title: Iminosugar MON-DNJ modulation of transciptomic response to dengue virus and LPS in primary human macrophages

city: Oxford

first: Andrew

middle: Cameron

last: Sayce

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Protocols for the treatment of sepsis and septic shock are restricted to early administration of appropriate antibiotics and supportive organ care. To date, there has been limited success in addressing the characteristically dysregulated host response once it is underway. Furthermore, virus-induced sepsis remains poorly appreciated, and treatment strategies are similarly limited to supportive measures. Prior in vitro and murine studies demonstrate antiviral efficacy of iminosugars against diverse viral pathogens, but translational approaches to humans are missing. Here we show successful iminosugar-mediated inhibition of dengue virus, bacterial lipopolysaccharide, and fungal antigen stimulated cytokine responses in human macrophages. Iminosugar treatment mediated a sustained reduction in oxidative stress and the secretion of proinflammatory cytokines, particularly IFN-g and TNF-a. Transcriptome analysis suggests that the mechanism behind this reduction involves endoplasmic reticulum (ER) stress via early, pathogen-independent induction of a robust unfolded protein response (UPR). Based on these findings, we propose that iminosugars have the potential to fill the treatment gap in controlling symptoms and complications of a wide variety of inflammatory disorders associated with excessive cytokine secretion.

overall_design: Primary human monocyte-derived macrophages from 4 donors were matured in the presence of recombinant human IL-4 (25 ng/mL) for 3 days. After 3 days, media was removed and samples were infected with dengue virus (DENV-2 16681) at MOI of 1 or treated with lipopolysaccharide (Salmonella enterica, 200 ng/mL) for 90 minutes. Uninfected controls were incubated in X-VIVO medium. Virus was removed and samples were treated with N9-methoxynonyl-deoxynojirimycin (MON-DNJ, 25 μM) or untreated. LPS-treated samples were diluted to a final concentration of 100 ng/mL LPS for the time period following the initial 90 minute incubation and were treated with MON-DNJ or untreated. Samples were collected at 6 hours and 24 hours post-initiation of infection for a total of 12 treatments in biological quadruplicate for 48 total samples.

middle: C

first: Joanna

last: Miller

first: Fernando

middle: O

last: Martinez

first: Raymond

last: Dwek

first: Nicole

last: Zitzmann


title: Id4 maintains quiescence of adult hippocampal stem cells

status: Public on Oct 18 2019

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

type: Expression profiling by high throughput sequencing

summary: Quiescence is essential for the long term maintenance of adult stem cells and tissue homeostasis. However, how stem cells maintain quiescence is still poorly understood. Here we show that stem cells in the dentate gyrus of the adult hippocampus actively transcribe the proactivation factor Ascl1 regardless of their activation state. We found that the inhibitor of DNA binding protein Id4 suppresses Ascl1 activity in neural stem cell cultures. Id4 sequesters Ascl1 heterodimerisation partner, promoting the degradation of Ascl1 protein and neural stem cell quiescence. Accordingly, elimination of Id4 from stem cells in the adult hippocampus results in abnormal accumulation of Ascl1 protein and premature stem cell activation. We also found that multiple signalling pathways converge on the regulation of Id4 to control the activity of hippocampal stem cells.  Id4 therefore maintains quiescence of adult neural stem cells, in sharp contrast with its role of promoting the proliferation of embryonic neural progenitors.

overall_design: 6 samples, each in triplicate (3 biological repeats). 'FGF_GFP' and 'BMP_GFP' are the control samples for 'FGF_ID4' and 'BMP_E47', in which wildtype adult hippocampal neural stem cells (AHNSCs) were nucleofected with expression constructs and FACS sorted. 'FGF' and 'BMP' samples refer to wildtype AHNSCs, non-transfected; these samples were paired-end sequenced, 'R1' refers ro read 1, 'R2' to read 2.

first: Isabelle

last: Blomfield

first: Debbie

last: van den Berg

first: François

last: Guillemot

first: Noelia

last: Urbán


title: Tbx3 governs a transcriptional program to maintain atrioventricular conduction system form and function [RNA-Seq]

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

summary: Rationale: The atrioventricular conduction system controls ventricular activation and is delineated by expression of Tbx3. Genome-wide association studies identified genetic variants near TBX3 associated with conduction velocities (PR interval and QRS duration), suggesting minor changes in TBX3 dose affect conduction system function. Objective: To assess whether and how Tbx3 dose reduction affects the integrity of the atrioventricular conduction system. Methods and Results: Electrocardiograms revealed a PR interval shortening and prolonged QT interval and QRS duration in heterozygous Tbx3 mutants compared to wild-types. We observed that the atrioventricular bundle and proximal bundle branches of Tbx3+/- mice after birth became hypoplastic, whereas the size of the atrioventricular node was not affected. The transcriptomes of wild-type and Tbx3+/- atrioventricular nodes were analyzed using BAC-Tbx3-Egfp mice enabling specific isolation of the atrioventricular node by laser capture microdissection followed by RNA-sequencing. Hundreds of genes were slightly but consistently deregulated. Cross-referencing with transcriptome data of isolated cardiomyocytes of the conduction system and chamber myocardium derived from Tbx3+/Venus;BAC-Nppb-Katushka hearts revealed that a set of chamber-enriched genes, including Kcne1 (MinK), Ryr2, and Scn5a, were upregulated in Tbx3+/- atrioventricular nodes, whereas conduction system-enriched genes, including Hcn4 and Cacna2d2, were downregulated. We performed ATAC-sequencing on purified fetal Tbx3+ atrioventricular cardiomyocytes to identify potential atrioventricular-specific regulatory DNA elements on a genome-wide scale, and identified regulatory elements mediating the Tbx3-dependent regulation of Ryr2 and other target genes in the atrioventricular node. Conclusions: Tbx3 dose reduction results in deregulation of a large number of genes affecting the electrical properties of the atrioventricular node and causes failure to maintain the structural integrity of the atrioventricular bundle. These data provide a mechanism underlying differences in PR interval and QRS duration in individuals carrying associated variants in the TBX3 locus.

overall_design: Laser capture microdissection of AVNs from Tbx3-CreERT2;BAC-Tbx3-GFP (n=6) and Tbx3-WT;BAC-Tbx3-GFP (n=6)

first: Rajiv

last: Mohan

first: Karel

last: van Duijvenboden


title: Expression data from livers of female wild-type mice subjected to warm bilateral renal artery ischemia-reperfusion injury (RIR) in comparison to livers of female wild type mice subjected to sham surgery.

status: Public on Oct 17 2019

city: Pittsburgh

first: Anne

last: Barbosa Diniz

state: PA

address: 3501 Terrace St

department: Pharmaceutical Sciences

country: USA

institute: University of Pittsburgh

summary: RIR leads to ischemic acute kidney injury (AKI). Women below the age of menopause have a lower incidence of AKI. It is bellieved that estrogens are protective. Many genes were shown to be altered in female wild-type mice subjected to IRI.

overall_design: We used microarrays to detail the global differences of gene expression in the livers of female wild-type mice subjected to 30 minutes of warm renal ischemia reperfusion injury (RIR) in comparison to livers of female wild-type mice subjected to sham surgery.

first: Yanping

last: Yu

first: Wen

last: Xie


title: Expression data from kidneys of male EST KO mice in comparison to kidneys of male wild type mice subjected to warm bilateral renal artery ischemia-reperfusion injury

summary: EST KO mice are protected from ischemic acute kidney injury (AKI). Many genes were shown to be altered in this group.

overall_design: We used microarrays to detail the global differences of gene expression in the kidneys of male EST KO mice subjected to 30 minutes of warm renal ischemia reperfusion injury (RIR) in comparison to  kidneys of male wild-type mice subjected to RIR.


title: RNA-seq and ChIP-seq analysis to understand the mechanistic role of NCoR1 as a tolerogenic program suppressor in dendritic cells

city: Bhubaneswar

first: Sunil

middle: Kumar

last: Raghav

state: Odisha

address: Nalco Square

department: Infectious Disease Biology

country: India

institute: Institute of Life Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression data from livers of male wild-type mice subjected to warm bilateral renal artery ischemia-reperfusion injury (RIR) in comparison to livers of male wild type mice subjected to sham surgery.

summary: RIR leads to ischemic acute kidney injury. Many genes were shown to be altered in this group.

overall_design: We used microarrays to detail the global differences of gene expression in the livers of male wild-type mice subjected to 30 minutes of warm renal ischemia reperfusion injury (RIR) in comparison to livers of male wild-type mice subjected to sham surgery.


title: An integrated transcriptomics and metabolomics study of the immune response of newly hatched chicks to the CpG-ODN stimulation

city: Pierre Bénite

first: Jeremie

middle: FC

last: Becker

address: Centre Hospitalier Lyon Sud, Bâtiment 3F

department: Medical diagnostic Discovery department

country: France

institute: bioMérieux

summary: This study aims at identifying a dual transcriptomics and metabolomics blood signature following administration of CpG-ODN (cytosine-phosphate-guanine oligodeoxynucleotides), a reference immune-stimulatory molecule. A clinical study was conducted with chicks and transcriptomics and metabolomics analyses were performed on whole-blood and plasma samples respectively. Statistical analyses resulting in lists of differentially expressed genes and metabolites with different abundance were identified in chicks treated with CpG-ODN. The results showed that CpG-ODN activates the innate immune systems within hours following administration and its effect lasts over time, as metabolomic and transcriptomic profiles are still varying at 6 days after administration.

overall_design: CpG-ODN 2007, a prototypal immunomodulator, described as one of the most efficient agonists of chTLR21, the counterpart of mammalian TLR9, was injected at day of hatch and systemic changes were monitored in blood at different time points post injection. An early time point of 3h (D0+3h) post injection was chosen to secure early signature following CpG-ODN injection. As the immunomodulatory properties of CpG-ODN have been evaluated up to 4 days post-injection in the spleen, two additional time points to frame this timing at day three (D3) and day six (D6) were chosen to assess its functional effects over time

first: Djomangan

last: Ouattara

first: Lydie

last: REMOLUE

first: Jérémie

last: BECKER

first: Magali

last: PERRET

first: Andrei

last: BUNESCU

first: Kristin

last: HENNIG

first: Emeline

last: BILIAUT

first: Annemanuelle

last: BADIN

first: Cesarino

last: GIACOMINI

first: Frédéric

last: REYNIER

first: Christine

last: ANDREONI

last: BEQUET

first: Patrick

last: LECINE

first: Karelle

last: De LUCA


title: Arabidopsis slim1 response to arsenic and cadmium

city: Cologne

first: Timothy

middle: Owen

last: Jobe

state: DE

address: Zulpicher Str 47b

department: Botanical Institute

country: Germany

institute: University of Cologne

summary: 14 day old slim1-1 and Col-0 seedlings treated with arsenic or cadmium

overall_design: 3 biological reps of all treatments

first: Julian

middle: I

last: Schroeder


title: Expression data from human oligodendroglia cells expressing shRNA targeting ADAR2 or control.

