oocytes and PGCLCs in Zglp1 knockout/over expression and Stra8 KO lines

first: So

middle: I

last: Nagaoka

first: Fumio

last: Nakaki

first: Hidetaka

last: Miyauchi

first: Yoshiaki

last: Nosaka

first: Hiroshi

last: Ohta

first: Kazuki

last: Kurimoto

first: Katsuhiko

last: Hayashi

first: Tomonori

last: Nakamura

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Adhesion, motility and matrix-degrading gene expression changes in CSF-1-induced mouse macrophage differentiation

city: Perth

first: James

middle: Harvey

last: Steer

state: Western Australia

address: Hospital Avenue, QEII Medical Centre, M Block

country: Australia

institute: University of Western Australia

summary: Migratory macrophages play critical roles in tissue development, homeostasis and disease so it is important to understand how their migration machinery is regulated. Whole-transcriptome sequencing revealed that CSF-1-stimulated differentiation of bone marrow derived precursors into mature macrophages is accompanied by widespread, profound changes in the expression of genes regulating adhesion, actin cytoskeletal remodeling and extracellular matrix degradation. Significantly altered expression of almost 40% of adhesion genes, 60–86% of Rho family GTPases, their regulators and effectors and over 70% of extracellular proteases occurred. The gene expression changes were mirrored by changes in macrophage adhesion associated with increases in motility and matrix-degrading capacity. IL-4 further increased motility and matrix-degrading capacity in mature macrophages, with additional changes in migration machinery gene expression. Finally, siRNA-induced reductions in the expression of core adhesion proteins, paxillin and leupaxin, decreased macrophage spreading and adhesion numbers with distinct effects on adhesion numbers and their distribution and on matrix degradation. Together, the datasets provide an important resource to increase our understanding of the regulation of migration in macrophages and to develop therapies targeting disease enhancing macrophages.

overall_design: Analysis of mRNA transcripts as macrophages differentiate in the presence of CSF1.  Analysis of mRNA transcripts of mature macrophages exposed to IL4 for 48h.

first: Michael

middle: W

last: Murrey

first: Jame

middle: H

first: Eloise

middle: L

last: Greenland

first: Julie

last: Proudfoot

first: David

last: Joyce

first: Fiona

last: Pixley


title: RNA sequence analysis to compare Elf5+ and Elf5- tumor cells in C3-T; Elf5-GFP reporter mice tumors

city: Philadelphia

first: Andres

last: Blanco

state: PA

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

institute: University of Pennsylvania

summary: The data generated here shows increased interferon gamma gene signatures in Elf5- tumor cells in  C3-T; Elf5-GFP reporter mice tumors

overall_design: Examination of Elf5+(n=2) and Elf5-(n=4) tumor cells from C3-T; Elf5-GFP  tumors

first: John

last: Tobias

first: Rumela

last: Chakrabarti


title: Expression analysis of chimeric antigen receptor-transduced T cells following antigenic stimulation

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

summary:
Adoptive transfer of anti-CD19 chimeric antigen receptor (CAR)-engineered T cells has shown impressive clinical responses in patients with refractory B-cell malignancies.  However, therapeutic effects of CAR-T cells targeting other hematologic malignancies and solid tumors are not yet satisfactory.  Although inefficient tumor trafficking and multiple immunosuppressive molecules impede CAR-T cell effector responses, signals delivered by the current CAR constructs may still be insufficient to fully activate antitumor T cell functions.  Optimal T cell activation and proliferation requires multiple signals including T cell receptor (TCR) engagement (signal 1), costimulation (signal 2), and cytokine engagement (signal 3).  CAR genes developed to date contain a CD3z domain and costimulatory domain(s), but not a domain to transmit signal 3.
In this study, we have developed a novel CAR construct capable of inducing cytokine signaling in an antigen-dependent manner.  The new generation CD19 CAR encodes a cytoplasmic domain of IL-2RB and STAT3-binding YXXQ motif together with CD3z and CD28 domains (28-IL2RB-z (YXXQ)).  The 28-IL2RB-z (YXXQ) CAR-T cells showed antigen-dependent JAK-STAT, especially the STAT3-mediated pathway activation, which promoted their proliferation and prevented terminal differentiation.  The 28-IL2RB-z (YXXQ) CAR-T cells demonstrated superior in vivo persistence and antileukemia effects compared with the currently used CARs in multiple tumor models.

