title: TCDD exposure in control and slincR zebrafish morphants at 48 hpf

status: Public on Oct 25 2018

city: Corvallis

first: Gloria

last: Garcia

state: OR

institute: Oregon State University

summary: Background: A structurally diverse group of chemicals, including polycyclic aromatic hydrocarbons (PAHs), can inappropriately activate the aryl hydrocarbon receptor (AHR) and lead to adverse health effects. In the zebrafish model, repression of sox9b has a causal role in several AHR-mediated toxic responses, including craniofacial cartilage malformations; however, the mechanism of sox9b repression remains unknown. We previously identified a long non-coding RNA, slincR, which is increased (in an AHR-dependent manner) by multiple AHR ligands and is required for the AHR-activated repression of sox9b.   Objective: Enhance our understanding of the signaling events downstream of AHR activation that contribute to toxic responses. To understand slincR’s role in the TCDD-induced toxicity pathway, we performed RNA-sequencing and gene ontology enrichment analysis on 48 hpf control and slincR morphants exposed to 0.1% DMSO or 1 ng/mL TCDD.

overall_design: Each biological sample consisted of 20 embryos with 4 biological replicates per condition, for a total of 16 samples

first: Robert

last: Tanguay


title: Colonic single-cell RNA-seq experiment

status: Public on Oct 23 2018

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

country: USA

institute: Vanderbilt University

type: Expression profiling by high throughput sequencing

summary: WT untreated C57Bl6 mouse

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 3 replicates from different mice in single sequencing run

middle: S

first: Alan

middle: J

last: Simmons


title: Transcriptomic analysis of Col and arf7 responding to auxin

status: Public on Nov 10 2018

city: Qingdao

first: feng

last: zhang

state: Shandong

address: 72 Binhai Road

country: China

institute: shandong university

summary: The goal of this study is to clarify the function of ARF7 in the pathway of auxin inducing lateral root development. We isolated total RNA from the roots of 8-day-old Col-0 and arf7 seedlings. New genes act downstream of ARF7 after responding to auxin treatment, during the lateral root formation, are discovered.

overall_design: We isolated total RNA from the roots of 8-day-old Col-0 and arf7 seedlings with or without auxin treatment.

first: Feng

last: Zhang

first: ZhaoJun

last: Ding


title: Volatile profiles and transcriptomic variation in Cabernet Sauvignon grapes in response to various sunlight exposure strategies in a warm climate

status: Public on Oct 14 2018

city: Beijing

first: Lei

last: He

address: No. 17 Tsinghua east road

institute: China Agricultural University

summary: Basal leaf removal has been widely practiced to increase cluster sunlight exposure, control berry rot and eventually improve grape berry quality. Early leaf removal performed in cool region appeared to benefit the accumulation of norisoprenoids and monoterpenes. However, effects of this canopy management and leaf moving on volatile profiles and transcriptome of grape berry in warm region characterized with strong sunshine and arid climate were paid less attention. To cope with multiple possible effects caused by global warming, researches in warm region are urgently needed to provide a guide for adjusting the sunlight exposure treatment to adapt the climate change.In Manas county of Xinjiang province, sunlight exposure treatments performed in this study resulted in decreased β-carotene and lutein, which mainly responsible for the reduced norisoprenoids in ripening grapes. Substrate competition due to the up-regulation of VvTPS-a and VvNCED3 may contribute to the decreased concentration of monoterpenes in exposed berries. The notable increased C6 alcohols in the grape berries treated by leaf removal applied at veraison (LR-V), was mainly attribute to the enhanced substrate availability of linoleic acid and linolenic acid together with the higher expression of VvLOXO and VvADH1. Free C6 aldehyde was reduced by half leaf removal applied at veraison (HLR-V), leaf moving at veraison (LM-V) and leaf removal applied at berry pepper-corn size (LR-PS). Moreover, transcriptomic analysis indicated that both LR-V and LM-V treated grape berry implemented multiple stress-mitigation strategies to acclimate the improved sunlight exposure. Interestingly, photosynthesis-related genes in grape berry were primarily up-regulated by LR-V as a consequence of carbohydrate source removal rather than improved sunlight exposure. Weighted gene co-expression network analysis (WGCNA) suggested that the genes encoding malate synthase and 3-oxoacyl-(acyl carrier protein) reductase show a significant correlation with the accumulation of C6 alcohol.

overall_design: Nine grape berry sample groups were used for RNA sequencing in this study, consisting of LR-V, LM-V and the control at the E-L 36, E-L 37 and E-L 38 stages, respectively.

first: Xiao-Qing

last: Xu

first: Yu

last: Wang

first: Wei-Kai

last: Chen

first: Run-Ze

last: Sun

first: Guo

last: Cheng

first: Bin

last: Liu

first: Wu

first: Chang-Qing

last: Duan

first: Jun

first: Qiu-Hong

last: Pan


title: Whole mesenteric lymph nodes (mLN) RNA-seq from MNV or Reovirus infected C57BL/6 mice

status: Public on Oct 01 2018

city: Cambridge

first: Mukund

last: Varma

state: MA

address: 415 Main Street

institute: Broad Institute

summary: mRNA profiles of 8 weeks old C57BL/6 mice 2 days after infections with 5e7 pfu of various strains of murine norovirus (MNV) or 1e8 pfu of T1L reovirus were evauated

first: Romain

last: Bouziat

first: Scott

last: Biering


title: TRIM28 protects TRIM24 from SPOP-mediated degradation and promotes prostate cancer progression [ChIP-seq]

status: Public on Oct 05 2018

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, proteomic profiling of TRIM24 interactome in conjunction with shRNA screening of TRIM24 top-interactors nominated that   TRIM28 is indispensable for TRIM24 protein stability. We showed that TRIM28 stabilizes TRIM24 against SPOP-mediated ubiquitination and   degradation. TRIM28 promotes TRIM24 and AR transcription activity, androgen-dependent and -independent PCa growth.   In addition, we demonstrated that TRIM28 level in high in advanced PCa, which drives TRIM24/AR transcription activity in a similar manner   to SPOP mutation, which implies that TRIM28 potentially dictates the therapeutic outcome of TRIM24-targeted therapy.

overall_design: genetic modification design

first: Ka-wing

last: Fong


title: Molecular consequences of Dlx3 deletion in mouse enamel organ as determined by microarray analysis

status: Public on Sep 14 2018

city: Bethesda

first: Hong-wei

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary:
DLX3 is a homeodomain transcription factor involved in ameloblast differentiation and enamel formation. Mutations in DLX3 in human lead to defects in enamel.
However, the downstream targets of Dlx3 transcriptional activity in the enamel organ have not been identified yet.
In this study, we compared the transcriptome of enamel organs where Dlx3 has been deleted to control tissues.

overall_design: Total RNA was extracted from enamel organs (mandibular incisors) from Dlx3-WT (N=3) and Dlx3-K14cKO (N=3) mice at P10. Microarray analysis was performed using Affymetrix Mouse 430.2 arrays

first: Olivier

last: Duverger

first: Maria

last: Morasso

first: Weiping


title: TRIM28 protects TRIM24 from SPOP-mediated degradation and promotes prostate cancer progression

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

overall_design: Refer to individual Series


title: DNA and Histone Methyltransferase Inhibitors Cooperate to Increase Viral Mimicry in Ovarian Cancer Cells

status: Public on Sep 30 2018

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: Total RNA sequenceing method was used to compare the differential expression of genes in A2780, CAOV3, PEO14, and OAW42 cells with G9Ai, 5-aza-CdR and combination treatment compared to untreated cells

overall_design: Examination of total RNA expressed after cells with G9Ai, 5-aza-CdR and combination treatment compared to untreated cells

first: Minmin


title: Structural, biochemical, and molecular analyses of cambial stem cells reveal longevity mechanisms in old Ginkgo biloba trees

status: Public on Sep 08 2018

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: High-throughput RNA, sRNA and degradome sequencing were performed to identify a large number of mRNA, miRNAs and their targets in  G. biloba cambium at different ages to provide useful information for uncovering the regulatory networks of ageing in long-lived old trees.

overall_design: RNA, sRNA and degradome sequencing in cambium of G. biloba

first: Li

first: Jiawen

last: Cui


title: RNA sequencing for candidate gene identification for habitat specific clock varaition in natural ecotypes of Neurospora discreta

status: Public on Sep 18 2018

city: Camden

first: Kwangwon

last: Lee

state: New Jersey

address: 200 Federal St.