city: Kyoto

first: Mako

last: Yanai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Institute for Frontier Life and Medical Sciences

country: Japan

institute: Kyoto university

summary:
To assess whether antiviral genes are upregulated by ADAR2 knockdown, we performed a comprehensive analysis using a microarray system for oligodendroglia cells introduced shRNA against ADAR2 or control.
The inflammation- and immune response-related genes were upregulated in ADAR2-knockdown cells.

overall_design: The oligodendroglia cells stably expressing shRNA targeting ADAR2 or control were subjected to RNA extraction and microarray analysis.  Four samples were analyzed (two biological repricates).

first: Akiko

last: Makino

first: Keizo

last: Tomonaga


title: Medroxyprogesterone acetate alters the vaginal microbiota and microenvironment in humans and increases susceptibility to HIV-1 in humanized mice

city: Hamilton

first: Jocelyn

middle: M

last: Wessels

state: Ontario

address: 1280 Main Street West

department: Obstetrics and Gynecology

country: Canada

institute: McMaster University

summary: The hormonal contraceptive medroxyprogesterone acetate (MPA) is associated with increased risk of human immunodeficiency virus (HIV), via incompletely understood mechanisms. Increased diversity in the vaginal microbiota modulates genital inflammation and is associated with increased HIV-1 acquisition. However, the effect of MPA on diversity of the vaginal microbiota is relatively unknown. In a cohort of female Kenyan sex workers, negative for sexually transmitted infections (STIs), with Nugent scores <7 (N=58 of 370 screened), MPA correlated with significantly increased diversity of the vaginal microbiota as assessed by 16S rRNA gene sequencing. MPA was also significantly associated with decreased levels of estrogen in the plasma, and low vaginal glycogen and α-amylase, factors implicated in vaginal colonization by lactobacilli, bacteria that are believed to protect against STIs. In a humanized mouse model, MPA treatment was associated with low serum estrogen, low glycogen and enhanced HIV-1 susceptibility. The mechanism by which the MPA mediated changes in the vaginal microbiota may contribute to HIV-1 susceptibility in humans appears to be independent of inflammatory cytokines and/or activated T cells. Altogether, these results suggest MPA-induced hypo-estrogenism may alter key metabolic components that are necessary for vaginal colonization by certain bacterial species including lactobacilli, and allow for greater bacterial diversity in the vaginal microbiota.

overall_design: Vaginal bacterial profiles of Kenyan sex workers were generated by 16S rRNA gene sequencing using the Illumina MiSeq platform.

first: Charu

last: Kaushic


title: Gene expression profile of HMT3522 S1 cells grown on 2D and in 3D matrix in response to the death ligand TRAIL

status: Public on Oct 16 2019

city: Taipei City

first: Kelvin

middle: Kun-Chih

last: Tsai

address: 7F, 250 Wuxing St, Xinyi Dist

department: Graduate Institute of Clinical Medicine, College of Medicine

country: Taiwan

institute: Taipei Medical University

summary: The series represent gene expression profiles of HMT3522 S1 mammary epithelial cells cultured as 2D monolayers or in 3D reconstituted basement membrane (rBM) and treated with the death ligand TRAIL.  Keywords: Genetic modification; response to death induction

overall_design: Three replicated cultures were established for each of the 4 experiment groups, including S1 cells grown as 2D monolayers (S1-2D CA, S1-2D CB, S1-2D CC), S1 cells grown as 2D monolayers and treated with TRAIL (S1-2D TA, S1-2D TB, S1-2D TC), S1 cells embedded in 3D rBM (S1-3D CA, S1-3D CB, S1-3D CC), S1 cells embedded in 3D rBM and treated with TRAIL (S1-3D TA, S1-3D TB, S1-3D TC). Cells were embeded in rBM for 12 days and then treated with TRAIL (1 μg/mL) or vehicle for 8 hours before the collection of RNA samples.

middle: K

first: Valerie

last: Weaver


title: mtefd1 and wt roots and nodules-Analysis of Medicago truncatula transcriptomes for roots and nodules at different developmental stages, in wild type and efd1-1 mutant backgrounds

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: 12plex_medicago_2012-03 - mtefd1 and wt roots and nodules - Identification of genes affected by a KO mutation in a transcription factor involved in root and nodule development, MtEFD1. - Comparison of wild type and efd-1 transcriptomes in non inoculated nitrogen-starved control roots and nodules at 4 dpi, 6 and 11 dpi. Comparison of wild type nodule (11 dpi) and root transcriptomes, using mixed random primed and polydT primed probes.

overall_design: 8 dye-swap - gene knock out,time course

first: Ludivine

last: Taconnat

first: Sandrine

last: Balzergue

first: Pascal

last: Gamas

first: Marie-Laure

last: Martin-Magniette


title: Metabolic Reprogramming Associated with Aggressiveness Occurs in the G-CIMP-High Molecular Subtypes of IDH1mut Lower Grade Gliomas

city: Bethesda

first: Mioara

last: Larion

state: Maryland

address: 37 Convent Drive, Building 37

department: NCI, CCR

institute: National Institutes of Health

type: Methylation profiling by genome tiling array


title: DNA Methylation of BT142 and TS603 cell lines

summary: We report the DNA methylation status of IDH1-mutant cell lines

overall_design: Cell lines were grown either in normoxia (N) or hypoxia (H) for at least 3 days before collecting for subsequent DNA methylation analysis


title: RNA sequencing of BT142 and TS603 cell lines

summary: We report the levels of the transcripts arising from the RNA sequencing analysis of IDH1-mutant cell lines

overall_design: Cell lines were cultured in parallel for 3 days for subsequent RNAseq analysis


title: Single cell RNA sequencing of multiple myeloma I

city: Seoul

first: Daeun

last: Ryu

address: 81, Irwon-ro

country: South Korea

institute: Samsung Genome Institute

summary: To understand molecular events associated with myeloma progression, we applied single-cell RNA sequencing to myeloma cells in the bone marrow and extramedullary sites. Transcriptome analysis, at single cell level, demonstrates that proliferation and alterations in antigen presentation are associated with myeloma progression whereas NF-kB pathway activation has an anti-correlation. While these alterations are prominent in most of the extramedullary myeloma cells, some myeloma cells in the bone marrow show gene expression signatures resembling extramedullary cells even when the myeloma cells were taken at stable disease. Altogether single-cell transcriptome analysis reveals both common transcriptional programs and heterogeneity turned on during myeloma progression.

overall_design: We performed single cell RNA sequencing (RNA-seq) for multiple myeloma from the bone marrow and/or extramedullary sites from 10 patients. Additional bulk RNA sequencing was performed with CD138-negative non-myeloma populations from the same patients. Data contain 477 single-cell RNA-seq and 11 bulk RNA-seq.

first: D

first: H

last: Lee

first: K

last: Kim

first: W

last: Park


title: Global Long Noncoding RNA and mRNA Expression Changes between Ovarian Granulosa Cell Treatment with GnRH agonist(Alarelin) and antagonist(Cetrorelix) in goose

city: Chongqing

first: Gao

last: Guangliang

address: Street Address, No. 51 Changlong Avenue Rongchang County

country: China

institute: Chongqing Academy of Animal Sciences

summary: Gonadotropin-releasing hormone (GnRH) might combine with other reproductive hormones to affect follicular development by regulation of the cell cycle in granulosa cells (GCs).To investigate the function of GnRH in GCs, we examined the effects of a GnRH agonist (alarelin acetate) and an antagonist (cetrorelix acetate) on the proliferation of primary goose (Anser cygnoides) ovarian GCs by colorimetry and 5-ethynyl-2¢-deoxyuridine (EdU) cell proliferation assays. Differently expressed genes (DEGs) affected by these GnRH analogues in goose GCs were detected by RNA-seq and the results were verified using quantitative reverse transcription polymerase chain reaction (RT–qPCR) and western blotting. The optical densities in  the colorimetry assays and the S phase cell cycle ratio of GCs in the EdU cell proliferation assays gradually increased and decreased with increasing concentrations in the alarelin-treated and cetrorelix-treated cells in dose-dependent manners, respectively. Statistically significances were achieved at concentrations of 10−5 mol/L alarelin and 1 mg/L cetrorelix acetate RNAseq analysis showed that 134 DEGs and 226 DEGs were detected following GC treatment with 10−5M GnRH alarelin (76 downregulated and 58 upregulated) and 1 mg/L cetrorelix (90 downregulated and 136 upregulated). Many of these DEGs are involved in the actions of genes encoding G protein-coupled hormone receptors, such as estrogen receptor 2 (ESR2), oxytocin receptor (OXTR), and prolactin receptor (PRLR), which are essential for folliculogenesis. The mRNA and protein expression levels of ESR2 in GCs were decreased and increased by the GnRH agonist and antagonist, respectively. Interestingly, ESR2 was increasingly expressed in pre-hierarchical follicles, most strongly expressed in GCs of F5 stage follicles and reduced in preovulatory follicles, which implicates a potential role in follicle selection. Thus, GnRH might act as an autocrine or paracrine factor to regulate GC proliferation by interacting with some key steroid hormone G protein-coupled receptors genes participating in follicular development.

overall_design: Ovaries were collected 2 hr before laying for cell culture and isolation of ovarian GCs from preovulatory follicles and pre-hierarchical follicles (4–12 mm diameter) in 40W Sichuan white goose. The cell were treated with different concentrations of GnRH agonist (alarelin acetate) and an antagonist (cetrorelix acetate). The proliferation assay were performance by the colorimetry and 5-ethynyl-2¢-deoxyuridine (EdU) cell proliferation assays. The cell treatment with optimal concentration of GnRH analogues were collected and frozen immediately in liquid nitrogen and stored at -80°C until required for RNA extraction, sequencing and transcriptome analysis.

first: zheshan

last: zhang

first: guanglaing

last: gao

first: xianzhi

last: zhao

first: qin

last: li

first: hang

last: zhong

first: youhui

last: xie

first: qigui

last: wang


title: Relief of tumor hypoxia unleashes the tumoricidal potential of neutrophils

city: San Francisco

first: Karim

last: Mahiddine

state: CA

address: 513 Parnassus avenue

department: Laboratory medicine

institute: University of Califiornia San Francisco

summary:
Our objective was to identify the genes in tumor-associated neutrophils that are differentially expressed when uterine tumor-bearing "PRPL" mice are subjected to respiratory hyperoxia versus normoxia housing conditions.
Six samples were spread across thw two housing conditions, each with 3 biological replicates.  Sequencing provided was 372 million total reads with an average of 81.9% of these reads aligning uniquely to the mouse genome. Reads uniquely mapped to known mRNAs were used to identify gene expression changes between housing conditions using DESeq2.
We found that 423 protein-coding genes were differentially expressed (FDR<0.05, excluding genes whose normalized read counts were less than 50 across all six samples) in tumor-associated neutrophils from 4-wk old PRPL mice housed under hyperoxia versus normoxia conditions.