overall_design: Human CD8+ T cells derived from three different healthy donors were retrovirally transduced with individual anti-CD19 CAR genes (28-z, 28-BB-z and 28-IL2RB-z (YXXQ)) and were stimulated with K562 cells expressing CD19.  RNA was collected 4 days after stimulation and gene expression profiles were analyzed by Affymetrix Human Gene 2.0 ST Array (gene-level analysis).

first: Naoto

last: Hirano


title: Loss of Tmem106b leads to myelination deficits: implications for FTD treatment strategies

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: Genetic variants that define two distinct haplotypes at the TMEM106B locus have been implicated in multiple neurodegenerative diseases and in healthy brain aging. In frontotemporal dementia (FTD), the high expressing TMEM106B risk haplotype was shown to increase susceptibility for FTD with TDP-43 inclusions (FTD-TDP) and to modify disease penetrance in progranulin mutation carriers (FTD-GRN). To further elucidate the biological function of TMEM106B and determine whether lowering TMEM106B may be a viable therapeutic strategy, we performed brain transcriptomic analyses in 8-month-old animals from our recently developed Tmem106b-/- mouse model. We included 10 Tmem106b+/+ (WT), 10 Tmem106b+/- and 10 Tmem106-/- mice. The most differentially expressed genes (153 down-regulated and 60 upregulated) were identified between Tmem106b-/- and WT animals, with an enrichment for genes implicated in myelination-related cellular processes including axon ensheathment and oligodendrocyte differentiation. Co-expression analysis also revealed that the most downregulated group of correlated genes was enriched for myelination-related processes. We further detected a significant loss of Olig2-positive cells in the corpus callosum of Tmem106b-/- mice, which was present already in young animals (21 days) and persisted until old age (23 months), without worsening. qPCR revealed a reduction of differentiated but not undifferentiated oligodendrocytes cellular markers. While no obvious changes in myelin were observed at the ultrastructure levels in unchallenged animals, treatment with cuprizone revealed that Tmem106b-/- mice are more susceptible to cuprizone-induced de-myelination and have a reduced capacity to re-myelinate, a finding which we were able to replicate in a newly generated Tmem106b CRISPR/cas9 knock-out mouse model. Finally, using a TMEM106B HeLa knock-out cell line, we determined that loss of TMEM106B leads to abnormalities in the distribution of lysosomes and PLP1 trafficking but not to differences in MOG trafficking which is lysosome-independent. Together these findings reveal an important function for TMEM106B in myelination with possible consequences for therapeutic strategies aimed at lowering TMEM106B levels.

overall_design: We performed brain transcriptomic analyses in 8-month-old animals from our recently developed Tmem106b-/- mouse model. We included 10 Tmem106b+/+ (WT), 10 Tmem106b+/- and 10 Tmem106-/- mice.

first: Xiaolai

last: Zhou

first: Alexandra

last: Nicholson

first: Mieu

last: Brooks

first: Peizhou

last: Jiang

first: Aamir

last: Zuberi

first: Hung

middle: N

last: Phuoc

first: Ralph

middle: B

last: Perkerson

first: Billie

last: Matchett

first: Tammee

last: Parsons

first: NiCole

last: Finch

first: Wenlang

last: Lin

first: Wenhui

last: Qiao

first: Monica

last: Castanedes-Casey

first: Virginia

last: Phillips

first: Ariston

last: Librero

first: Yan

last: Asmann

first: Guojun

last: Bu

first: Melissa

last: Murray

first: Cathleen

last: Lutz

first: Dennis

last: Dickson

first: Rosa

last: Rademakers


title: F-53B and PFOS treatments skew human cardiac differentiation towards epicardial cells by in part disrupting the WNT signaling pathway

city: 北京市

first: Renjun

last: Yang

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

overall_design: To dissect the potential developmental cardiac toxicity of F-53B and PFOS, we performed RNA-seq analyses for day 8 and 12 cardiac differentiation samples treated with 60 µM F-53B/PFOS. RNA sequencing were performed with BGISEQ-500 platform