department: Department of Biology

institute: Rutgers University

summary:
Purpose: The goal of the current study was to find the candidate genes responsible for the habita specific clock variation in N. discreta.
Methods: We performed RNA-seq experiment using four strains ; African parent (FGSC8831),  North American parent (FGSC 8578) and two representative progeny representing African clock phenotype (N309-89) and North American clock phenotype (N309-50).
Results: We identified one candidate gene that meets our criteria; confirmed it's expression by qPCR and it's expression pattern is associated with parent genotype.
Conclusions: Our approach using the expression profiles and SNP data of two parents and two representative progeny led us to identify a candidate gene for a complex clock adaptation phenotype.

overall_design: Samples are prepared from cells at different time of the cycling environement, 12 h light: 12 h dark; 2h dark phase (2DK),  and 15m, 1h and 2h  light phase. We also used the identified SNPs in the transcripts to perform association study.

first: Bala

last: Koritala

first: Yaping

last: Feng

first: Dibyendu

last: Kumar


title: Mechanisms of Adaptive Evolution of Aneuploid Cells

status: Public on Aug 31 2018

city: Boston

first: Alaattin

last: Kaya

address: 77 Avenue Louis Pasteur

institute: Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA

summary: Alteration of normal ploidy (aneuploidy) is an important mechanism of evolution of species. It has been linked to a rapid response to stress and is regarded as a hallmark of cancer. While increased genomic instability of aneuploid cells can accelerate genetic diversification and facilitate adaptation, these cells also face the adverse effects of gene imbalance, resulting in fitness cost. Here, to understand the mechanisms through which cells respond to aneuploidy and develop tolerance leading to fitness restoration, we subjected disomic (i.e. with an extra chromosome copy) strains of yeast to long-term experimental evolution, forcing disomy maintenance with selection markers. We characterized mutations, karyotype alterations and gene expression changes throughout adaptive evolution, and analyzed them to dissect the associated molecular strategies. Cells with different extra chromosomes accumulated mutations at distinct rates, and endured a diverse array of adaptive events. Despite remarkable diversity of these events, cells tended to evolve towards normal ploidy through both chromosomal DNA loss and changes in gene expression. We identified genes commonly altered during the evolution of disomic strains, and genes recurrently mutated in multiple lines. Our analyses revealed protein translation, amino acid biosynthesis, transcription regulation, stress response, and nucleotide and protein degradation as key pathways for the adaptive response to aneuploidy and identified transcription factors that mediate this response. Together, these findings define cellular strategies that underlie tolerance to aneuploidy.

overall_design: We compared the transcriptome data of laboratory evolved (600 generations) and unevolved disomic yeast strains to find the signatures of aneuploidy adaptation

first: Marco

last: Mariotti


title: m6A profile in cardiomyocytes

status: Public on Aug 29 2018

city: Columbus

first: Federica

last: Accornero

address: 473 W 12th Ave

institute: OSU

summary: To determine the role of m6A methylation in the heart we isolated primary cardiomyocytes and performed m6A immunoprecipitation followed by RNA sequencing. We measured the level of m6A methylation on cardiomyocyte mRNA, and found a significant increase in response to hypertrophic stimulation, suggesting a potential role for m6A methylation in the development of cardiomyocyte hypertrophy. Analysis of m6A methylation showed significant enrichment in genes that regulate kinases and intracellular signaling pathways. Inhibition of METTL3 completely abrogated the ability of cardiomyocytes to undergo hypertrophy when stimulated to grow, while increased expression of the m6A RNA methylase METTL3 was sufficient to promote cardiomyocyte hypertrophy both in vitro and in vivo. Our study identified METTL3-mediated methylation of mRNA on N6-adenosines as a dynamic modification that is enhanced in response to hypertrophic stimuli and is necessary for a normal hypertrophic response in cardiomyocytes.

first: Lisa

last: Dorn


title: Epigenetic changes of the thioredoxin system in the tx-j mouse model and in patients with Wilson disease

status: Public on Jul 25 2018

city: Davis

first: Charles

middle: E

last: Mordaunt

state: CA

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

type: Methylation profiling by high throughput sequencing

summary: Wilson disease (WD) is caused by mutations in the copper transporter ATP7B, leading to copper accumulation in the liver and brain. Excess copper inhibits S-adenosyl-L-homocysteine hydrolase, leading to variable WD phenotypes from widespread alterations in DNA methylation and gene expression. Previously, we demonstrated that maternal choline supplementation in the Jackson toxic milk (tx-j) mouse model of WD corrected higher thioredoxin 1 transcript levels in fetal liver. Here, we investigated the effect of maternal choline supplementation on genome-wide DNA methylation patterns in tx-j fetal liver by whole-genome bisulfite sequencing (WGBS). Tx-j Atp7b genotype-dependent differences in DNA methylation were corrected by choline for genes including, but not exclusive to, oxidative stress pathways. To examine phenotypic effects of postnatal choline supplementation, tx-j mice were randomized to one of six treatment groups: with or without maternal and/or continued choline supplementation, and with or without copper chelation with penicillamine (PCA) treatment. Hepatic transcript levels of thioredoxin 1 and peroxiredoxin 1 were significantly higher in mice receiving maternal and continued choline with or without PCA treatment compared to untreated mice.  A comparison of WGBS of human WD liver compared to tx-j mouse liver demonstrated a significant overlap of differentially-methylated genes associated with ATP7B deficiency. Further, eight genes in the thioredoxin pathway were differentially methylated in human WD liver samples. In summary, Atp7b deficiency and choline supplementation have a genome-wide impact, including on thioredoxin system-related genes, in tx-j mice. These findings could explain the variability of WD phenotype and suggest new complementary treatment options for WD.

overall_design: Investigation of DNA methylation with whole-genome bisulfite sequencing (WGBS) in liver from tx-j and C3H mice at E17, with and without maternal choline supplementation. Tx-j mice carry a homozygous Gly712Asp missense mutation in Atp7b. Dams were fed normal or high choline diet for 2 weeks before mating and through gestation. Tx-j pups were fostered by C3H dam with sam diet that gave birth on the same day. Fetal livers of pups from the same litter were pooled. Pooled liver samples: C3H + control diet (n=4), C3H + choline diet (n=4), tx-j + control diet (n=4), tx-j + choline diet (n=4)

first: Janine

middle: M

last: LaSalle

first: Valentina

last: Medici


title: Aortic Effects of Thyroid Hormone in Male Mice

status: Public on Aug 28 2018

city: Lübeck

first: Jens

last: Mittag

address: Ratzeburger Allee 160

department: Department of Internal Medicine I

country: Germany

institute: University of Lübeck

summary:
Test for thyroid hormone regulation of genes expressed in the abdominal aorta of C57Bl6 mice.
Comparison between mice treated with 1mg/L Thyroxin in drinking water for 4 days compared to controls.

overall_design: 2 group comparison


title: Changes in gene expression in human skeletal stem cells transduced with constitutively active Gsα correlates with hallmark histopathological changes seen in fibrous dysplastic bone

status: Public on Jul 01 2018

city: Rome

first: domenico

last: raimondo

address: Viale Regina Elena 324

department: Molecular Medicine

country: Italy

institute: Sapienza University of Rome

summary:
In order to dissect pathways enchained in skeletal stem/progenitors by Fibrous Dysplasia mutations, we engineered human skeletal stem/progenitors with the mutation and performed transcriptomic analysis. FD mutation profoundly alters the properties of skeletal stem/progenitors by pushing hBMSCs towards formation of disorganized bone with a concomitant lack of fat development. In addition, the mutation created an altered in trans environment that pushed the overall system towards neovascularization, inflammation and osteoclastogenesis.
We used microarrays to detail the global programme of gene expressionc of human skeletal progenitors containing the Gsα activating mutation R201C

overall_design: Human bone marrow stromal cells (hBMSCs) (derived from bone marrow aspirates) from three independent healthy donors were isolated. Lentiviral vectors (LV-GSαR201C and LV-ctr) were generated, produced and titrated.  The LV-vector integrated copy number was calculated by Q-PCR as described and was established as ~1 copy of integrated lentiviral sequence per transduced cell. hBMSCs were transduced with LV-GSαR201C and LV-ctr or mock treated.