overall_design: mRNA profiles of neutrophils sorted from uteri of 4-wk old PRPL mice (housed in normoxia or hyperoxia conditions for the last 10 days prior to sacrifice) were generated by next generation sequencing using Illumina HiSeq 4000.

first: Adam

last: Blaisdell

first: Stephany

last: Ma

first: Amandine

last: Créquer-Grandhomme

first: Clifford

middle: A

last: Lowell

first: Adrian

last: Erlebacher


title: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-seq2]

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary: Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remain largely unexplored. Here, we show that the RNA helicase DDX6 is crucial for the dissolution of the pluripotency-specific transcriptional network in mouse and human embryonic stem cells (ESCs). We further demonstrate that epigenetic silencing of DDX6 endows primed ESCs with a differentiation-resistant, “hyper-pluripotent” state, which readily reprograms to a naïve state resembling the preimplantation embryo. In addition to directing cell fate in ESCs, we find that DDX6 plays a key role in adult progenitors where it controls the balance between self-renewal and differentiation in a context-dependent manner. Specifically, DDX6 loss blocks the differentiation of mouse intestinal stem cells and human neural stem cells, while it favors exit from the progenitor state in human muscle and mesenchymal progenitors. Mechanistically, we show that DDX6 coordinates the storage and translational suppression of target mRNAs in P-bodies. Upon loss of DDX6 or mutation of its helicase domain, P-bodies dissolve and release mRNAs encoding fate-instructive transcription and chromatin factors that subsequently re-enter the ribosome pool. Increased translation of these targets impacts cell fate by rewiring the enhancer, heterochromatin and DNA methylation landscapes of human undifferentiated cell types. Collectively, our data establish a novel link between P-body homeostasis, chromatin organization and cellular potency across diverse stem and progenitor cell populations.

overall_design: DDX6 overexpression in the GEN1C hiPSCs cells (GEN1C DDX6 OE) was achieved by infection with a lentiviral vector expressing the wt DDX6 cDNA (Vector Builder). For the TGFβi assay, cells were incubated in differentiation media for 48 hours for the TGFβi condition.

first: Bruno

last: Di Stefano

first: Ruslan

last: Sadreyev

first: Konrad

last: Hochedlinger


title: Re-masking of fungal cell wall PAMPs in response to environmental pH is regulated by multiple processes

city: Birmingham

first: Rebecca

last: Hall

address: University of Birmingham, School of Biosciences

department: IMI

institute: University of Birmingham

summary: Candida albicans is a commensal yeast of the human gut, which is tolerated by the immune system, but has the potential to become an opportunistic pathogen. One way in which C. albicans achieves this duality is through the concealing, or exposure of cell wall associated pathogen-associated molecular patterns (PAMPs) in response to host derived environment cues (pH, hypoxia, lactate). This cell wall remodelling allows C. albicans to evade or hyperactivate the host’s innate immune responses leading to disease. Previously we identified that adaptation of C. albicans to acidic environments, conditions encountered during colonisation of the female reproductive tract, induce significant cell wall remodelling resulting in the exposure of two key fungal PAMPs (glucan and chitin). Here we report that this pH-dependent cell wall remodelling is a highly dynamic process, requiring periods of both cell wall unmasking, with peak PAMP exposure occurring between 2-4 hrs, followed by subsequent PAMP remasking. b-glucan remasking was mediated via the cell density dependent fungal quorum sensing molecule farnesol, while chitin remasking was mediated via a small, heat-stable, non-proteinaceous secreted molecule(s). Transcript profiling identified a core set of 42 genes significantly regulated by pH over time, and linked the transcription factor Efg1p to being the main regulator of chitin exposure through regulation of CHT2. This dynamic cell wall remodelling, influenced innate immune recognition of C. albicans, suggesting that during infection C. albicans can manipulate the host innate immune responses.

overall_design: Transcriptional response of C. albicans (SC5314) to YPD buffered at pH4 or pH6 over a 8h period.

first: Fabien

last: Cottier

first: Sarah

last: Sherrington

last: Cockeril

first: Stephen

last: Kissane

first: Valentina

last: Delolmo

first: Helene

last: Tournu

first: Christian

last: Pérez

first: Glen

last: Palmer

first: Luisa

last: Orsini


title: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [ChIP-Seq]

city: Cambridge

first: Jocelyn

last: Charlton

state: MA

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Analysis of adult and embryonic stem cells depleted for DDX6. Results provide insight into the regulation of human stem cell self-renewal and differentiation by the RNA-binding protein DDX6.

overall_design: ChIP-seq


title: Cis-regulatory basis of sister cell type divergence in the vertebrate retina

city: Saint Louis

first: Daniel

last: Murphy

state: MO

address: 660 S. Euclid

institute: Washington University School of Medicine

summary: Multicellular organisms evolved via repeated functional divergence of transcriptionally related sister cell types, but the mechanisms underlying sister cell type divergence are not well understood. Here, we study a canonical pair of sister cell types, retinal photoreceptors and bipolar cells, to identify key cis-regulatory features that mediate the transcriptomic and functional differences between them. We generated open chromatin maps and transcriptome profiles of mouse ON and OFF bipolar cells isolated by fluorescence-activated cell sorting (FACS) and compared them to similar data from rod and cone photoreceptors. We found that photoreceptors and bipolar cells have divergent transcriptional profiles, and yet share remarkably similar cis-regulatory grammars. The predominant cis-regulatory motifs in the enhancers of both cell classes are K50 homeodomain binding sites, which are required for activity. These motifs are bound by two transcription factors (TFs), CRX and OTX2, which are expressed in both photoreceptors and bipolar cells. In contrast, cell type-specific open chromatin regions are distinguished by enrichment of E-box motifs in bipolar cells, and Q50 homeodomain motifs in photoreceptors. In bipolar cells, Q50 motifs are thought to mediate repression of photoreceptor-specific genes through the bipolar-specific TF VSX2. We show that converting selected K50 motifs to Q50 motifs represses reporter expression in bipolar cells, while photoreceptor expression is maintained. These findings suggest that partitioning of Q50 motifs within cell type-specific CREs was likely a critical step in the divergence of the bipolar transcriptome from that of photoreceptors, facilitating the emergence of the complex interneuronal circuitry of the vertebrate retina.

overall_design:
ATAC-seq of adult (6-8wk) mouse bipolar cells, including aggregate, ON, and OFF populations (two biological replicates each) purified from transgenic reporter lines via fluorescence-activated cell sorting (FACS). RNA-seq of adult (6-8wk)  mouse bipolar cells, including aggregate, ON, and OFF populations (three biological replicates each) purified from transgenic reporter lines via FACS.

Photoreceptor samples are re-analyzed from GSE83312.

middle: P

first: Andrew

middle: E

last: Hughes

first: Karen

last: Lawrence

first: Connie

last: Myers

first: Joseph

last: Corbo


title: Genome-wide screening of drought-responsive long noncoding RNAs in rice

city: Pyeongchang

first: Choonkyun

last: Jung

state: Gangwon

address: 1447 Pyeongchang-ro, Daehwa

department: Department of International Agricultural Biotechnology

institute: Seoul National University

summary: RNA-seq analyses of drought-treated rice leaves were performed to screen long noncoding RNAs showing differential expression in a time-dependent manner.

overall_design: Eight transcriptome profiles of drought-treated 5-week-old rice leaves were generated by deep sequencing using Illumina HiSeq 4000.

first: Pil

middle: J

last: Chung

first: Nuri

last: Oh


title: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-Seq]

first: Fei

last: Ji

summary: Analysis of adult progenitor cells depleted for DDX6. Results provide insight into the regulation of human stem cell self-renewal and differentiation by the RNA-binding protein DDX6

overall_design: RNA-seq

first: Bruno

last: Di Stefano

first: Ruslan

last: Sadreyev

first: Konrad

last: Hochedlinger


title: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [CLIP-Seq]

city: La Jolla

first: En-Ching

last: Luo

address: 9500 Gilman St

institute: UCSD

summary: Analysis of human embryonic stem cells and induced pluripotent stem cells depleted for DDX6. Results provide insight into the regulation of human stem cell self-renewal and differentiation by the RNA-binding protein DDX6

overall_design: CLIP-seq

first: Stefan

last: Aigner


title: The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]

summary: Analysis of DDX6 eCLIP in human skeletal myoblasts to identify DDX6 target genes, and binding locations.

overall_design: Enhanced crosslinking and immunoprecipitation (eCLIP) was performed on Human Skeletal Myoblast cells


title: In Vivo Profiling of Leukemic Stem Cell Fitness

first: Jiantao

last: Shi

address: 3 Blackfan Circle

institute: dana farber cancer institute

summary: By transplanting in competition multiple pre-leukemic clones in a cohort of primary recipients, we observed emergence of dominant clones during the development of AML. By sampling “winner” clones at different time points, we could observe the gradual acquisition a of cell-intrinsic growth advantage that was preserved in secondary transplantation, whereas control “loser” clones grew at a significantly lower rate. Functional characterization of the winner clones demonstrated a higher engraftment rate in vivo, whereas the self-renewal potential and growth rate in vitro was similar among winner and loser clones. By comparing the gene expression profile of leukemic stem cells isolated from various clones, we observed that the most aggressive clones share a common signature characterized by activation of multiple metabolic pathways, such as steroid biosynthesis and response to oxidative stress.

overall_design: A pre-leukemic cell line was generated by isolating murine granulocyte-macrophage progenitors from a male B6.SJL-Ptprc<a> Pepc<b>/BoyJ and infecting with a MSCV-MLL/AF9-IRES-NeoR retrovirus. Single clones of that cell line were labeled with lentiviruses driving the expression of multiple fluorescent proteins (iRFP, GFP, Sapphire and BFP). This pool of clones was transplanted in multiple recipients (M784, M798 and M800). Disease competition and evolution was tracked prospectively in primary recipients through repeated sampling of blood and bone marrow at different time points (T0: pre-transplantation; T2: 65 days; T3: 88 days; T4:98 days). Secondary leukemic cell lines were established from individual clones, harvested at serial time points during growth in vivo. In order to study the cell-intrinsic characteristics acquired following exposure to the bone marrow microenvironment, these secondary cell lines were transplanted into additional recipients to measure engraftment potential, growth rate, cell cycle and apoptosis, gene expression profile and acquisition of secondary mutations. Leukemic burden was defined as fraction of leukemic cells in BM of secondary recipients.

first: Francois

last: Mercier


title: Gene expression of adherent and spheroid cells derived from both D-WT and D-MT cells

first: Kang-Yell

last: Choi

state: State...

address: 50 Yonsei Ro, Seodemun-Gu Seoul 120-749, Korea

institute: Yonsei University

summary: Mutant KRAS activates cancer stem cells (CSCs) contributing transformation of colorectal cancer (CRC) cells harboring adenomatous polyposis coli (APC) mutations. The factors mediating activation of CSCs by KRAS mutation were systematically investigated through a microarray analysis of the APC-mutated isogenic DLD-1 CRC cells harboring homogeneous wild-type KRAS (D-WT) or mutant KRAS (D-MT). The objective of the study was to find the factors specifically induced in the spheroids harboring both APC and KRAS mutations.