first: Shuyu

last: Liu

first: Xiaoxing

last: Liang

first: Nuoya

last: Yin

first: Ting

last: Ruan

first: Linshu

last: Jiang

first: Francesco

last: Faiola


title: RNA sequence analysis to compare alteration in transcriptome upon Elf5 loss in C3-T+ tumors

first: Andres

last: Blanco

summary: The data generated here shows increased interferon gamma gene signatures in C3-T+ tumors with loss of Elf5

overall_design: Examination of C3-T+ Elf5+/+ (n=2) and C3-T+ Elf5+/-(n=2) tumors

first: John

last: Tobias

first: Rumela

last: Chakrabarti


title: RNA sequencing in ALS patient fibroblasts with a mutation in CHCHD10

city: Montreal

first: Isabella

last: Straub

state: QC

address: 3801 University

institute: McGill University

summary: Purpose: Comparing patient and rescue (Pat-OE) cells

overall_design: Patient and rescue (Pat-OE) fibroblasts were cultured in glucose and galactose medium and harvested in triplicates

middle: R

first: Eric

last: Shoubridge


title: Hydrogen incubation on the mechanical injury of spinal cord neurons

city: Jiangyin

first: Longjuan

last: Qin

state: Jiangsu

address: Sha shan road no. 85

institute: puhebio

summary: We report the application of mRNA sequencing technology for high-throughput profiling of genes expression changes in spinal cord neurons with or without hydrogen incubation.In model group, we mechanically injured neurons. In control group, neurons were cultured without any intervention. In treatment group, after neurons were injured mechanically, hydrogen incubation(75%) was performed.

overall_design: Examination of mRNA modifications in 3 groups

first: Chen

last: Xiao

first: Wang

last: Ying


title: Single-cell RNA-sequencing of differentiation myeloid cells

status: Public on Feb 14 2020

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

summary: During granulocyte-macrophage colony-stmulating factor (GM-CSF) driven ex vivo myeloid differentiation of mouse hematopoietic stem/progenitor cells defined as Lineage negative cKit positive Sca-1 postive (LSK) cells,  LSK cells after Cxxc5 knockdown makes more granulocytic cells than monocytic cells. To study this effect of Cxxc5 knockdown during myeloid cell differentiation, we performed a single-cell RNA sequencing of differentiating myeloid cells and analyzed the transcriptome of these cells.

overall_design: Stem/progenitor cells enriched bone marrow cells from five C57BL/6 mice were infected with retrovirus to knockdown Cxxc5. Retrovirus that does not target any mouse genes was used as a control. Infected LSK cells (GFP positive LSK) were flow-sorted and cultured in a differentiation media containing cytokines GM-CSF and SCF. Cells were collected three days post growth in the myeloid differenation media, pooled (5 control samples pooled as one control and 5 knock-down samples pooled as one knock-down sample) and used for single-cell RNA sequencing with 10X Genomics.

first: Hemant

last: Joshi

first: Christopher

middle: J

last: Conley

first: Attila

last: Kumanovics


title: RNA sequencing LSK cells after Cxxc5 knockdown

summary: To study the effect of knockdown of Cxxc5 on stem/progenitor cells, we used retrovirus to knockdown Cxxc5 expression in the LSK cells. We used this as a surrogate to study the function of Cxxc5 in mouse/stem progenitor cells.

overall_design: Stem/progenitor cells enriched bone marrow cells from BALB/c mice were transduced with retrovirus to knockdown Cxxc5. Retrovirus that does not target any mouse genes was used as a control. Infected LSK cells (GFP positive LSK) were flow-sorted. Sorted infected LSK cells from multiple animals were pooled together for RNA isolation.


title: Expression profiling of circular RNA in the cumulus cells of patients with polycystic ovary syndrome

city: Qingdao

first: Zhi

last: Ma

address: No.308 Ningxia Rd

institute: Qingdao University

summary: Polycystic ovary syndrome (PCOS) is the most common and heterogeneous endocrine disorder in women of reproductive age.Depending on different criteria and populations,the prevalence of PCOS ranges from 6 to 8% with the NIH criteria,  and up to 20% with the Rotterdam criteria.Further, it accounts for approximately 75% of anovulatory infertility.Circular RNAs (circRNAs) mediate the posttranscriptional regulation of multiple genes by functioning as microRNA (miRNA) sponges. This study aimed to detect the novel expression of circRNAs in the cumulus cells (CCs) of PCOS patients and their potential significance in the pathogenesis of PCOS.