first: Domenico

last: Raimondo

first: Cristina

last: Remoli

first: Letizia

last: Astrologo

first: Romina

last: Burla

first: Mattia

last: La Torre

first: Fiammetta

last: Verni’

first: Enrico

last: Tagliafico

first: Alessandro

last: Corsi

first: Pamela

middle: G

last: Robey

first: Mara

last: Riminucci

first: Isabella

last: Saggio

first: Agnese

last: Persichetti

first: Simona

last: Del Giudice

first: Giuseppe

last: Giannicola


title: Single-cell RNA sequencing of proliferative stem cell population from juvenile Schistosoma mansoni worms

status: Public on Jul 12 2018

city: Stanford

first: Yuan

last: Xue

address: 318 Campus Drive

institute: Stanford University

summary: The rise of single-cell RNA sequencing (scRNAseq) technologies has enabled researchers to classify cell types, delineate cell developmental trajectories, and measure molecular responses to external perturbations. These technologies all rely on the premise that cell-to-cell variations arising from the biological processes of interest are clearly distinguishable from the intrinsic transcriptional and technical noise. However, for datasets in which the biologically relevant differences between cells are subtle, this assumption does not always hold. Here we present the self-assembling manifold (SAM) algorithm, which iteratively rescales gene expression to extract these subtle signals in a robust and unsupervised manner. We demonstrate its advantages over other state-of-the-art methods with experimental validation in identifying novel stem cell populations of Schistosoma, one of the most prevalent parasites that infects hundreds of millions of people worldwide. Extending our analysis to a total of 56 datasets, we show that SAM is generalizable and consistently outperforms other methods in a variety of biological and quantitative benchmarks.

overall_design:
[N402Barcode samples] We applied Smart-Seq2 protocol to sequence 370 single stem cells isolated from 2.5 weeks old Schistosoma mansoni worms, which infect millions of people worldwide. We discovered new stem cell sub-populations using a novel single-cell RNA sequencing analysis method (Self-assembling manifolds, SAM). We found differential expressions in a few transcription factors and marker genes that distinguish these sub-populations. We hope this will be a useful resource for the community interested in the developmental biology of Schistosoma at large.
Transcriptome sequencing of 370 single stem cells of Schistosoma

[YX samples] We applied Smart-Seq2 protocol to sequence 367 single stem cells isolated from 3.5 weeks old Schistosoma mansoni worms, which infect millions of people worldwide. We discovered new stem cell sub-populations using a novel single-cell RNA sequencing analysis method (Self-assembling manifolds, SAM). We found differential expressions in a few transcription factors and marker genes that distinguish these sub-populations. We hope this will be a useful resource for the community interested in the developmental biology of Schistosoma at large.
Transcriptome sequencing of 367 stem cells of Schistosoma

first: Stephen

middle: R

last: Quake

first: Bo

last: Wang


title: mRNA-seq in MCF7 cells in response to 4-hydroxytamoxifen (OHT)

status: Public on Oct 12 2018

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

summary:
Purpose: Study the temporal effect of OHT on gene expression in MCF7 cells using mRNA-seq.
Methods: MCF7 cells were treated with 100nM OHT for 2h, 6h and 24h or 24h with vehicle alone (ethanol). Six biological replicates of each time point were included in the analysis. For the library preparation the Illumina TruSeq Stranded mRNA Library Prep Kit High Throughput was used and 2 lanes of SE50 were run on HiSeq 4000.
Results: We identify 27,520 genes of which 1,187 were significantly regulated in response to OHT in at least one time point. This included transcriptional repression of cell cycle genes as well as a number of known ERα target genes.
Conclusions: We demonstrate a  transcriptional response to OHT in MCF7 cells, with ERa target genes and genes linked to cell cycle progression being repressed.

overall_design: MCF7 cells were grown in DMEM supplemented with 10% FBS, 50U/ml penicillin, 50μg/ml streptomycin and 2mM L-glutamine. MCF7 cells were treated with 100nM OHT for 2h, 6h and 24h or 24h with vehicle alone (ethanol). Six biological replicates for each time point were included in the analysis.

first: Evangelia

last: Papachristou

first: Kamal

last: Kishore


title: Expression data after knockdown of MYB-NFIB and IGF1R/INSR inhibition in ACC cells

status: Public on Jun 01 2018

city: Gothenburg

first: Mattias

last: Andersson

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

summary:
The MYB-NFIB gene is a driver-mutation in the majority of adenoid cystic carcinomas (ACCs) and believed to control a large number of genes involved in tumorigenesis.
This experiment investigates the effects on gene expression after siRNA knock-down of MYB-NFIB and/or inhibition of IGF1R/INSR signaling in ACC cells.

overall_design: A total of 18 samples are analyzed of which 6 are control samples (control siRNA and DMSO control).

middle: K

first: Göran

last: Stenman


title: Expression data from human macrophages

city: Edinburgh

first: John

middle: Alexander

last: Marwick

address: 47 Little France Crescent

department: Center for Inflammation Research

institute: University of Edinburgh

summary:
Experimental set 1: To evaluate the impact of apoptotic neutrophils on TLR4-induced inflammatory pathways in human macrophages.
Experimental set 2: To compare the activation of inflammatory pathway between alveolar macrophages (AM) from idiopathic pulmonary fibrosis (IPF) patients and alveolar macrophages from respiratory bronchiolitis interstitial lung disease (RB-ILD) patients

overall_design:
Experimental set 1: (n=4 per group, 4 match paired groups): Human monocyte-derived macrophages (MDM) co-colture +or- apoptotic neitrophils and +or- LPS (1ng/ml) for 9 hours. RNA isolated using Qiagen RNeasy Kit
Experimental set 2: (n=4 per group, 2 groups):AM from IPF and RB-ILD patients isolated from bronchoalveolar lavage by cell sorting, RNA isolated using Qiagen RNeasy Kit


title: Stabilizing Heterochromatin by DGCR8 Alleviates Senescence and Osteoarthritis (miRNA-Seq)

status: Public on Jun 30 2018

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor complex for microRNA biogenesis. However, the non-canonical functions of DGCR8 have not been studied. Here, we demonstrate that DGCR8 plays an important role in maintaining heterochromatin organization and preventing aging. An N-terminal-truncated version of DGCR8 (DR8dex2) accelerated senescence in human mesenchymal stem cells (hMSCs) independent of its miRNA-processing activity, which is mediated by its C-terminal domain. Further studies revealed that DGCR8 maintained heterochromatin organization by interacting with the nuclear envelope protein Lamin B1, and heterochromatin-associated proteins, KAP1 and HP1g Overexpression of any of these proteins, including DGCR8, reversed premature senescent phenotypes in DR8dex2 hMSCs. Finally, DGCR8 was downregulated in pathological and naturally aged hMSCs, whereas DGCR8 overexpression alleviated hMSC aging and osteoarthritis in mice. Taken together, these analyses uncovered a novel, miRNA-independent role for DGCR8 in maintaining heterochromatin organization and preventing senescence. DGCR8 may therefore represent a new therapeutic target for alleviating human aging-related disorders.

overall_design: microRNA-seq profiles of DR8dex2 and WT hMSCs

first: Guanghui


title: Characterization of Lgr6+ Cells as an Enriched Population of Hair Cell Progenitors Compared to Lgr5+ Cells for Hair Cell Generation in the Neonatal Mouse Cochlea

status: Public on May 05 2018

city: Shanghai

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

institute: Fudan University

summary: Our previous studies showed that Lgr6+ cells are a subpopulation of Lgr5+ progenitor cells and that both Lgr6+ and Lgr5+ progenitors can regenerate Myosin7a+ HCs in vitro. Thus we hypothesized that Lgr6+ cells are an enriched population of cochlear progenitor cells. However, the detailed distinctions between the Lgr5+ and Lgr6+ progenitors have not been researched. Here, we systematically compared the proliferation, HC differentiation, and detailed transcriptome expression profiles of these two progenitor populations. We found that when isolated by flow cytometry, the same number of Lgr6+ progenitors generated significantly more Myosin7a+ HCs than Lgr5+ progenitors; however, Lgr5+ progenitors formed more epithelial colonies and more spheres than Lgr6+ progenitors in vitro. Using RNA-Seq, we compared the transcriptome differences between Lgr5+ and Lgr6+ progenitors and identified a list of significantly differential expressed genes which may regulate the proliferation and differentiation of these HC progenitors.

first: Yanping

last: Zhang


title: Microbial signatures in prostate cancer

status: Public on May 01 2018

city: Philadelphia

first: Sagarika

last: Banerjee

address: 3610 Hamilton Walk

institute: University of Pennsylvania

summary: Investigationg microbiome specifically associated with prostate cancer compared to non-cancerous prostate controls.

overall_design: 50 prostate cancer tissues were screened individually, and 15 non-cancerous prostate control tissues were screened in pools of 5 by PathoChip, a metagenomic array comprising probes for all known micro-organisms in NCBI database. Both genomic DNA (gDNA) and total RNA (cDNA) from prostate cancer and control tissues were co-amplified, labelled with Cy3 and hybridized on the PathoChip.