overall_design: D-WT and D-MT cells were grown under both adherent and spheroid conditions for 72 h. Each of the four groups contained three biological replicates.

first: Junyong

last: Yoon

first: Jeong-Ha

last: Hwang


title: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [polysome RNA-seq]

summary: Analysis of adult and embryonci stem cells depleted for DDX6. Results provide insight into the regulation of human stem cell self-renewal and differentiation by the RNA-binding protein DDX6.

overall_design: Polysome cells were treated with cycloheximide (CHX) at 100 µg/ml for 5 min at 37°C. And then resuspend in polysome lysis buffer,  loaded on the sucrose gradient and centrifuged at 35,000 x g (Beckman, rotor SW41) at 4 °C for 3 h.  500 µl fraction were collected using a FC203B (Gilson) fraction collector. Fractions containing monosome(MONO), light polysome (LITE), medium polysome (MID), heavy polysome (HEAVY), and total polsome (POLY) were pooled.


title: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [ATAC-Seq]

summary: Analysis of adult and embryonci stem cells depleted for DDX6. Results provide insight into the regulation of human stem cell self-renewal and differentiation by the RNA-binding protein DDX6

overall_design: ATAC-seq


title: Genome-wide analysis of gene expression after AML1-ETO and Ezh1 knock down in leukemia

city: M

first: L

last: D

state: M

address: District

department: Department of Hematology

institute: Hospital

summary: The chimeric protein AML1-ETO is subjected to an array of posttranslational modifications that crucially regulate its functions. Enhancer of zeste homolog 1 (Ezh1) regulates gene expression through its histone methyltransferase activity. In this study, we test the impact of Ezh1 on AML1-ETO regulating target gene expression.  Results provide important information of the response of Ezh1 knock down, AML1-ETO knock down or both.

overall_design: Total RNA obtained from SKNO-1 cells with AML1-ETO knock down or Ezh1 knock down compared to scrambled control cells.


title: SIX1 regulates aberrant endometrial epithelial cell differentiation and cancer latency following developmental estrogenic chemical exposure

status: Public on Oct 15 2019

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Female mice exposed neonatally to the synthetic estrogen diethylstilbestrol (DES) develop metaplastic and neoplastic uterine changes as adults. Abnormal endometrial glands express the oncofetal protein sine oculis homeobox 1 (SIX1) and contain cells with basal (cytokeratin [CK]14+/18-) and poorly differentiated features (CK14+/18+), strongly associating SIX1 with aberrant differentiation and cancer. Here we tested whether SIX1 expression is necessary for abnormal endometrial differentiation and DES-induced carcinogenesis by using Pgr-cre to generate conditional knockout mice lacking uterine Six1 (Six1d/d). Interestingly, corn oil (CO) vehicle treated Six1d/d mice develop focal endometrial glandular dysplasia and features of carcinoma in situ as compared with CO wildtype Six1 (Six1+/+) mice. Furthermore, Six1d/d mice neonatally exposed to DES had a 42% higher incidence of endometrial cancer relative to DES Six1+/+ mice. While DES Six1d/d mice had >10-fold fewer CK14+/18- basal cells within the uterine horns as compared with DES Six1+/+ mice, the appearance of CK14+/18+ cells remained a feature of neoplastic lesions. We have employed whole genome microarray expression profiling as a discovery platform to identify genes associated with the phenotypic changes described above. Expression of three genes (Ihh, Krt14, and Trp63) were quantified by real-time PCR, confirming low variability between samples as well as the predicted response pattern.

overall_design: Gene expression analysis was conducted on uterine horn tissue from four independent biological replicates for each exposure group (CO and DES) and genotype (Six1+/+ or Six1d/d) at 6 months-of-age (mos).

first: Alisa

last: Suen

first: Wendy

last: Jefferson

first: Carmen

last: Williams


title: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RRBS]

first: Kendell

last: Clement

address: 7 Divinity Ave.

type: Methylation profiling by high throughput sequencing

overall_design: Human induced pluripotent stem cells depleted for DDX6.


title: LncRNA Expression Profiling  in sinonasal squamous cell carcinomas

city: Harbin

first: Yanan

last: Sun

state: Heilongjiang

address: No. 246, Baojian Road

department: The Second  Affiliated Hospital, Harbin Medical University

institute: Department of Otorhinolaryngology, Head and Neck Surgery

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

summary: Long non-coding RNAs (lncRNAs) play important roles in various biological progresses of carcinogenesis. However, the function of lncRNAs in human sinonasal squamous cell carcinoma (SNSCC) remains greatly unclear. In the current study, lncRNA AC091729.7 expression was examined in SNSCC samples by using microarray.The human 8 × 60 K lncRNA array was produced by Arraystar Company (USA). Over 25,000 lncRNAs were gathered from the canonical data sources encompassing UCSC, NCBI RefSeq, RNAdb, and NRED.

overall_design: LncRNA Expression Profile analysis was performed in five patients who had sinonasal squamous cell carcinomas and underwent  surgical resection. Paired cancerous and adjacent normal tissues were collected.


title: Gene analysis of major signaling pathways regulated by gonadotropins in human ovarian granulosa cells

city: Québec

first: Patricia

middle: G

last: Tremblay

state: Québec

address: 2440 Hochelaga Blvd

department: Sciences animales

institute: Laval University

summary: RNA seq analysis of protein kinase A, protein kinase B and protein kinase C signalling pathways in human tomoural granulosa cells (KGN).

overall_design: Cells treated with specific activators for each signalling pathway with gene functional analysis

first: Marc-André

last: Sirard


title: TIP60/KAT5 is required for the maintenance of homeostasis in hippocampal CA1

city: Goettingen

first: Vakhtang

last: Elerdashvili

address: Von-Siebold Str.3a

institute: German Center for Neurodegenerative Diseases

summary: ChIP-Seq for H4K12ac from the hippocampal neuronal nuclei of Tip60 cKO and control mice.

overall_design: 12 samples

first: Cemil

last: Kerimoglu

first: M

last: Sadman Sakib


title: A novel miRNA-4484 is up-regulated on microarray and associated with increased MMP-21 expression in serum of systemic sclerosis patients

city: Lublin

first: Marta

last: Rusek

address: Radziwillowska 11

department: Dept. of Dermatology

country: Poland

institute: Medical University of Lublin

summary:
Systemic sclerosis (SSc) is a complex, heterogeneous connective tissue disease, characterized by fibrosis and ECM deposition in skin and internal organs, autoimmunity, and changes in the microvasculature. Profiling of circulating miRNAs in serum has been found to be changed in pathological states, creating new possibilities for molecular diagnostics as blood-based biomarkers. This study was designed to identify miRNAs that are differentially expressed in SSc and might be potentially contributing to the disease etiopathogenesis or be used for diagnostic purposes. Thus, we compared the expression pattern of multiple miRNAs in serum of 10 SSc patients to 6 healthy controls using microarray analysis, and RT-qPCR to confirm the obtained results. In addition, bioinformatics analysis was performed to explore miRNAs target genes and the signaling pathways that may be potentially involved in SSc pathogenesis.
Our study shows a different expression of 15 miRNAs in SSc patients. We identified that miR-4484, located on chromosome 10q26.2, was an 18-fold up-regulated in SSc patients compared to a control group. Bioinformatics analysis of the miR-4484 target genes and the signaling pathways showed that it might be potentially involved in the TGF-β signaling pathway, ECM-receptor interaction, and metalloproteinases expression. Based on the chromosomal location, the most interesting target gene of miR-4484 may be MMP-21. We found that the expression of MMP-21 significantly increased in SSc patients compared to healthy subjects (P<0.05). Our results suggest that miR-4484, and MMP-21 might be novel serum biomarkers that may correspond to pathological fibrosis in SSc, but it needs to be validated in further studies.

overall_design: The expression pattern of multiple miRNAs in serum of 10 SSc patients to 6 healthy controls using microarray analysis was performed.

first: Małgorzata

last: Michalska-Jakubus

last: Kowal

first: Jerzy

last: Bełtowski

first: Dorota

last: Krasowska


title: Gene expression in dorsal halves of Apcdd1-depleted Xenopus laevis embryos

city: Rochester

first: Alin

last: Vonica

state: NY

address: 4245 East Avenue

department: Biology

institute: The Nazareth College

summary: apcdd1, a gene mutated in hereditary hypotrychosis simplex, is a maternally expressed gene in Xenopus embryos, required for correct formation of anterior and dorsal structures. Initial data suggested Apcdd1 functions as zyogtic Wnt inhibitor. Here we indentify genes regulated by Apcdd1 in the organizer area of early gastrula stage embryos

overall_design: 4 cell stage embryos were injected marginally in each of the dorsal blastomeres with 10ng anti apcdd1 MO or control MO. apcdd1-depleted embryos were also labeled on the ventral side with Nile Blue crystals, because some of the dorsally-depleted embryos displayed a delay in dorsal lip formation. At stage 10.5, when the dorsal lip is clearly marked, the vitelline membrane was removed with tweezers and the dorsal half sectioned with a hair knife. Three batches of 10 embryos were prepared for each condition (control and depletion).

first: A

last: Christiano


title: Gene expression profiling via RNA sequencing of patient brain tumors cultured in 3D bioengineered cultures

city: Medford

first: David

middle: L.

last: Kaplan

address: 4 Colby Street

institute: Tufts University

summary: Using pediatric ependymoma and adult glioblastoma (GBM) as examples, it was shown that the 3D brain ECM-containing microenvironment with a balance of cell-cell and cell-matrix interactions supports distinctive phenotypes, which are associated with tumor type-specific and ECM-dependent patterns in the tumor cells’ transcriptomic profiles. 3D model’s culture conditions affect tumor tissue’s gene expression profiles, and suggest that these genetic changes underlie the phenotypic outcomes of tumor growth in the different microenvironments. In particular, 3D tissue models with brain-ECM containing hydrogels (i.e. derived from fetal or adult brain sources) differed from those with non-brain derived ECM hydrogels (i.e. unsupplemented collagen I) for both ependymoma and GBM.

overall_design: Examination of patient anaplastic ependymoma across three experimental categories: media type (FBS versus serum free), time point in culture (0.5, 1.5 and 4 months), and ECM (fetal brain ECM enriched collagen I- FECM, adult brain ECM enriched collagen I-AECM or plain collagen I- CLG1) and patient GBM across the three ECM conditions. n=1 for each experimental category (and n=2 for GBM samples) were sequenced.