overall_design: CircRNAs in the cumulus cells from 6 PCOS patients and 6 normal control individuals were collected for microarray analysis, and an independent cohort study including 25 PCOS patients and 25 normal control individuals was conducted  to validate the circRNA microarray results using quantitative real-time polymerase chain reaction. Spearman’s rank correlation and receiver operating characteristic (ROC) were performed to delineate the potential correlation between  novel circRNAs and patients’ clinical characteristics and their potential efficacy for the diagnosis of PCOS. Bioinformatics analysis was applied to investigate the potential roles of circRNAs in the pathogenesis of PCOS.

first: Cuifang

last: Hao


title: LSK cells after Cxxc5 knockdown


title: Analysis of mRNA Changes in the prelimbic cortex of Rat with Chronic Neuropathic Pain

city: Xi'an

first: Guohong

last: Cai

address: NO.169 Changle West Road

institute: Fourth Military Medical University

summary: Neuropathic pain (NP) is a complex, chronic pain condition caused by injury or dysfunction affecting the somatosensory nervous system. This study aimed to identify crucial mRNA in prelimbic cortex (PL) involved in NP rats. mRNA  microarrays were applied in the present study.

overall_design: 3 spared nerve injury (SNI) samples and 3 control samples

first: Shengxi

last: Wu

first: Jing

last: Huang

first: Yuanyuan

last: Zhu


title: Deciphering Regulatory SNPs from ATAC-seq

city: indianapolis

first: siwen

last: xu

state: IN

address: 410 W 10th St

institute: Indiana University

summary:
Background: Expression quantitative trait loci (eQTL) studies are a valuable approach for identifying genetic variants correlated with gene expression. However, identifying the causal variants is challenging due to linkage disequilibrium amongst variants in the same haplotype block. In this study, we aim to identify functional SNPs in key regulatory regions that alter transcriptional regulation and thus, potentially impact cellular function. The majority of disease-associated single-nucleotide polymorphisms (SNPs) are located in regulatory regions, which can result in allele-specific binding (ASB) of transcription factors and differential expression of the target gene alleles. Here, we present regSNPs-ASB, a generalized linear model-based approach to accurately identify regulatory SNPs that are located in transcription factor binding sites from ATAC-seq data.
Results: Using regSNPs-ASB, we identified 53 regulatory SNPs in human MCF-7 breast cancer cells and 125 regulatory SNPs in human mesenchymal stem cells (MSC). By integrating the regSNPs-ASB output with RNA-seq experimental data and publicly available chromatin interaction data from MCF-7 cells, we found that these 53 regulatory SNPs were associated with 74 potential target genes and that 32 (43%) of these genes showed significant allele-specific expression (ASE). By comparing all of the MCF-7 and MSC regulatory SNPs to the eQTLs in the Genome-Tissue Expression (GTEx) Project database, we found that 30% (16/53) of the regulatory SNPs in MCF-7 and 43% (52/122) of the regulatory SNPs in MSC were also eQTLs. The enrichment of regulatory SNPs in eQTLs indicated that many of them are likely responsible for allelic differences in gene expression (chi-square test, p-value < 0.01). In sum, we conclude that regSNPs-ASB is a useful tool for identifying causal variants from ATAC-seq data. This new computational tool will enable efficient prioritization of genetic variants identified as eQTL for further studies to validate their causal regulatory function. Ultimately, identifying causal genetic variants will further our understanding of the underlying molecular mechanisms of disease and the eventual development of potential therapeutic targets.

overall_design: ATAC-seq assays were performed on two human cell lines, MCF-7 breast cancer cells and MSC (Mesenchymal Stem Cells). We generated 3 ATAC-seq libraries in MCF-7 cells and each individual libraries were derived from three technical replicates. We also generated 3 ATAC-seq libraries in MSC and each individual libraries were derived from two technical replicates. RNA-seq assays were performed on MCF-7 breast cancer cells. We generated 2 RNA-seq libraries which were each sequenced in three lanes to create three technical replicates per library.