first: Tian

last: Tian

first: Zhi

last: Wei

first: Natalie

last: Shih

first: Michael

middle: D

last: Feldman

first: James

middle: C

last: Alwine

first: Erle

last: Robertson


title: Gene expression profiling in human ACTH-secreting pituitary tumors

status: Public on Jun 18 2018

city: Cusano Milanino

first: Francesca

last: Pecori Giraldi

state: Milan

address: via Zucchi 18

department: Neuroendocrinology Research Laboratory

institute: Istituto Auxologico Italiano

summary: Corticotropin (ACTH)-secreting pituitary adenomas give rise to a severe endocrinological disorder, i.e., Cushing’s disease, with multifaceted clinical presentation and treatment outcomes. Experimental studies suggested that disease variability is inherent to the pituitary tumor, thus pointing to the need for further studies into tumor biology. Aim of the present study was to evaluate transcriptome expression pattern in a large series of ACTH-secreting pituitary adenoma specimens, in order to identify molecular signatures of these tumors. Gene expression profiling of formalin-fixed paraffin-embedded specimens from 40 human ACTH-secreting pituitary adenomas revealed significant expression of genes involved in protein biosynthesis and ribosomal function, in keeping with neuroendocrine cell profile. Unsupervised cluster analysis identified three distinct gene profile clusters and several genes were uniquely overexpressed in a given cluster, accounting for different molecular signatures. Of note, gene expression profiles were associated with clinical features such as age and size of the tumor. Altogether, our study shows that corticotrope tumors are characterized by neuroendocrine gene expression profile and present subgroup-specific molecular features.

overall_design: gene expression analysis of 40 RNA obtained from formalin-fixed paraffin-embedded pituitary human tissue

first: Maria

middle: F

last: Cassarino

first: Alberto

last: Ambrogio

first: Andrea

last: Terreni

first: Davide

last: Gentilini

first: Marco

last: Losa

first: Antonella

last: Sesta

first: Francesco

last: Cavagnini


title: Rapid high-resolution measurement of DNA replication timing by droplet digital PCR

status: Public on May 16 2018

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary: Time of DNA replication is inversely proportional to the relative DNA copy number. Sort-seq is a technique that uses deep short read sequencing to determine relative copy number across genome from sorted S phase cells. We have applied sort-seq to HeLa cells and report their relative copy number profile. The high (close to 2) value means the region replicates early in S phase; the low (close to 1) value means the region is replicated late in S phase.

overall_design: Proliferating HeLa cells were sorted to enrich for G1 and S phase cell cycle stages (based on propidium iodide staining). Extracted DNA was fragmented and sequenced on Illumina NextSeq platform.

first: Dzmitry

last: Batrakou

first: Emma

last: Heron


title: Transcriptomic profile of the retinal ganglion cell type J-RGC in Tbr1 KO and control mice

status: Public on Apr 09 2018

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: The goal of this experiment is to identify genes with altered expression in Tbr1 mutant J-RGCs.

overall_design: J-RGCs were labeled with Green Fluorescent Protein using a J-RGC specific transgenic line and isolated by flow cytometry. 5 samples from 4 control animals (JRGC_WT_2 and JRGC_WT_3 are from the same animal) and 6 samples from 4 mutant animals (JRGC_KO_1 and JRGC_KO_2 are from the same animal, JRGC_KO_3 and JRGC_KO_4 are from the same animal) were collected. RNA was extracted and libraries prepared for Illumina sequencing.

first: Joshua

last: Sanes


title: Transcriptome profile of rice genotypes IR24 and IRBB67 in interaction with Xanthomonas oryzae pv. oryzae under two temperature regimes

status: Public on Mar 31 2018

city: Metro Manila

first: Sylvestre Gerbert

last: Dossa

address: DAPO Box

department: Genetics and Biotechnology

country: Philippines

institute: International Rice Research Institute

summary: We report about the effects of temperature increase on rice response to Xanthomonas oryzae pv. oryzae using high throughput sequencing (RNA-Seq). The time course transcriptomic analysis revealed that temperature enhanced IRBB67 resistance to combined heat and Xoo. Our findings highlight altered cellular compartment by Xoo and heat stress in both susceptible (IR24) and the resistant (IRBB67). Interestingly, up-regulation of trehalose-6-phosphatase gene and low affinity cation transporter in IRBB67 suggest that IRBB67 maintained a certain homeostasis under high temperature to have its resistance enhanced. The interplay of both heat stress and Xoo responses as determined by up-regulated and down-regulated genes demonstrates how resistant plant cope with combined biotic and abiotic stresses. This study provides an understanding of how IRBB67 mediated resistance to Xoo under temperature get insight to cross talk in abiotic and biotic stress regulatory pathway.

overall_design: Leaf mRNA profile of 21 days old plants of IR24 (susceptible) and IRBB67 (resistant) inoculated with Xanthomonas oryzae pv. oryzae strain PXO145 under two temperature regimes. Samples were collected at three time points (3hours post inoculation, hpi; 72 hpi and 120 hpi).

first: Sylvestre

first: Ian

last: Quibod

first: Ruby

last: Burgos

first: Ricardo

last: Oliva

first: Edgar

last: Maiss

first: Vera

last: Casiana

first: Kerstin

last: Wydra


title: Emory University African American Microbiome in Pregnancy Cohort [Methylation]

status: Public on Mar 19 2018

city: Atlanta

first: Anna

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University

type: Methylation profiling by genome tiling array

summary: All subjects were enrolled from Grady Memorial and Emory Midtown Hospitals. Subjects provided blood samples at two timepoints during pregnancy. Medical record abstraction was used to determine the presence of fetal intolerance of labor.

overall_design: Subjects provided blood samples at two timepoints during pregnancy, which were processed into peripheral blood mononuclear cells (PBMC). DNA was extracted usingthe AllPrep RNA/DNA Mini Kit (Qiagen). DNA methylation was assessed on the Human Methylation450 BeadChip.

first: Alicia

last: Smith

first: Anne

middle: L

last: Dunlop


title: Separable recruitment of DNA Polymerase α for leading- and lagging-strand replication initiation

status: Public on Jun 16 2018

city: New York

first: Duncan

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

summary: Okazaki fragments were purified and sequenced from asynchronous S. cerevisiae at various DNA polymerase alpha levels in the presence or absence of interactions with Ctf4. The sequencing data was used to quantify efficiencies of replication origins.

overall_design: We enriched Okazaki fragments by depletion of DNA ligase I, and sequenced the resulting enriched single-stranded/nicked DNA.

first: Sarina

middle: Y

last: Porcella

first: Natasha

last: Morse

first: Colin

middle: P

last: Tang

first: Daphne

middle: N

last: Kramer

first: Priyanka

last: Srivastava


title: Comparison of the transcriptome response within the tracheobronchial lymph node  following infection with Porcine Reproductive and Respiratory Syndrome Virus, Porcine  Circovirus 2 or Swine Influenza A Virus.

status: Public on Mar 03 2018

city: Ames

first: Laura

last: Miller

state: Iowa

address: 1920 Dayton Ave

department: Virus and Prion Research Unit

institute: USDA-ARS-National Animal Disease Center

summary: The aim of this study was to acquire a better understanding of porcine   reproductive and respiratory syndrome (PRRS) disease through a deeper knowledge of   gene expression changes that occur in pulmonary lymph nodes by comparing PRRS virus   (PRRSV), porcine circovirus type 2 (PCV-2), and swine influenza virus (IAV-S)   infections. The PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in   these domestic pigs typical of experimental infection of young pigs with these viruses.   PRRSV isolate SDSU-73 was pathogenic in this study inducing fever, anorexia,   listlessness, and dyspnea.

overall_design:
Differentially expressed tags (with respect to control) at all   time points were ascertained. The experimental results were integrated with previous   studies to develop a robust model of swine respiratory virus infection.
Here we identified and compared gene expression changes in tracheobronchial  lymph nodes (TBLN) following viral infection using Digital Gene Expression Tag  Profiling (DGETP). Pigs were infected with 1 x 10^5 cell culture infectious dose 50%  per pig of PRRSV (strain SDSU73), porcine circovirus type 2 (PCV2; group 2), or swine  influenza A virus (IAV-S; A/SW/OH/511445/2007). Pigs were allotted to one of 4  treatment groups: sham inoculated control, PRRSV-challenge, PCV2-challenge, or  IAV-S-challenge.