first: Disha

last: Sood

middle: L


title: m6A profiles in shCTRL, shMETTL3 HeLa cells

city: Beijing

first: Bao-Fa

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: Cells were washed with cold PBS twice and scraped from the plates, then centrifuged at 1000 rpm for 5 min to pellet cells. Washed cells were lysed with 400 L of cell lysis buffer (10 mM Tris-HCl pH7.5, 150 mM NaCl, 0.15% NP-40 and proteinase inhibitor cocktail) and incubated on ice for 10 min. The suspension was carefully add at the top of sucrose buffer (10 mM Tris-HCl pH7.5, 150 mM NaCl, 24% sucrose), and centrifuged at 3200g for 10 min to collect nuclear pellets. Pellets were resuspended in 250 L of Glycerol buffer (20 mM Tris-HCl pH7.5, 75 mM NaCl, 0.5 mM EDTA pH8.0, 50% glycerol), then then immediately add 250 μl Nuclear lysis buffer (10 mM Tris-HCl pH7.5, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA pH8.0, 1% NP-40, 1M urea). Mix by vortexing for 4 s and incubate on ice for 2 min. Centrifuge the lysate at 13,000 × g for 2 min to precipitate the chromatin–RNA complex. Brieﬂy rinse the chromatin pellets with PBS-EDTA. RNA was extracted with Trizol reagent.  RNA libraries were prepared according to manual of SMARTer smRNA-Seq Kit for Illumina (Clontech, 635031).

overall_design: Examination of m6A levels in zebrafish embryo.

first: Xin

last: Yang

first: Yuigui


title: NET-seq analysis of pSer2-Pol II profile in shCTRL, shMETTL3 and shDDX21 HeLa cells

summary: The chromatin fraction was isolated from 5x107 HeLa cells. Chromatin was digested in 100 mL of MNase (40 units/ mL ) reaction buffer for 3 min at 37 °C in a thermomixer (1,400 rpm). After addition of 10 L EGTA (25mM) to inactivate MNase, soluble digested chromatin was collected by 13,000 rpm centrifuge for 5 min. 10 mg of Pol II antibody was conjugated to magnetic protein A beads. The supernatant was diluted with 400 mL of NET-2 buffer and pSer2-Pol II antibody-conjugated beads were added. Incubated the IP reaction at 4 °C for 1 hr. The beads were washed with 1 mL of NET-2 buffer six times and 100 mL of 1xPNKT (1xPNK buffer and 0.05% Triton X-100) buffer once. Washed beads were incubated in 50 mL PNK reaction mix (1xPNKT, 1 mM ATP and 0.05 U/ml T4 PNK (NEB)) in Thermomixer at 37 °C, 1,400 rpm for 6 min. Beads were washed with 1 mL of NET-2 buffer once and RNA was extracted with Trizol reagent. RNA was suspended in urea Dye (7M Urea, 1xTBE, 0.1% BPB and 0.1% XC) and resolved on 6% TBU gel (Invitrogen) at 200 V for 5 min. Gels with 30-160 nt RNAs were collected. 0.2 mL tube was prepared with holes made with 25G needle and placed in a 1.5 mL tube. Gel fragments were placed in the layered tube and broken down by centrifugation at 12,000 rpm for 1 min. The small RNAs were eluted from gel using RNA elution buffer (1 M NaOAc and 1 mM EDTA) at 25 °C for 1 hr in Thermomixer (900 rpm). Eluted RNA was puriﬁed with SpinX column (Coster) with 2 glass ﬁlters (Millipore) and the ﬂow-through RNA was ethanol precipitated.

overall_design: Examination of pSer2-Pol II profile


title: Hypocretin-specific CD4+ T cells in narcolepsy patients and controls: in vivo clonal expansion and phenotypes

city: Stanford

first: Wei

last: Jiang

address: 269 Campus Dr. CCSR1200

department: Pediatrics

institute: Stanford University

summary: Individuals with narcolepsy suffer from abnormal sleep patterns due to loss of neurons that uniquely supply hypocretin (HCRT). Previous studies found the associations of narcolepsy with human leukocyte antigen (HLA)-DQ6 allele and T-cell receptor α (TRA) J24 gene segment and also suggested that in vitro-stimulated T cells can target HCRT. However, DQ6+ individuals generate DQ6-HCRT tetramer+/TRAJ24+ TCRs. Without a proof that an HCRT-reactive cell expressing such TCRs has expanded in vivo, T cell-mediated autoimmunity in narcolepsy remains speculative. Here, we isolated DQ6-HCRT tetramer+/CD4+ T cells (low frequency, <0.04%) from DQ6+ individuals with/without narcolepsy. Within 74 informative TRAJ24+ TCRαβ from 8/12 patients and 11/12 controls, we identified a conserved family of clonotypes shared by 2 patients and 2 controls using identical α/β genes. TRAJ24-G allele+ clonotypes only expanded in the two patients, whereas a TRAJ24-C allele+ clonotype expanded in a control. A representative tetramer+/G-allele+ TCR showed signaling reactivity to the physiologically modified form of the epitope HCRT87-97. Clonally expanded G-allele+ T cells also exhibited an unconventional effector phenotype. In vivo expansion of HCRT-reactive TRAJ24-G allele+ cells provides critical evidence for an autoimmune contribution to narcolepsy development.

overall_design: DQ6/hypocretin peptide tetramer+/CD4+ T cells were isolated from the peripheral blood of 12 narcoleptic patients and 12 DQ6 allele-matched controls. Four different tetramers were used.

first: Elizabeth

middle: D

last: Mellins


title: H3K27ac ChIP-seq in LNCaP cell line overexpressing WT or mutant FOXA1

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston

summary: Our data suggested  that FKHD-MSs impair the chromatin binding of FOXA1 to AR-dependent enhancers and thus suppress AR transcriptional activity, and promote PCa progression through increasing FOXA1 binding to a subset of AR-independent enhancers that regulates transcription of genes mediating EMT and metastasis

overall_design: We generated LNCaP stable cells with tetracycline-inducible expression of V5-tagged FKHD-MSs or WT FOXA1. H3K27ac ChIP-seq experiments were performed on these cell lines

first: Shuai

last: Gao

first: Dong

last: Han

first: Sujun

last: Chen

first: Housheng

middle: H

last: He


title: RNA-seq in LNCaP cell line overexpressing WT or mutant FOXA1

overall_design: We generated LNCaP stable cells with tetracycline-inducible expression of V5-tagged FKHD-MSs or WT FOXA1. RNA-seq experiments were performed on these cell lines with or without DHT


title: FOXA1 ChIP-seq in LNCaP cell line overexpressing WT or mutant FOXA1

overall_design: We generated LNCaP stable cells with tetracycline-inducible expression of V5-tagged FKHD-MSs or WT FOXA1. FOXA1 ChIP-seq experiments were performed on these cell lines


title: ssDRIP-seq analysis of R-loop level in shCTRL, shMETTL3 and shDDX21 HeLa cells

last: Sun

summary: gDNA was estracted and digested with cocktail of restrict enzymes MseI, DdeI, AluI, MboI, incubated at 37°C for 6 h. After purified by phenol/chloroform extraction, fragmented DNA was resuspended by TE, and quantified by Qubit 3.0 (Invitrogen). For each sample, 20 μg input DNA was immunoprecipitated overnight at 4°C in a shaker, with 1× DRIP binding buffer (10 mM NaPO4 pH 7.0, 140 mM NaCl, 0.05% Triton X-100) and 10 μg S9.6 antibody (ATCC, HB-8730). After adding 50 μl Dynabeads Protein G (Invitrogen, 10004D) and incubated for 4 h, the beads with antibody were washed by 1× DRIP binding buffer for 4 times at room temperature, each wash takes 10 min. Added 250 μl elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) and 5 U Proteinase K to beads/antibody complexes, incubated for 40 min in an Eppendorf ThermoMixer at 55°C, 1,000 rpm. Purified by phenol/chloroform extraction, and moved supernatant to a new tube, followed by adding 1/10 volume 3 M NaAc, 1 μl GlycoBlue (Invitrogen) and 1 volume isopropanol, precipitated at -20°C for 3 h and then centrifuged. After washed by 70% ethanol and dried, the DRIPed DNA pellet was resuspended by 75 μl low EDTA TE buffer (10 mM Tris-HCl 8.0, 0.1 mM EDTA). NGS libraries were constructed using Accel-NGS® 1S Plus DNA Library Kit (Swift Biosciences).

overall_design: Examination of R-loop in Hela cells


title: Forkhead domain mutations in FOXA1 drive prostate cancer cell progression

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of self-reactive B cells Transcriptomes in PPs

city: San Diego

first: Ashima

last: Shukla

address: 10901 N Torrey Pines Rd, La Jolla, La Jolla

institute: Sanford Burham Prebys Medical Discovery

summary:
Purpose: The purpose of this study is to identify novel regulator of B cell tolerance to gut associated self antigens using HEL system. The goals of this study are to compare NGS-derived (RNA-seq) differentially expressing genes in antigen encountered self-reactive B cells to non-antigen expirenced cells from different tissues.
Methods: Self-reactive (HEL binding) cells were sorted from the spleen, mesenteric lymph nodes and Peyer's Patches of VillinCre-mDelloxp-SWHEL mice. RNA was isolated and cDNA librabries were made using SMART (Switching Mechnaism at 5' End RNA template) technology followed by NGS using Nextera from Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10). RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of self-reactive B cells in gut transcriptomes, with biologic and technical replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Self-reactive B cells in gut transcriptomes

first: Robert

middle: C

last: Rickert

first: John

middle: R

last: Apgar


title: NR2F2 study

city: Shanghai

first: Guojuan

state: Shanghai

address: Ruijin er road

department: School of Medicine

institute: Shanghai Jiaotong University


title: Genome-wide maps of chromatin accessibility before and after NR2F2 knock down using ATAC-seq.

summary: FOXA1 and GATA3 can remodel chromatin accessibility, we further explored what effect of NR2F2 would have on chromatin properties. ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing) is widely used to map chromatin accessibility genome-wide. Thus, We perform ATAC-seq without oestrogen stimulation before and after NR2F2 depletion.Covalent modifications are a main chromatin property.To test whether NR2F2 favoured histone modification deposition on chromatin, we profiled ChIP-Seq of H3K4me1, H3K4me3, and H3K27ac following NR2F2 depletion in oestrogen-starved MCF-7 cells to gain comprehensive histone medication landscape.

overall_design: Study of chromatin accessibility in WT and NR2F2 KO MCF-7 cells by deep sequencing using Illumina xten.

first: Xinrui

last: Wang


title: m6A facilitates transcription termination by promoting R-loop formation


title: Gene expression analysis of hematopoietic stem/progenitor cells in the zebrafish kidney

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

institute: Kanazawa University

summary: Hematopoietic stem cells (HSCs) maintain the entire blood system throughout the life and are utilized for a therapeutic component of blood diseases. The zebrafish is an elegant genetic model for the study of hematopoiesis due to its many unique advantages. We have developed the method to isolate zebrafish HSCs by a combination of two HSC-related transgenic lines, gata2a:GFP and runx1:mCherry. In this study, we performed RNA-seq analysis in three distinct hematopoietic cell populations in the adult kidney, gata2a+ runx1+ cells (HSCs), gata2a− runx1+ cells (erythroid- and/or myeloid-primed progenitors), and gata2a+ runx1− cells (lymphoid-primed progenitors).