first: Yunlong

last: Liu

first: Yue

last: Wang

first: Hongyu

last: Gao


title: The RNA-binding protein ATXN2 controls cellular processes during megakaryopoiesis.

city: Amsterdam

first: Emile

middle: van den

last: Akker

address: Plesmanlaan 125

institute: Sanquin

summary: Megakaryocytes accumulate mRNA during their maturation, which is required for the correct spatio-temporal production of cytoskeletal proteins, membranes and platelet-specific granules, and for the subsequent shedding of thousands of platelets per cell. Gene expression profiling  identified the RNA binding protein ATAXIN2 (ATXN2) as a putative novel regulator of megakaryopoiesis. ATXN2 expression is high in CD34+/CD41+ megakaryoblasts and sharply decreases upon maturation to megakaryocytes. ATXN2 associates with DDX6 suggesting that it may mediate repression of mRNA translation during early megakaryopoiesis. Comparative transcriptome and proteome analysis on megakaryoid cells (MEG-01) with differential ATXN2 expression identified ATXN2 dependent gene expression of mRNA and protein involved in processes linked to coagulation. Mice deficient for Atxn2 did not display differences in bleeding times, but expression of key surface receptors on platelets, such as ITGB3 (carries the CD61 antigen) and CD31 (PECAM1), were deregulated and platelet aggregation upon specific triggers was reduced.

overall_design: Comparison in the megakaryocyte cell line (MEG-01) the effect of ATXN2 depletion by small interference RNA (shRNA) after 16 days (Puro selected). Two different shRNA targeting ATXN2 (also confirmed on protein level), one shRNA scrambled and one non-transduced control.

first: M

last: Hansen

first: S

last: Zeddies

last: Meinders

first: F

last: di Summa

first: E

last: Damrath

last: van Alphen

first: K

middle: S

last: Moore

last: Halbach

first: L

last: Gutierrez

last: van den Biggelaar

first: D

middle: C

last: Thijsen-Timmer

first: G

last: Auburger

last: van den Akker

last: von Lindern


title: Feces 16S rRNA seq of mice treated by AZ1 with 2.5% DSS or H2O

city: wuhan

first: xiaomeng

last: wang

address: Donghu Road 115

institute: Wuhan University

summary: Feces 16s rRNA seq experiments is required to demonstrate the AZ1 doesn’t impact the intestinal microbiota.

overall_design: V4 region of the bacterial 16S rRNA was sequenced with the 515F and 814R primers in an Illumina NovaSeq sequencer

first: Xiaomeng

last: Wang

first: Bo

last: Zhong


title: Single cell RNA-Seq of Ewing Sarcoma PDX data (PDX_Chromium)

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of 5 Ewing Sarcoma PDX (PDX-184, 352, 856, 861 and 1058) with the 10X Genomics Chromium technology.

overall_design: Study of transcriptomic heterogeneity of Ewing Sarcoma models and comparison with control cell models. Raw data not submitted due to patient privacy concerns.

last: Aynaud

first: O

last: Mirabeau

first: N

last: Gruel

last: Grossetête

first: A

last: Zinovyev


title: Single cell RNA-Seq of Ewing Sarcoma PDX data (PDX_C1)

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of 3 Ewing Sarcoma PDX (PDX-83, 84 and 111) with the Fluidigm C1 technology.


title: Human cytomegalovirus promoting endothelial cell proliferation by targeting regulator of G-protein signaling 5 hypermethylation and downregulation

city: Shihez

first: xiaoni

last: zhang

address: Shihezi, China

institute: Medical College of Shihezi University

summary:
Interactions between human cytomegalovirus (HCMV) infection and environmental factors can increase susceptibility to essential hypertension (EH). Although endothelial dysfunction is the initial factor of EH, the epigenetic mechanisms through which HCMV infection induces endothelial cell dysfunction are poorly understood.
Here, we evaluated whether HCMV regulated endothelial cell function and assessed the underlying mechanisms. Microarray analysis in human umbilical vein endothelial cells (HUVECs) treated with HCMV AD169 strain in the presence of hyperglycemia and hyperlipidemia revealed differential expression of genes involved in hypertension.

overall_design: We use microarray to describe the differentially expressed genes induced by human cytomegalovirus infection in detail, providing a target for the prevention and treatment of hypertension.