first: Damarius

last: Fleming

first: Gregory

last: Harhay

first: Marcus

last: Kehrli

first: Kelly

last: Lager


title: Expression profiling of lncRNAs/mRNA for 16 human samples derived from patients with altrophic gastritis(Hp+) or gastric cancer(Hp+)

status: Public on Mar 14 2018

city: Beijing

first: Taotao

last: Han

state: Beijing

address: NO.5 Dong Dan San Tiao, Dongcheng District

department: Department of Biochemistry and Molecular Biology

institute: Peking Union Medical College & Chinese Academy of Medical Sciences

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

summary: H.pylori was a well known risk factor for gastic cancer. In this study, we used high-throughtput lncRNA microarray to screen dysregulated lncRNA in gastric cancer, and to investigate the biological function fully understood lncRNA.

overall_design: A  sixteen chip study using total RNA extracted from four normal mucosa tissues, six atrophic gastritis (Hp+)  tissues and six gastric cancer (Hp+) tissues

first: Juan

last: Shi


title: Expression data from sorted mouse E17.5 lung ciliated cells

status: Public on Mar 30 2018

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: We purified the differentiating ciliated cells from E17.5 mouse lungs and used Affymetrix microarrays to obtain their gene expression profiles.

overall_design: Ciliated cells were isolated by flow cytometry as GFP+ cells from FOXJ1-GFP mouse lungs at E17.5

first: Emma

last: Rawlins


title: Herpesvirus-encoded microRNAs alter  transcriptome of oral keratinocytes

status: Public on Feb 15 2018

city: Chicago

first: Afsar

last: Naqvi

state: IL

address: 801 S Paulina, Room 561B

department: Periodontics

institute: University of Illinois at Chicago

summary:
We investigated the impact of on miR-H1 and miR-K12-3-3p- on host transcriptome focusing on gingival epithelial cells that are target sites for various HHV.
Results: More than 1300 genes were altered by miR-H1 and miR-K12-3-3p expressing HOK.

overall_design: Primary oral keratinocytes were transfected with miR-H1, miR-K12-3-3p or control mimic for 48 hours. Total RNA isolated from cells (n=4) was assessed for global transcriptome changes using Affymetrix Gene array .

first: Alexandra

last: Seal

first: Jennifer

last: Shango

first: Salvador

last: Nares


title: MicroRNAs associated with reverse left ventricular remodeling in humans identify pathways of heart failure progression

status: Public on Feb 01 2018

city: Boston

first: SAUMYA

last: Das

address: 185 Cambridge Street

institute: MGH

summary: Plasma miRNAs associated with LVRR in humans are dysregulated in animal HF and target clusters of genes involved in mechanisms implicated in HF. A translational approach integrating human HF, bioinformatics, and model systems may uncover novel pathways involved in HF.

overall_design: Plasma circulating miRNAs were measured in patients with and without remodeling (15% reduction in LVESVI ) by the ABCAM FirePlex platform

first: Saumya

first: Ashish

last: Yeri


title: Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis

status: Public on Feb 07 2018

city: Basel

first: Andreas

last: Moor

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

summary: The intestinal epithelium is a highly structured tissue composed of repeating crypt-villus units. Enterocytes, which constitute the most abundant cell type, perform the diverse tasks of absorbing a wide range of nutrients while protecting the body from the harsh bacterial-rich environment. It is unknown if these tasks are equally performed by all enterocytes or whether they are spatially zonated along the villus axis. Here, we performed whole-transcriptome measurements of laser-capture-microdissected villus segments to extract a large panel of landmark genes, expressed in a zonated manner. We used these genes to localize single sequenced enterocytes along the villus axis, thus reconstructing a global spatial expression map. We found that most enterocyte genes were zonated. Enterocytes at villi bottoms expressed an anti-bacterial Reg gene program in a microbiome-dependent manner, potentially reducing the crypt pathogen exposure. Translation, splicing and respiration genes steadily decreased in expression towards the villi tops, whereas distinct mid-top villus zones sub-specialized in the absorption of carbohydrates, peptides and fat. Enterocytes at the villi tips exhibited a unique gene-expression signature consisting of Klf4, Egfr, Neat1, Malat1, cell adhesion and purine metabolism genes. Our study exposes broad spatial heterogeneity of enterocytes, which could be important for achieving their diverse tasks.

overall_design: Bulk RNA sequencing of laser-capture-microdissected villus epithelium fragments.

first: Yotam

last: Harnik

first: Shani

last: Ben-Moshe

first: Efi

last: Massasa

first: Kehern

last: Bahar Halpern

first: Shalev

last: Itzkovitz


title: Reduced chronic lymphocyte activation following Interferon-α blockade in the acute phase of SIV infection in rhesus macaques

status: Public on Feb 19 2018

city: Cleveland

first: Peter

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: Pathogenic HIV/SIV infection of humans and rhesus macaques (RMs) induces persistently high production of type-I interferon (IFN-I) which is thought to contribute to disease progression. To elucidate the specific role of IFN in SIV pathogenesis, 12 RMs were treated prior to i.v. SIVmac239 infection with a high or a low dose of an antibody (AGS-009) that neutralizes most IFN subtypes, and compared with six mock-infused, SIV-infected controls. Plasma viremia was measured post infection to assess the effect of IFNα blockade on virus replication, and peripheral blood and lymphoid tissue samples were analyzed by immunophenotypical staining. Consistent with the known antiviral effect of IFN-I, high-dose AGS-009 treatment induced a modest increase in acute phase viral loads vs. controls. 4 out of 6 RMs receiving a high dose of AGS-009 also experienced an early decline in CD4+ T cell counts which was associated with progression to AIDS. Interestingly, 50% of animals treated with AGS-009 (6/12) developed AIDS within one year of infection, compared with 17% (1/6) of untreated controls.  Finally, blockade of IFN decreased the levels of activated CD4+ and CD8+ T cells, as well as B-cells, as measured by PD-1 and/or Ki67 expression. The lower levels of activated lymphocytes in IFN-blockade animals supports the hypothesis that IFN signaling contributes to lymphocyte activation during SIV infection, and suggests that this signaling pathway is involved in controlling virus replication during acute infection. The potential anti-inflammatory effect of IFN blockade should be explored as a strategy to reduce immune activation in HIV-infected individuals.

overall_design: 107 Rhesus macaque whole blood samples were hybridized to Illumina Human RefSeq-12 V4 BeadChips.

first: Diane

last: Carnathan

first: Benton

last: Lawson

first: Joana

last: Yu

first: Kalpana

last: Patel

first: James

last: Billingsley

first: Gregory

last: Tharp

first: Olivia

last: Delmas

first: Reem

last: Dawoud

last: Nicolette

first: Mark

last: Cameron

first: Rafick-Pierre

last: Sekaly

first: Steven

last: Bosinger

first: Guido

last: Silvestri

first: Thomas

middle: H

last: Vanderford


title: Comparison between drugs- and unfolded proteins-induced responses reveals early induction of components of an ER-resident multimeric complex binding unfolded proteins

status: Public on Feb 16 2018

city: Bellinzona

first: Andrea

last: Rinaldi

state: Ticino

address: via vela 6

institute: IOR - oncology institute of southern switzerland

summary: We compared gene and protein expression profiles in cells challenged with ER stress-inducing drugs or expressing model polypeptides. Drugs titration to limit up-regulation of the endogenous ER stress reporters BiP/HSPA5 and HERP/HERPUD1 to levels comparable to luminal accumulation of unfolded proteins substantially reduced the amplitude of transcriptional and translational responses.

overall_design: GEP analysis of HEK cell lines

first: Timothy

last: Bergmann

first: Ilaria

last: Fregno

first: Maurizio

last: Molinari


title: Comparing gene expression of Lentigo to perilesional normal

status: Public on Jan 30 2018

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Ajou University School of Medicine

summary: Analyze of gene expression of Lentigo and perilesional normal and compare gene expression of Lentigo to gene expression of perilesional normal.

overall_design: We have 2 sample (two patient), we collected Lentigo and perilesional normal region in each patient, extract RNA and analyze exon array. We compare of gene expression of Lentigo and gene expression of perilesional normal.