overall_design: mRNA profiles of isolated gata2a+ runx1+ cells, gata2a− runx1+ cells, and gata2a+ runx1− cells in the zebrafish kidney were generated by Quartz-seq using Illumina NextSeq500.

first: Shiori

last: Yamamori


title: Transcriptional profiling of PBMC from patients with aGvHD and patients without aGvHD after alloHSCT

first: Aijie

last: Huang

address: 168, Changhai road

institute: Changhai Hospital

summary: The goal of this study are to identify critical biomarkers distinguishing alloHSCT recipients with aGvHD from alloHSCT recipients without aGvHD in two separate cohorts. Total RNA was isolated from the peripheral blood mononucleated cells and then quantified on a Bioanalyzer. Whole transcriptome sequencing libraries (3 pairs of aGvHD and controls, 6 libraries in total) were prepared following the manufacturer’s instructions for the Whole Transcriptome Sample Prep Kit (Illumina) by GENEWIZ Company. 1148 presented significant alterations in cases with aGvHD (t test, FDR corrected P < 0.05, |fold change|>1.5). Transcriptomic pathway analysis showed that the GPL metabolism pathway was one of the most significant pathways with Bonferroni correction P value (Q value) less than 0.001, indicating that it was a critical pathway related to the development of aGvHD.

overall_design: To identify critical biomarkers distinguishing alloHSCT recipients with aGvHD from alloHSCT recipients without aGvHD in two separate cohorts.

first: Yue

last: Liu

first: Qi

first: Xiaofei

first: Yang

last: Fei

first: Xiaoming

last: Zhao

first: Weiping

last: Zhang

first: Zhanying

last: Hong

first: Zhenyu

last: Zhu

first: Jianmin

first: Yifeng

last: Chai

first: Xiaoxia

last: Hu


title: Transcriptome Sequencing of Solid Fermentation under Different Induced Carbon Sources

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary: Here comparative transcriptomic analyses of Penicillium oxalicum grown on wheat bran (WB), WB plus rice straw (WR) and WB plus Avicel (WA) as the sole carbon source under solid-state fermentation (SSF) revealed that most of differentially expressed genes (DEGs) were involved in metabolism specifically carbohydrate metabolism.

overall_design: Identification of key transcription factors regulating cellulase and hemicellulase in solid-state fermentation of Penicillium oxalate HP7-1 by differential transcriptome analysis

first: Shuai

first: Xu-Zhong

last: Liao


title: MicroRNA expression data from an epithelial-mesenchymal transition (EMT) model of triple negative breast cancer (TNBC).

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Triple-negative breast cancer (TNBC) is the most aggressive form of breast  cancer due to lack of effective targeted therapies. Here, we report that the expression of  miR-4417 is suppressed during the progression of TNBC cells from non-malignant to the  malignant stage. miR-4417 is localized to chromosome 1p36, a region with high loss of  heterozygosity in multiple cancers, and its biogenesis is DICER-dependent. Low  expression of miR-4417 is significantly associated with worse prognosis in TNBC  patients, while overexpression of miR-4417 is sufficient to inhibit migration and  tumorigenecity of TNBC cells in vitro. Overall, our findings suggest that miR-4417 exerts a  tumor suppressive effect and thereby could serve as a prognostic biomarker and  therapeutic tool against TNBC.
We used microarrays to profile the global miRNA changes during EMT to identify putative tumor suppressors and prognostic biomarkers for TNBC.

overall_design: Three biological replicates for each cell line (mesechymal MIIIshGFP vs epithelial MIIIshSMAD2) were selected for RNA extraction.

first: Chen

last: Wong

first: Sam

last: Thiagalingam


title: A comprehensive PDX gastric cancer collection captures cancer cell intrinsic transcriptional MSI traits.

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

summary:
Gastric cancer (GC) is the world's third leading cause of cancer mortality. In spite of significant therapeutic improvement, the clinical outcome for patients with advanced GC is poor; thus, the identification and validation of novel targets is extremely important from a clinical point of view.
We generated a wide, multi-level platform of GC models, comprising 100 Patient-derived xenografts (PDXs), primary cell lines and organoids. Samples were classified according to their histology, microsatellite stability (MS) and Epstein-Barr virus status, and molecular profile.
This PDX platform is the widest in an academic institution and it includes all the GC histologic and molecular types identified by TCGA. PDX histopathological features were consistent with those of patients’ primary tumors and were maintained throughout passages in mice. Factors modulating grafting rate were histology, TNM stage, copy number variation of tyrosine kinases/KRAS genes and MSI status. PDX and PDX-derived cells/organoids demonstrated potential usefulness to study targeted therapy response. Finally, PDX transcriptomic analysis identified a cancer cell intrinsic MSI signature, which was efficiently exported to gastric cancer, allowing the identification -among MSS patients- of a subset of MSI-like tumors with common molecular assets and significant better prognosis.
We generated a wide gastric cancer PDX platform, whose exploitation will help identify and validate novel 'druggable' targets and define the best therapeutic strategies. Moreover, transcriptomic analysis of GC PDXs allowed the identification of a cancer cell intrinsic MSI signature, recognizing a subset of MSS patients with MSI transcriptional traits, endowed with better prognosis.

overall_design:
Expression profiling of frozen primary, patient derived xenograft, cells and organoids from gastric cancer as indicated in the sample titles:
Cells = frozen cells derived from XenoGrafts
Organoids = XenoGraft derived organoids?
PR = Primary tumor
PRX = parient derived xenograft

first: Simona

last: Corso

first: Claudio

last: Isella

first: Silvia

last: Giordano


title: Differential chromatine state and ER binding potentially induced by NR2F2 depletion.

first: Guojuan

last: Jiang

summary: ERα binding activity largely depends on access to binding sites on chromatin, which is facilitated in part by Pioneer Factors (PFs).We show that most binding events of NR2F2  occur together with the ERα binding sites.To explore whether NR2F2 may act as potential pioneer factor of ER, we performed a series of ChIP-seq genome wide in MCF-7. Since NR2F2 associates with chromatin prior to estrogen treatment and its depletion in MCF-7 cells did not affect ERα expression, we hypothesize NR2F2 may inhibit estrogen-dependent growth by modulating ERα recruitment. We performed ChIP-seq genome wide gainst ERα before and after NR2F2 depletion.Covalent modifications are a main chromatin property.To test whether NR2F2 favoured histone modification deposition on chromatin, we profiled ChIP-Seq of H3K4me1, H3K4me3, and H3K27ac following NR2F2 depletion in oestrogen-starved MCF-7 cells to gain comprehensive histone medication landscape.

overall_design: Examination of 3 histone modifications and ER, FOXA1 binding in WT and NR2F2 KO MCF-7 cells.

first: Xinrui

last: Wang


title: Estrogen response in breast cancer cell line MCF-7 is dependent on NR2F2 [RNA-seq]

summary: We show that most binding events of NR2F2  occur together with the ERα binding sites.To address the functional relationship between NR2F2 and ERα, we assessed the role of NR2F2 in oestrogen-induced growth in ER positive cell line MCF-7. The MTT experiment showed that inhibition of NR2F2 prevented the oestrogen-induced proliferation of MCF-7 cells.To further explore the effect of NR2F2 on estrogen response, We expanded our knockdown studies by performing RNA-seq analysis for MCF-7 cells transfected with control or NR2F2 shRNAs with or without E2.

overall_design: Study of gene expression in WT and NR2F2 KO in MCF-7 cells before and after estroge treatment


title: Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses (ATAC-seq)

city: New York

first: Hideo

last: Watanabe

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Mesenchymal tumor subclones secrete cytokines that promote tumorigenesis and chemoresistance, but the mechanism that underlies this phenomenon remains poorly understood. Here we identify a de-repressed subclass of endogenous retroviruses (ERVs) that engage innate immune signaling in mesenchymal cancer cells. These Stimulated 3 Prime Antisense Retroviral Coding Sequences (SPARCS) are oriented inversely in 3’UTRs of certain interferon-inducible genes, generating dsRNA following IFN exposure. Sensing of this dsRNA by MAVS fuels activation of TBK1, IRF3, and STAT1 signaling. SPARCS induction in human tumors is tightly associated with B2M and MHC class 1 antigen expression, mesenchymal markers, and downregulation of chromatin modifying enzymes. Cell lines poised to induce high levels of SPARCS expression are associated with an AXL positive mesenchymal cell state. These data unveil a novel subclass of ERVs whose derepression triggers pathologic innate immune signaling in cancer.

overall_design: Examination of chromatin accessibility in H69 and H69AR cells

first: Israel

last: Cañadas

first: David

last: Barbie


title: The transcription factor IRF4 plays a critical role in plasma cell identity and function

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: IRF4 regulates the plasma cell signature but also regulates plasma cell metabolism

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcriptional profiling of plasma cells in mice and cell lines with and without IRF4 intact using RNA sequencing

first: Michael

last: Low

first: Yang

last: Tarlinton


title: Microarray analysis of the wildtype and recombinant E. coli strain containing an ncRNA nfiS to H2O2 shock

first: Yongliang

last: Yan

state: Haidian

address: 12th Zhongguancun Nanjie

institute: Chinese Academy of Agricultural Sciences

summary:
The aim of this study was to investigate the expressional changes profiles of the wildtype and recombinant Escherichia coli strain which contains an non-coding RNA nfiS from the nitrogen-fixing Pseudomonas stutzeri A1501 after hydrogen peroxide shock, so as to lay a theoretical foundation for further clarifying the mechanism of this ncRNA to enhance the resistance ability of E.coli to oxidative stress.
In our early research, an ncRNA named NfiS from the nitrogen fixing bacteria Pseudomonas stutzeri A1501 was identified to play an important role in the response to oxidative as well as osmotic stress. In this work, the nifS gene was transferred to E. coli Trans10. Heterologous expression of the nfiS in Trans10 enhanced its tolerance to salt stress and oxidative stress. To further study the effect of nfiS on gene expression in E. coli, microarray assay was performed to delineate the transcriptome difference between nfiS-expressing strain and wild type under H2O2 shock treatment.

overall_design: E. coli Trans10 and the derivatives strain Trans10-nfiS were cultured in LB broth at 30 °C overnight and then transferred into fresh LB broth the next day till the OD600 was raised to 0.6. Subsequently, 20 mM H2O2 was added into the medium and incubated at 30 °C, 220 rpm for 10 min. Cells were collected by centrifugation and stored in - 80 °C refrigerator for subsequent research.