first: X

last: Zhang

last: Tang

last: Xi

first: Q

last: Feng

first: Y

last: Liu

first: H

last: He


title: Single cell RNA-Seq of Neuroblastoma cell line (CLB-berlud)

summary:
We report the application of single-molecule-based sequencing technology for high-throughput profiling of Neuroblastoma cell line (CLB-berlud)
Examination of gene expression in Neuroblastoma cell line (CLB-berlud), as a negative control

overall_design: Study of transcriptomic heterogeneity of Ewing Sarcoma models and comparison with control cell models

first: M

first: S


title: Single cell RNA-Seq from bone marrow Ewing patients

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of bone marrow Ewing patients


title: Characterization of the specific EWSR1-FLI1 activity signature

address: 26 rue d'ulm

summary: We report the application of ChIP sequencing technology for high-throughput profiling of genes directly regulated  and the active histone mark modification (H7K27ac) under EWSR1-FLI1 expression in A673/TR/shEF

overall_design: Examination of gene regulation and histone modification upon EWSR1-FLI1 expression

first: Marie-Ming

first: Nadège

first: Sandrine

first: Andrei


title: Gene expression analysis of skeletal muscle of control and mesenchymal progenitor-depleted mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Comprehensive analyses of mRNA expression were performed using skeletal muscle from control and mesenchymal progenitor-depleted mice to investigate the role of mesenchymal progenitors in skeletal muscle maintenance.

overall_design: PDGFRa+ mesenchymal progenitors were depleted using Pdgfra-CreER:R26-DTA mice, and WT:R26-DTA littermate mice were used as control. Skeletal muscle of these mice were quickly frozen and RNA was extracted. Gene expression analysis was performed to identify genes that show altered expression in mesenchymal progenitor-depleted muscle.

first: Akiyoshi

last: Uezumi


title: Next generation sequencing facilitates quantitative analysis of control samples and nervous necrosis (VNN) virus infection samples orange-spotted grouper transcriptomes

city: xiamen

first: hui

last: Ge

state: fujian

address: No.361012, haishan road no.7, huli district

institute: Fisheries Research Institute of Fujian

summary:
Purpose:To study the molecular mechanism of nerve necrosis (VNN) virus infection, and to provide help for molecular breeding and further development of Marine fishery
Results: we found that 17,939 genes are elevated after NNV infection compared with control group, suggesting that NNV infection can strongly induce the expression of immune associated genes. In summary, we obtained high quality transcriptome of orange-spotted grouper and comparative analysis of transcriptome analysis reveals dramatically perturbation of gene expression with NNV infection.

overall_design: mRNA profiles of 20-day old control and  nervous necrosis (VNN) virus infection orange-spotted groupers (Epinephelus coioides)  were generated by deep sequencing, in triplicate, using  HiSeq 4000.

first: Hui


title: Gene expression analysis of skeletal muscle

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

overall_design: Refer to individual Series


title: Analysis of miRNA Changes in the prelimbic cortex of Rat with Chronic Neuropathic Pain

status: Public on Feb 13 2020

first: Guohong

last: Cai

summary: Neuropathic pain (NP) is a complex, chronic pain condition caused by injury or dysfunction affecting the somatosensory nervous system. This study aimed to identify crucial miRNA in prelimbic cortex (PL) involved in NP rats. miRNA  microarrays were applied in the present study.

overall_design: 3 SNI samples and 3 control samples

first: Shengxi

last: Wu

first: Jing

last: Huang

first: Yuanyuan

last: Zhu


title: Single cell RNA-Seq of A673/TR/shEF cell line - time course

first: Olivier

last: Delattre

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of genes regulated under EWSR1-FLI1 expression in A673/TR/shEF. EWSR1-FLI1 specific small hairpin RNA was induced in A673/TR/shEF cells by adding DOX at 1 ug/mL. After 7 days, DOX was removed to allow silencing of the shRNA and induction of EWSR1-FLI1. Cells were harvested at seven different times points: 0 day (d7), 2 days (d9), 3 days (d10), 4 days (d11), 7 days (d14), 10 days (d17) and 15 days (d22) after DOX removal.

last: Aynaud

first: O

last: Mirabeau

first: N

last: Gruel

first: A