title: Waveband Specific Transcriptional Control of Select Genetic Pathways in Xiphophorus maculatus Skin

status: Public on Apr 30 2018

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

summary: Changes in the transcriptional profiles of Xiphophorus maculatus skin was assessed by RNA-Seq after exposure to fluorescent (i.e., FL, 4,100K or “cool white”), or narrow wavelength regions of light between 300-600 nm (i.e., 50 nm or 10 nm regions, herein termed ”wavebands”).   Exposure to varied 50 nm wavebands allowed identification of waveband specific transcriptional modulation within gene sets representing discrete functional pathways within Xiphophorus skin. For example, exposure to either 350-400 or 450-500 nm wavebands resulted in opposite transcriptional effects in necrosis and apoptosis gene sets that predict selective differential suppression or activation of these pathways (i.e., 350-400 nm; necrosis suppression, apoptosis activation, and 450-500 nm; apoptosis suppression, necrosis activation).   Further investigation of waveband specific transcription employing successive 10 nm waveband exposures within the genetically responsive 500-550 nm waveband show; (a) greater numbers of genes may be transcriptionally modulated after 10 nm exposures, than observed for either 50 nm or FL exposures. (b) the 10 nm wavebands incite greater functional specificity than either 50 nm or FL exposures. (c) The principal genetic effects of FL are primarily due to the 30 nm between 500 to 530 nm.

overall_design: Xiphophorus maculatus fish were exposed to 4,100K fluorescent light, 50 nm wavelength window (waveband) between 300 to 600 nm wavelength region, or 10 nm waveband between 500 and 550 nm wavelength region. Gene expression were profiled by mRNA-Seq following exposure to each type of light exposre and were compared to the baseline gene expression (i.e., no light exposure)

first: Ronald

last: Walter

first: Mikki

last: Boswell

first: Jordan

last: Chang

first: William

first: Kaela

last: Novarro

first: Sean

first: Dylan

first: Raquel

last: Salinas

first: Markita

last: Savage


title: anti-NONO RIP seq in liver nuclei after fasting and re-feeding

status: Public on Jan 18 2018

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary:
In order to identify the RNAs bound by NONO complexes in different nutritional conditions, we carried out RNA immunoprecipitation followed by sequencing (RIP-seq) of NONO from mouse liver nuclei collected at three different times of the day.
Samples were collected after fasting (ZT10), 2h after re-feeding (ZT14) and towards the end of the feeding period (ZT22).
The co-immunoprecipitated RNA (along with input RNA and unspecific IgG bound RNA) was sequenced.

overall_design: Livers were collected at 3 different time points. RIP and Input RNA were sequenced for each time point and one IgG control for a total of 8 samples. Each sample is a pool of 2 independent experiments.

first: Giorgia

last: Benegiamo

first: Satchidananda

last: Panda


title: Nanopore and Illumina sequencing of limited MNase digests to map chromatin regularity and linker length

status: Public on Feb 20 2018

city: Planegg-Martinsried

first: Sandro

last: Baldi

address: Großhaderner Strasse 9

department: BMC Molecular Biology

institute: LMU Munich

summary: The nature of chromatin as regular succession of nucleosomes has gained iconic status. However, since most nucleosomes in metazoans are poorly positioned it is unknown to which extent the bulk genomic nucleosome repeat length (NRL) reflects the regularity and spacing of nucleosome arrays at individual loci. We describe a new approach to map nucleosome fiber regularity and spacing through sequencing oligonucleosome-derived DNA by classical as well as emergent nanopore-technology. This revealed modulation of chromatin regularity and NRL depending on functional chromatin states independently of nucleosome positioning and even in unmappable regions. We also found that that nucleosome arrays downstream of silent promoters are considerably more regular than those downstream of highly expressed ones, despite most extensive nucleosome phasing of the latter. Our approach is generally applicable and provides an important parameter of chromatin organisation that so far had been missing.

overall_design: Chromatin from Drosophila BG3-c2 or Kc cells was digested with MNase to oligonucleosomal ladders. Total digested DNA was either sequenced on Oxford Nanopore Minion devices, or the tetranucleosomal band was cut out and the purified DNA sequenced paired-end on an Illumina 1500 HiSeq machine to measure nucleosome repeat length along the genome with high resolution.

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Peter

middle: B

last: Becker


title: Diurnal liver transcriptome in wt and nono-/- mice

summary:
The liver circadian transcriptome results from the combined action of a circadian clock and feeding/fasting rhythms.
Since we found that (1) the number of NONO-containing speckles increases in response to feeding, (2) NONO interacts with RNA processing factors and (3) it binds to the introns of a large number of protein coding genes, we hypothesized that NONO may contribute to the daily rhythm of hepatic gene expression.
To address whether NONO contributes to rhythmic gene expression in response to feeding/fasting, diurnal liver transcriptomes were assessed in nono-/- and wt littermate mice fed a normal diet during the night time (ZT12-24).
We habituated mice to a 12:12 LD cycle with food available only at lights off (ZT12-24) for one week and in the second week collected mice every 2h throughout the 24h day. Both total and nuclear RNAs were sequenced after ribosomal RNA depletion

overall_design: Livers were collected at 12 different time points during a 24h day (ZT0-ZT22). For each liver sample, total and nuclear RNA were extracted for a total of 48 samples. Each sample is a pool of 2 mice.


title: Expression data for human colon cancer cell line HCT116 transfected with siRNA targeting YAP1.

status: Public on Jan 01 2018

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

summary: Yes-associated protein 1 (YAP1) is an effector of Hippo pathway, which is critical for regulating organ size, cell proliferation and tumor growth in mammals. YAP1 is known to be involved in tumorigenesis in several tissues, yet its role in colorectal cancer(CRC) is not established. To investigate the effect of YAP1 in CRC, we used microarrays to compared human colon cancer cell line HCT116 transfected with a control non-targeting siRNA to cells and transfected with siRNA targeting YAP1.

overall_design: Human colon cancer cell line HCT116 was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting YAP1 for 36 hours in DMEM medium (with 2% serum). Total RNA were extracted and detected by Affymetrix Human Genome U133 Plus 2.0 Array. 3 independent biological replicates were plated, transfected in parallel for each control and siRNA.

first: Chunlin

last: Ou

first: Zhenqiang

last: Sun

first: Guiyuan

last: Li


title: Human iPSC derived posterior gut progenitors are expandable and capable of forming gut and liver organoids

status: Public on Jan 10 2018

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

country: Japan

institute: Yokohama City University

summary: Organoid technology provides a revolutionary paradigm towards therapy, yet to be applied in humans mainly because of the reproducibility and scalability challenges. Here, we overcome these limitations by evolving scalable organ bud production platform entirely from human induced pluripotent stem cells (iPSC). By conducting massive ‘reverse’ screen experiments, we identified effective triple progenitor populations for generating liver buds in a highly reproducible manner: hepatic endoderm, endothelial and septum mesenchyme progenitors. Furthermore, we achieved human scalability by developing an omni-well-array culture platform for mass-producing homogenous and miniaturized liver buds on a clinically relevant large scale (>108-cell scale). Vascularized and functional liver tissues generated entirely from iPSC significantly improved subsequent hepatic functionalization potentiated by stage-matched developmental progenitor interactions, enabling functional rescue against acute liver failure via transplantation. Overall, our study provides a stringent manufacture platform for multi-cellular organoid supply, thus facilitating clinical and pharmaceutical applications especially for the treatment of liver diseases through multi-industrial collaborations.

overall_design: Transcriptome profiling of iPSC derived-DE, -HE and PGECs.

first: Ran-Ran

last: Zhang

first: Masaru

last: Koido

first: Takanori

last: Takebe

first: Hideki

last: Taniguchi


title: CSL RNA-Seq on HKC and SCC cell lines

status: Public on Dec 15 2017

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

institute: SIB Swiss Institute of Bioinformatics

summary: Down-modulation or loss-of-function mutations of the Notch 1 and 2 genes are associated with development of squamous cell carcinoma (SCC), a very frequent and therapy-resilient malignancy in skin, head/neck (H/N), lung and other surface epithelia. In this context, surprisingly little is known on the role of CSL (RBP-Jk), key effector of canonical Notch signaling endowed with intrinsic transcription repressive function. CSL expression is decreased in upper epidermal layers and differentiating primary human keratinocytes (HKCs), while it is up-regulated in premalignant and malignant SCC lesions and SCC cell lines from skin, Head/Neck and lung. Increased CSL levels enhance proliferation and self-renewal potential of HKCs and SCC cells, while its silencing induces growth arrest and apoptosis. In vivo, SCC cells with increased CSL levels give rise to rapidly expanding tumors, while upon CSL silencing they form smaller and more differentiated tumors with enhanced inflammatory infiltrate. Global transcriptomic analysis of HKC and SCC cells plus/minus CSL silencing reveals major modulation of apoptotic, cell cycle and pro-inflammatory genes, with no significant association with Notch or keratinocyte differentiation gene signatures. KDM6B, a histone demethylase gene with highly context dependent functions, is a direct CSL negative target, with an inverse role of CSL in HKC and SCC self-renewal and tumorigenesis, with IL6 as a target of likely significance. CSL / KDM6B protein expression could be used as biomarkers of SCC development and novel indicators of cancer treatment.