first: Min

last: Lin

first: Guihua

last: Hu

first: Tao


title: Defining the Expression of piRNAs and Transposable Elements in Drosophila Ovarian Germline Stem Cells and Niche Cells

city: Heidelberg

first: Benjamin

middle: Andrew

last: Story

address: Meyerhofstrasse 1

department: Genomics

institute: European Molecular Biology Laboratory (EMBL)

type: Non-coding RNA profiling by high throughput sequencing

summary: Summary: Piwi-interacting RNAs (piRNAs) are important for repressing transposable elements (TEs) and modulating gene expression in germ cells, thereby maintaining genome stability and germ cell function. Here, we show that the canonical piRNA clusters are more active in GSCs (germline stem cells) and their early progeny than late germ cells, and identify new piRNA clusters using deep RNA sequencing. We show that GSCs have higher piRNA levels and lower TE levels than niche cells. Furthermore, many mRNA 3’UTR also exhibit the production of sense, antisense or dual-stranded piRNA. Finally, we show that there are extensive differences in alternative promoter usage and splicing which are likely to modulate gene function in GSCs and niche cells. Overall, this study serves as a major resource for the investigation of piRNA and TE dynamics in GSCs and niche cells.

overall_design: RNA-seq experiments isolating mRNA and smallRNA were performed for bam/bgcn/tkv, mutant ovaries and wildtype ovaries. The same type of sequencing was subsequently performed on GSCs and their surrounding niche cells.

first: Xing

last: Ma

first: Kazue

last: Ishihara

first: Marco

last: Blanchette

first: Hua

last: Li

first: Kathryn

last: Hall

first: Allison

last: Peak

first: Perera

last: Anoja

first: Jungeun

last: Park

first: Jeff

last: Haug

first: Ting

last: Xie


title: Hippocampal gene expression from Nr2f1 heterozygous knockout and WT mice

city: Cambridge

first: Ayush

middle: T

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

summary: Differential gene expression in the adult hippocampus of Nr2f1 heterozygous knockout mice.

overall_design: RNA-seq of hippocampus from Nr2f1 heterozygous knockout and WT mice.

first: Christian

last: Schaaf

first: Chun

last: Chen

first: Zhandong

last: Liu


title: Expression profiling reveals differential expressed genes between bovine IVF and SCNT embryos

city: Yangling

first: rui

last: cheng

address: No. 3, Taicheng Road

institute: Northwest A&F University

summary: Alternative splicing (AS) is generally observed in different developmental processes in mammals. In mammalian development, totipotency which is defined as the ability of a cell to give rise to all cell types of an entire organism is limited to early-stage preimplantation embryos. Somatic cell nuclear transfer (SCNT) can reprogram terminally differentiated cells into a totipotent state. However, studies addressing the functional role of AS in mammalian preimplantation embryonic development are lacking. Here we show that AS has important physiological functions in mammalian preimplantation embryonic development as a regulator. We discovered abundant AS transitions during both key events in preimplantation embryonic development, fertilization and embryonic genome activation. We also found that the RNA-binding protein hnRNPK govern the oocyte-to-embryo transition by regulating the MII oocyte-specific exon exclusion in mouse. Furthermore, we demonstrated that SCNT embryos had abnormal alternative splicing compared to in vitro fertilized (IVF) embryos in bovine. We used RNA-targeting system CRISPR-Cas13d to target cis elements of ABI2 pre-mRNA to operate alternative splicing, reducing abnormal isoform ratios of SCNT embryos and greatly improve the production of cloned cows. Our results advance the understanding of SCNT-mediated reprogramming and its potential applications for both reproductive and therapeutic cloning.

overall_design: RNA-Seq profiles from pools of 6 two-embryos from bovine IVF (3 replicates) and SCNT (3 replicates) and 3 MII-embryos (3 replicates) using Illumina HiSeq 4000.

first: Xu

first: Yong

last: Zhang

first: Rui

last: Cheng


title: Transcriptomic analysis of transformed murine hepatic progenitors depleted or not for CDK8 or CDK19 kinases

status: Public on Oct 14 2019

city: Montpellier

first: Damien

last: Grégoire

address: 1919, route de Mende

institute: CNRS

summary: We report transcriptomes of hepatic progenitors cells (BMEL) wild-type or transformed by the expression of H-RasG12V, depleted of CDK8 or CDK19 kinases by crispr/Cas9 mediated editing.

overall_design: mRNA profiles of BMEL cells transformed by Ras wt or depleted for CDK8 and CDK19 kinases were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

last: Gregoire

first: Daniel

last: Fisher

first: Urszula

last: Hibner

first: Katarina

last: Bacevic

first: Geronimo

last: Dubra


title: Microarray profiling of miRNA in Hepatocellular carcinoma

first: Ji-Min

last: Zhu

address: 180 Fenglin Road, Shanghai, China

institute: Zhongshan Hospital of Fudan University

summary: To explore the critical roles of miRNAs playing in the pathogenesis of hepatocellular carcinoma, the Agilent microarray was used to the profiling of miRNA expression in 7 pairs of HCC and matched adjacent tumor-free tissues.

overall_design: In total, seven pairs of HCC and matched adjacent tumor-free tissues were collected during the surgery from HCC patients admitted to Zhongshan Hospital of Fudan University between 2008 and 2009.


title: Oncogenic changes and EMT in normal human bile duct epithelial cells are caused by parasite-derived materials and N-nitrosodimethylamine

city: Seoul

first: Eunmin

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu

institute: Yonsei University

summary: A total of 1,301 differentially expressed genes were identified: 521 upregulated and 780 downregulated. Furthermore, p21 and PAI levels decreased, which coincided with decreases in E-cadherin and increases in fibronectin expression, in cells stimulated with Clonorchis sinensis excretory/secretory products (ESPs) and NDMA. Cancer-related proteins, such as EGFR, K-ras, and PCNA, were significantly upregulated in cells exposed to C. sinensis ESPs and NDMA. Our results showed that C. sinensis ESPs and a small amount of NDMA were sufficient to induce cancerous transformation and epithelial-mesenchymal transition (EMT) in normal H69 cholangiocytes.

overall_design: mRNA expression profiles of the 'Human Liver' by Illumina Hi-seq 2500.

first: Kim

last: Eun-Min

last: Tai-Soon


title: Expression data from IRF4 KO mouse carotid arteries in response to wire-injury

city: Wuhan

first: Hongliang

last: Li

state: Hubei

address: JieFang Road 238, Wuhan

department: Department of Cardiology

institute: Renmin Hospital of Wuhan University

summary:
IRF4 is mainly expressed in immune cells, including B cell, T cell, macrophage and dendritic cell. Previous study showed that IRF4 plays important roles in regulating the differentiation and maturation of immune cells.  Recently, our and other`s studies revealed that IRF4 involved in the pathogenesis of cardiac hypertrophy, cerebral ischemic reperfusion injury and metabolic disorder. However, the function of IRF4 in VSMC and neointima formation was largely unknown. We found that IRF4 expression was dramatically decreased in the VSMCs of mouse carotid artery. More importantly, using global IRF4 deficient mouse (KO), we demonstrated that IRF4 deficiency significantly increased VSMC proliferation, migration and neointima formation compared with wild type mice (WT) in response to injury. To evaluate the underlying mechanism by which IRF4 promotes VSMC proliferation and migration after vascular injury, IRF4 KO and WT mice were subjected to wire-injury and the carotid arteries were collected at 14 days post-injury. We combined 3-5 vessels for one sample, and 3 samples for each phenotype. Subsequently, a total of 400ng RNA was used following Affymetrix instruction and 10 ug of cRNA were hybridized for 16 hr at 45°. GeneChips were scanned using the Scanner 7G and the data was analyzed with Expression Console using Affymetrix default analysis settings and global scaling as normalization method. RMA analysis was employed to evaluate the gene expression.
We used microarrays to detect the global gene expression in the carotid arteries of IRF4 knockout mice (IRF4 KO) compared with wild type mice (WT) at 14 days post-injury and identified distinct classes of altered genes

overall_design: Wild type (WT) and global IRF4 knockout mice (IRF4 KO) were subjected to wire-injury and the carotid ateries were collected at 14 days post-injury. We combine 3-5 vessels in one tube and for a single Affymetrix microarray. Total RNA was extracted and a total of 400ng RNA was used following Affymetrix instruction. 3 biological samples for each genotype.

first: Peng

first: Wenlin


title: Transcriptome analysis of marigold color

first: Shiya

address: No. 2, Yuanmingyuan West Road, Haidian District

institute: China Agricultural University

summary: Marigold (Tagetes erecta L.) is an important ornamental plant with a wide variety of colors. Despite its economic value, there are few biochemical and molecular basic studies of flower color in marigold. To study the mechanism behind its color formation, metabolomics analysis and de novo cDNA sequencing was performed on marigold inbred line ‘V-01’ and its petal color mutant ‘V-01M’, in four flower developmental stages.

overall_design: The yellow variety 'V-01' and the orange variety 'V-01M' are divided into four stages for transcriptome sequencing.

first: Huali

first: Hua

first: Fang

last: Liang

first: Helan

last: Qin

first: Yue

first: Richen

last: Cong

first: Haibo

last: Xin

first: Zhao


title: Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [RNA-seq]

city: Los Angeles

first: Min

last: Yu

state: CA

address: 1450 Biggy Street, NRT 3507

department: USC Norris Comprehensive Cancer Center, Keck School of Medicine

institute: University of Southern California

summary: Hematogenous metastasis is initiated by a subset of circulating tumor cells (CTCs) shed from primary or metastatic tumors into the blood circulation. Thus, CTCs provide a unique patient biopsy resource to decipher the cellular subpopulations that initiate metastasis and their molecular properties. However, one crucial question is whether CTCs derived from patients recapitulate human metastatic disease in an animal model. Here, we show that CTC lines established from breast cancer patients are capable of generating metastases in mice with a pattern recapitulating most major organs from corresponding patients. Genome-wide sequencing analyses of metastatic variants identified novel organ tropism-associated markers identified from CTCs and facilitate the development of potential therapies targeting metastatis initiating cells in circulation.

overall_design: Profiling of 4 breast cancer CTC  lines (4-5 replicates each) and -derived metastatic variants from brains (8 samples), bones (7 samples), lungs (5 samples), ovaries (5 samples) and kidney (1 sample)

first: Yu

last: Min

first: Klotz

last: Remi

first: Thomas

last: Amal


title: Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [micro-environment]

summary: Hematogenous metastasis is initiated by a subset of circulating tumor cells (CTCs) shed from primary or metastatic tumors into the blood circulation. Thus, CTCs provide a unique patient biopsy resource to decipher the cellular subpopulations that initiate metastasis and their molecular properties. However, one crucial question is whether CTCs derived from patients recapitulate human metastatic disease in an animal model. Here, we show that CTC lines established from breast cancer patients are capable of generating metastases in mice with a pattern recapitulating most major organs from corresponding patients. To investigate the tumor microenvironment changes in different metastases, we used RNA-seq to analyze expression changes in stromal cells after tumor formation in the brain, lung and bone microenvironments relative to control stromal cells from tumor free mice.