overall_design: CSL RNA-Seq on HKC and  SCC cell lines. Each shCSL sample was performed in duplicate. For experiments on humna keratinocytes (HKC), duplicate samples were analyzed.

first: Dania

last: Al Labban

first: Seung-Hee

last: Jo

first: Paola

last: Ostano

first: Massimo

last: Bongiovanni

first: G

last: Dotto


title: RNA-seq transcriptomics of the Atp7b-/- mouse liver at six weeks of age

status: Public on Dec 01 2017

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

summary: We report liver transcript profiling by RNA sequencing of Atp7b-/- and wild type mice at six weeks of age. Transcriptional network analysis of RNA-seq data reveals a highly interconnected network of transcriptional activators with over-representation of zinc-dependent and zinc-responsive transcription factors.

overall_design: Wild type and Atp7b-/- Mice were maintained on strain C57BL x 129S6/SvEv. Housing was in shoebox cages and fed Mazuri Rodent diet (PMI Nutrition, Inc., Richmond, Indiana), containing 16 ppm Cu, 100 ppm Zn, and 235 ppm Fe and water ad libitum, with a 12-hour light/dark cycle. Six-week-old mice of both sexes were used for transcriptomic studies. Animals were sacrificed by carbon dioxide asphyxiation and liver tissue was harvested for RNA isolation. RNA sequencing was performed at the National Center for Genome Resources (NCGR) using the GAIIx platform. Average read quality was 38.  An initial dataset was generated using two wild type and two Atp7b-/- samples with singleton 1x54 runs with 15,823,058; 8,149,631; 22,931,967 and 9,538,147 reads. A second paired end (2x54) dataset was generated to augment the initial singleton dataset with one wild type and one Atp7b-/- run resulting in 36,360,686 and 38,366,743 reads, respectively.

first: Jason

last: Burkhead

first: María

last: Paz Cortés


title: Chromatin reprogramming in primordial germ cells requires Nanos-dependent down-regulation of the synMuvB transcription factor LIN-15B

status: Public on Dec 08 2017

city: Baltimore

first: Geraldine

last: Seydoux

state: MD

address: 725 N. wolfe St. PCTB 706

department: MBG

institute: Johns Hopkins University

summary: The Nanos family of RNA-binding proteins has been implicated in the specification of primordial germ cells (PGCs) in a wide range of metazoans, but the underlying mechanisms remain poorly understood. We have profiled the transcriptome of PGCs lacking the nanos homologues nos-1 and nos-2 in C. elegans using cell sorting and RNA-seq. nos-1nos-2 PGCs fail to silence hundreds of genes normally expressed in oocytes and somatic cells, a phenotype reminiscent of PGCs lacking the repressive PRC2 complex. The nos-1nos-2 phenotype depends on LIN-15B, a broadly expressed synMuvB class transcription factor known to antagonize PRC2 activity in somatic cells. LIN-15B is maternally-inherited by all embryonic cells and is down-regulated specifically in PGCs in a nos-1nos-2-dependent manner.  Consistent with LIN-15B being a critical target of Nanos regulation, inactivation of maternal LIN-15B restores fertility to nos-1nos-2 mutants. These studies demonstrate a central role for Nanos in reprogramming the transcriptome of primordial germ cells away from an oocyte/somatic fate by down-regulating an antagonist of PRC2 activity.

overall_design: 30 RNA-seq samples are inclued in this study. These include PGC transcriptomes from wild-type, nos-1(gv5)nos-2(RNAi), mes-2(RNAi), mes-4(RNAi), nos-1(gv5)nos-2(RNAi);lin15-B(RNAi) and biological replicates.

first: Chih-Yung

middle: S

last: Lee


title: Gene expression signatures for conophylline (CNP) treatment in human foreskin fibroblasts NB1RGB cells

status: Public on Nov 02 2017

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

summary: To investigate the effect of CNP on gene expression, we have employed whole genome microarray expression profiling using NB1RGB cells.

overall_design: The cells were plated at 80% confluence and cultured for 16 hours, CNP at each concentration (0.025, 0.1 μM) was added and the cells were incubated for 1 hour. TGF-β was then added, and cells were cultured for 6 hours. After washing with PBS,

first: Hideto

last: Watanabe


title: Microarray expression data from mouse embryonic stem cells differentiated into Nkx2-1+ lung and thyroid progenitors

status: Public on Oct 31 2017

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
The in vitro directed differentiation of pluripotent stem cells (PSCs) through stimulation of developmental signaling pathways can generate mature somatic cell types for basic laboratory studies or regenerative therapies.
We used microarrays to detail the global transcriptomes of mouse embryonic stem cells differentiated in vitro into putative thyroid vs lung epithelial lineages using serum-free media supplemented with either BMP4+FGF2 (thyroid media) or BMP4+Wnt3a (lung media.) Differentiated cells carried an Nkx2-1mCherry knock-in reporter to allow sorting of mCherry + vs - cells in each condition on day 14 of differentiation for global transcriptomic profiling.

overall_design: Mouse embryonic stem cells (carrying an mCherry reporter targeted to the Nkx2-1 3'UTR) were differentiated in serum-free conditions: the cells were first differentiated as embryoid bodies in suspension culture into definitive endoderm with Activin A, followed by differentiation into anterior foregut endoderm by day 6, and then each sample in monolayered 2D culture on gelatin-coated plates was treated on days 6-14 with the growth factor supplements to be tested for each condition (BMP4+FGF2 for thyroid induction media; and BMP4+Wnt3a for lung induction media.)

first: Maria

last: Serra

first: Darrell

last: Kotton


title: RIP-seq and RNA-seq in wt and nono-/- mice

first: Galina

last: Erikson

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

overall_design: Refer to individual Series


title: Clonal analysis of lineage fate in unperturbed hematopoiesis

status: Public on Jan 03 2018

first: Fernando

last: Camargo

address: 300 Longwood Ave

department: Stem Cell and Regenerative Biology

institute: Boston Children's Hospital

summary: The classical tenet of hematopoiesis posits well-accepted lineage trees that arise from progressively restricted oligopotent and unipotent progenitor populations. However, because fate in hematopoiesis has mostly been studied in the context of transplantation, it is unclear whether these lineage branches and such proposed oligopotent progenitors exist in an unperturbed hematopoietic system. Here, we utilize endogenous transposon tagging to trace the fate of thousands of progenitors and stem cells over time to re-evaluate these dogmas. Our results describe a novel clonal roadmap where the megakaryocyte lineage arises independently of lymphoid and myeloid/erythroid fates. Our data also demonstrate that true oligopotency is largely restricted to the multipotent progenitor (MPP) compartment. Analysis of thousands of stem cell and progenitor transcriptomes demonstrates that lineage determination starts at the MPP stage and identifies a functional hierarchy within this population that drives hematopoiesis. Finally, our results demonstrate that long-term hematopoietic stem cells behave physiologically as megakaryocyte lineage progenitors. Our data provide evidence for a substantially revised hematopoietic roadmap, and highlights unique properties of MPPs and HSCs in situ.

overall_design: Single-cell mRNA sequencing of hematopoietic stem cells and multipotent progenitor subsets from mouse bone marrow. Sample LTHSC represents 940 single cells. Sample MPP2 represents 776 single cells. Sample MPP3 represents 1372 single cells. Sample MPP4 represents 1016 single cells. Sample STHSC represents 837 single cells.

first: Alejo

middle: E

last: Rodriguez-Fraticelli

first: Samuel

last: Wolock

first: Caleb

last: Weinreb

first: Maja

last: Jankovic

first: Jianlong

last: Sun

first: Allon

last: Klein


title: Search for apoptosis-related transcriptome markers associated with herpesvirus infections in peripheral blood leukocytes

status: Public on Jan 31 2018

city: Nizhny Novgorod

first: Dmitry

last: Knyazev

address: Malaya Yamskaya, 71

country: Russia

institute: I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology

summary: Proteins encoded by the herpesviridae family members interfere with apoptotic pathways helping the viruses to evade immune surveillance. The aim of the study is to reveal mRNA markers which could be clinically relevant for monitoring of the herpesvirus infections. Majority of the genes being investigated fall within the following categories - death receptors, adaptors, caspases, mitochondrial proteins associated with apoptosis, kinanses involved in apoptosis regulation and execution, splicing factors, transcription factors.