overall_design: Expression changes in stromal cells after CTC-derived tumor formation in the brain (3 samples), lung (7 samples), and bone (13 samples) microenvironments relative to control stromal cells from tumor free mice (3 replicates for bone and 2 replicates for lung and brain)

first: Remi

last: Klotz

first: Amal

last: Thomas


title: Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [ATAC-seq]

summary: Hematogenous metastasis is initiated by a subset of circulating tumor cells (CTCs) shed from primary or metastatic tumors into the blood circulation. Thus, CTCs provide a unique patient biopsy resource to decipher the cellular subpopulations that initiate metastasis and their molecular properties. However, one crucial question is whether CTCs derived from patients recapitulate human metastatic disease in an animal model. Here, we show that CTC lines established from breast cancer patients are capable of generating metastases in mice with a pattern recapitulating most major organs from corresponding patients. We used ATAC-seq to assay chromatin accessibility in parental CTC and CTC-derived metastatic cells. Genome-wide sequencing analyses of metastatic variants identified novel chromatin accessibility domains predicting organ-specific metastasis identified from CTCs and facilitate the development of potential therapies targeting metastatis initiating cells in circulation.

overall_design: Profiling of 4 breast cancer CTC  lines (4-8 replicates each) and -derived metastatic variants from brains (7 samples), bones (8 samples), lungs (5 samples), ovaries (5 samples) and kidney (1 sample).


title: Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants

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

overall_design: Refer to individual Series


title: The profile of long non-coding RNAs in mouse testis and sperm after exposure to cadmium

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

institute: Nanchang University

summary: Increasing evidences have shown that cadmium could caused male infertility. However, the exhaustive mechanisms have not been elucidated in mammals. Here, the mice testes and sperm RNA were used to investigate lncRNA expression profiles by stranded-specific RNA-seq on the transcriptome levels after exposure to cadmium. More LncRNA expression have been changed than mRNA genes by cadmium. Furthermore, many novel LncRNA were inducible expression, suggesting that LncRNA might be a good candidate for indicating the reproductive toxicity of cadmium. The present study provides a preliminary database for further exploring the mechanisms of reproductive toxicity caused by cadmium in mammalians.

overall_design: LncRNA profiles of mice (3-5 months) were generated by stranded-specific RNA-seq, using Illumina HiSeqTM 4000 with PE100.

first: Fengxin

last: Gao


title: Lung collapse and respiratory distress in neonatal cloned cows is caused by surfactant homeostasis disorders

city: Beijing

first: Yifan

last: Rao

address: yuanmingyuanxi street

institute: Chinese academy of agricultural sciences

summary: Respiratory distress is one of the major causes of the high mortality rate in neonatal cloned animals. Although some therapeutic methods have been used to improve the survival of cloned neonatal animals, the mechanisms of their neonatal respiratory distress lacked thorough investigation. Pathological analyses including necropsy and histology were implemented to determine the precise disease phenotypes, by which not fully dilated lungs, alveolar collapse and thickened alveolar walls were detected in neonatal cloned cows dying of respiratory distress compared to naturally conceived neonatal cows. In addition, we compared mRNA expression profiles between the two groups and differentially expressed genes (DEGs) have been achieved. Based on DEGs, GO and KEGG pathway enrichment analyses were performed, which showed that processes and pathways associated with surfactant homeostasis were significantly enriched between the two groups (p < 0.05).

overall_design: Gene expression in eight age-matched newborn cows, including four cloned cows that died of respiratory failure within 4 days of birth and were slaughtered immediately after death, and four normal healthy neonatal cows as the control group, which were also slaughtered 4 days after birth.

first: Xiaojing

last: Jiang

first: Huabin

last: Zhu

first: Linhua

last: Huang

first: Weihua

last: Du

first: Haisheng

last: Hao

first: Xueming

last: Zhao

first: Dong

last: Wang

first: Qiuling

first: Yunwei

last: Pang

first: Xiuzhu

last: Sun

first: Yan

last: Liu


title: Next Generation Sequencing Facilitates Quantitative Analysis of UVB(20mJ/cm2 and 40mJ/cm2) exposed and untreated HaCaT keratinocytes Transcriptomes

status: Public on Oct 12 2019

city: Chengdu

first: lidan

last: Xiong

address: No. 5, Gong Xing Road

institute: West China Hospital

summary:
Purpose: To compare the transcriptomes of UVB (20mJ/cm2 and 40mJ/cm2) exposed and untreated HaCaT keratinocytes by RNA-Seq analysis, trying to find differences in gene expression between UVB exposed and untreated of keratinocytes and then elucidate the candidate genes that may play important roles in the differentiation of UVB-induced damage in keratinocytes.
Methods: HaCaT keratinocytes were subjected to 20mJ/cm2 and 40mJ/cm2 UVB irradiation.
Results: To better understand the effects of UVB (20 mJ/cm2), mRNA-sequecing (n=3) were completed by Novogene Inc. A total 891 differentially expressed genes (DEGs) were identified between UV group and control group with 604 down-regulated and 287 up-regulated. A total of 4036 differentially expressed genes (DEGs) which compared with untreated group were identified by RNA-Seq, which provided abundant data for further analysis.

overall_design: HaCaT mRNA profiles of UVB(20mJ/cm2 and 40mJ/cm2) and untreated group were generated by deep sequencing, in triplicate, using Illumina xten.

first: Lidan

first: Hailun

last: He


title: The host response of IBS patients to allogenic and autologous faecal microbiota transfer

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: In this randomised placebo-controlled trial, irritable bowel syndrome (IBS) patients were treated with faecal material from a healthy donor (n=8, allogenic FMT) or with their own faecal microbiota (n=8, autologous FMT). The faecal transplant was administered by whole colonoscopy into the caecum (30 g of stool in 150 ml sterile saline). Two weeks before the FMT (baseline) as well as two and eight weeks after the FMT, the participants underwent a sigmoidoscopy, and biopsies were collected at a standardised location (20-25 cm from the anal verge at the crossing with the arteria iliaca communis) from an uncleansed sigmoid. In patients treated with allogenic FMT, predominantly immune response-related genes sets were induced, with the strongest response two weeks after FMT. In patients treated with autologous FMT, predominantly metabolism-related gene sets were affected.

overall_design: Microarray analysis was performed on sigmoid biopsies from ucleansed colon at baseline, 2 weeks and 8 weeks after FMT .

first: Savanne

last: Holster

first: Robert

last: Brummer

first: Julia

last: König


title: Sequencing of the 3' end of RNA using BRB-seq in Drosophila heterozygous cross

city: Lausanne

first: Michael

middle: Vincent

last: Frochaux

address: Route Cantonale

department: SV-IBI

country: Switzerland

institute: EPFL

summary: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants are channeled through distinct molecular layers is still limited. To address this, we employed a systems genetics approach on the gut transcriptomes from 38 control and orally-infected DGRP lines, identifying a large number of condition-specific expression quantitative trait loci (cis-eQTLs). By assessing the allelic imbalance in the transcriptomes of 19 F1 hybrid lines from a large round-robin design, we could independently attribute a robust cis-regulatory effect to only 10% of the detected cis-eQTLs. These results therefore suggest that many context-dependent eQTLs that are assumed to act in cis, may act in trans instead. Further comparison of the transcriptomes of resistant and susceptible DGRP lines revealed Nutcracker (ntc) as the only differentially expressed gene between resistance classes. Interestingly, we found that ntc is linked to infection-specific eQTLs that not only correlate with its expression level, but also to enteric infection susceptibility. This is consistent with our findings that ntc expression is induced upon infection, whereas loss of ntc confers an overall greater susceptibility to infection, including lower innate immune activation as well as impaired infection-induced stem cell activity. Further mechanistic analysis revealed one ntc eQTL that significantly decreases the binding affinity for the repressor Broad, resulting into an allele-specific ntc expression increase. Our collective findings therefore point to a large number of infection-specific cis and trans-acting eQTLs in the DGRP, including one common non-coding variant that lowers enteric infection susceptibility by modulating ntc gene regulation through altered Broad repressor binding.

overall_design: 19 crosses, 2 conditions each with 2 biological replicates.

middle: V

first: Maroun

middle: B

last: Sleiman

first: Bart

last: Deplancke


title: Gene expression profiles of PGAM5-knockout brown adipose tissue

city: Bunkyo-ku

first: Sho

last: Sugawara

state: Tokyo

department: Pharmaceutical Sciences

institute: The University of Tokyo

summary: PGAM5 is a mitochondria-localized protein phosphatase. To analyze the effect on gene expression profiles by PGAM5 in iBAT, RNA-seq analysis was performed.

overall_design: Tissue samples were collected from 10-week-old male mice, and RNA samples derived from 3 (WT) or 4 (PGAM5 KO) individuals were analyzed.

first: Akinori

last: Takahashi

first: Lila

last: Maekawa

first: Tadashi

last: Yamamoto

first: Takao

last: Fujisawa

first: Kazuki

last: Hattori

first: Hidenori

last: Ichijo


title: The influence of CCL5 to the exprssion profile of tumor associated macrophages (TAMs)

city: Shanghai

first: Sheng

middle: Bo

last: Zhang

address: No.1954. Huashan rode

institute: Shanghai Jiao Tong University

summary: The aim of the dataset was to demonstrate that the gene expression profile of CD11bhiF4/80low TAMs are different from CD11blowF4/80hi TAMs in WT and CCL5-/-  BALB/c mice which subcoutinious incubated with CT26 WT or CT26 CCL5 knockdown cell line. Furthermore, we also want to determine the different gene expression profile of CD11bhiF4/80low TAMs which seperated from the colonrectal  tumor of WT mice and CCL5-/- mice

overall_design: The mRNA profiles of CD11bhiF4/80low TAMs and CD11blowF4/80hiTAMs which isolated from the colonrecatal tumor of WT mice or CCL5-/-mice were generated by deep sequencing, in duplicate, using Illumina HiSeq X Tten.

first: Wei

middle: Q

last: Gao

first: Yan


title: Expression data from human embryonic kidney 293 (HEK-293) cells transiently transfected with Human endogenous retrovirus (HERV) (K-HML2) Rec protein compared to empty expression vector control

city: Jena

first: Sven

last: Stengel

address: Am Klinikum 1

department: Clinic for Internal Medicine IV

institute: Jena University Hospital

summary:
HERV-K protein Rec functions as RNA transport protein shuttling unspliced viral genomic RNA  from the nucleus to the cytoplasm.
Rec was found to be expressed in several tumors and transformed cell lines and contributes to  cell transformation by inhibiting the transcription factor Promyelocytic Leukemia Zinc Finger Protein

overall_design: HEK-293 cells were transfected with Rec expression plasmid or empty vector control (in duplicates). Samples were collected 72h post transfection. Microarray hybridization was carried out at Atlas Biolaps GmbH Berlin according to manufactures protocol. Microarray data was analyzed using Bioconductor. Comparison of Rec expressing cells vs. Rec non-expressing cells.

first: Joachim

last: Denner