title: Expression data from Arabidopsis seedling

city: Hannover

first: Thomas

last: Pflannschmidt

address: Herrenhäuser Straße 2

institute: Leibniz-Universität Hannover

summary:
For establishing the photosynthetic apparatus plant cells must orchestrate the expression of genes encoded in both nucleus and chloroplast. Therefore a crosstalk between the two compartments is necessary.
We employed a trivalent gene expression profiling approach in order to elucidate the changes in gene expression that occur during the early steps of light-induced chloroplast biogenesis.

overall_design: The three conditions compared were: Arabidopsis thaliana wildtype Col-0 grown in dark for 4 days after germination. Arabidopsis thaliana mutant pap7 and wildtype col-0 for 5 days in light. Plants were grown separately on MS medium in Petri dish per condition. around 50 seedlings per petridish.

first: Björn

last: Grübler

first: Livia

last: Merendino

last: Pfannschmidt


title: Targeting the vulnerability of RB tumor suppressor loss in triple negative breast cancer

status: Public on Jan 05 2018

city: Tucson

first: Adam

middle: David

last: Grant

state: Arizona

address: 3760 E. Felix Blvd

department: Cancer Biology

institute: University of Arizona

summary: Approximately 30% of TNBCs exhibit loss of function of the RB tumor suppressor. The study used RNA sequencing to profile RB-proficient and RB-deficient TNBC cases that were defined based on immunostaining for RB and p16ink4a.   The analyses revealed that RB-deficient TNBC cases express elevated levels of DNA replication and mitotic genes that could serve as the basis for increased sensitivity to drugs targeting cell cycle checkpoints.

overall_design: The study compared normal tissue, RB-positive, and RB-deficient TNBC.    RNA sequencing was utilized to define differentially expressed genes.

first: Agnieszka

last: Witkiewicz

first: Erik

last: Knudsen


title: Mechano-sensitive Gene Expression with RNA-Seq: Revisiting the Osteocytic Cell Response to Fluid Flow

status: Public on Jul 23 2017

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Bone adaptation to mechanical loading is regulated via signal transduction by mechano-sensing osteocytes. Mineral-embedded osteocytes experience strain-induced interstitial fluid flow and fluid shear stress, and broad shifts in gene expression are key components in the signaling pathways that regulate bone turnover. RNA sequencing analysis, or RNA-Seq, enables more complete characterization of mechano-sensitive transcriptome regulation than previously possible. We hypothesized that RNA-Seq of osteocytic MLO-Y4 cells reveals both expected and novel gene transcript regulation in cells previously fluid flowed and analyzed using gene microarrays (Govey et al., J Biomech, 2014). MLO-Y4 cells were flowed for 2 h with 1 Pa oscillating fluid shear stress and post-incubated 2 h. RNA-Seq of original samples detected 58 fluid flow-regulated gene transcripts (p-corrected<0.05) versus 65 transcripts detected by microarray. However, RNA-Seq demonstrated greater dynamic range, with all 58 transcripts >1.5 fold-change whereas 10 of 65 met this cut-off by microarray. Analyses were complimentary in patterns of regulation, though only 6 transcripts were significant in both analyses: Cxcl5, Cxcl1, Zc3h12a, Ereg, Slc2a1, and Egln1. As part of a broad inflammatory response inferred by gene ontology analyses, we again observed greatest up-regulation of inflammatory C-X-C motif chemokines, and newly implicated HIF-1? and AMPK signaling pathways. Importantly, we detected both expected mechano-sensitive transcripts (e.g. Nos2, Ptgs2, Ccl7) and transcripts not previously identified as mechano-sensitive, e.g. Ccl2. We found RNA-Seq advantageous over microarrays because of its ability to analyze unbiased estimation of gene expression, informing our understanding of osteocyte signaling.

overall_design: Osteocyte-like MLO-Y4 cells were subjected to 2 hours of 10 dyn/cm^2 oscillating fluid flow in parallel-plate fluid flow chambers and harvested for analysis after an additional 2 hours post-flow incubation in fresh medium. Parallel control samples from sham treated cells were also collected. Triplicate samples of both flow and non-flow control conditions were collected to analyze flow vs. non-flow gene transcript regulation.

middle: I

last: Kawasawa

first: Peter

middle: M

last: Govey

first: Henry

middle: J

last: Donahue


title: Sequencing of the stomach-less ballan wrasse (Labrus berggylta) genome and transcriptomic characterization of the intestine

status: Public on Jun 01 2017

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

summary: Stomach-less fishes comprise a diverse phylogenetic group within the teleosts indicating that the organ has been lost several times during evolution. In the present project we have combined Illumina short read platform with the PacBio long read platform to sequence the ballan wrasse (Labrus bergylta) genome and its intestinal transcriptome. The genome was applied to investigate the elimination and conservation of genes related to stomach function and appetite regulation in wrasse in relation to the loss of stomach in this species. We have sequenced the transcriptome of four intestinal segments from six ballan wrasse (Labrus bergylta) for the purpose of identifying possible functional organization along the wrasse intestine. The transcriptomic reads were mapped against the newly assembled genome. The analysis revealed a transcriptional gradient showing genes involved in nutrient digestion and uptake being highly expressed in the anterior intestine and declining towards the end of the intestine. The last segment, hind-gut, had the most distinct expression between the four segments with increased expression of genes coding for proteins involved in lysosomal activity, antigen presenting and vitamin b12 uptake. Overall, our results suggests that the wrasse entire digestive system is comparable to the small intestine of mammals with regards to gene expression missing both a stomach and colon. Gene expression related to colon in humans such as MS4A12 were found in the last segment. The genome analysis also confirmed the lack of genes coding for gastric proteins such as gastric lipase, pepsin, gastrin and ghrelin. Although ghrelin is not only related to stomach, ghrelin was missing in all stomach-less fish species with the exception of cyprinid. Ghrelin is currently the only known orexigenic hormone.

overall_design: Six ballan wrasse (Labrus bergylta) were collected from a commercial fish farm. Four segments of the intestine from the anterior to the posterior part was sampled from each fish. RNA from each segment were sequenced seperatly and analyzed.

middle: K

first: Ole

last: Tørresen

first: Monica

last: Solbakken

first: Ave

last: Tooming-Klunderud

first: Lex

last: Nederbragt

first: Øystein

last: Sæle


title: Single cell RNAseq of hPSC derived V2a interneuron cultures

status: Public on Apr 24 2017

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

summary: The goal of this study is to perform an unbiased characterization of human pluripotent derived V2a interneuron cultures.

overall_design: 1 Sample

middle: C

first: Jessica

last: Butts


title: The Not4 ubiquitin ligase utilizes its conserved RNA binding domains to regulate global proteostasis and RNA polymerase II-dependent transcription

status: Public on Aug 03 2017

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: The conserved Ccr4-Not complex regulates all aspects of the RNA polymerase II (Pol II) gene expression pathway, while it also controls proteasome assembly and function. The Not4 RING domain ubiquitin ligase is a core subunit that also contains an RNA recognition motif (RRM) and C3H1 domain (collectively referred to as the RRM-C) whose function is unknown. Herein, we demonstrate that the Not4 RRM-C contributes to both Not4-dependent regulation of the proteasome and Pol II. Disruption of both Not4 ligase activity and the RRM-C domain simultaneously replicates the proteasome-dependent deubiquitylation and catalytic activity misregulation found in Not4-deficient cells. Transcriptome analysis reveals that the Not4 RRM-C affects a subset of Pol II-dependent genes involved in specific biological functions, including transcription elongation, cyclin-dependent kinase regulated nutrient responses, and ribosomal biogenesis. At these genes, the Not4 RRM-C negatively regulates Pol II binding. While Not4 RRM-C disruption modestly increases between Ccr4-Not and Pol II, a Not4 ligase mutant decreases Ccr4-Not association with Pol II, thus implicating Not4-dependent ubiquitylation in mediating Ccr4-Not interaction with Pol II. Collectively, our results suggests the cellular RNA environment may integrate control of global proteostasis and Pol II transcription through the Not4 ubiquitin ligase.

overall_design: There are two conditions analyzed in this study (cells expressing Not4WT or Not4RRM) with three replicates per condition.

first: Hongfeng

last: Chen

first: Tirupataiah

last: Sirupangi

first: Zhaohui

last: Wu

first: R

last: Laribee


title: PAIR-MaP visualizes RNA base pairing complexity in human and bacterial non-coding RNAs

status: Public on Aug 01 2019

city: Houston

first: Anthony

last: Mustoe

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Structure probing experiments were performed on in vitro transcripts and E. coli and human cell cultures under natively extracted (cell-free) and in-cell conditions to benchmark the performance of the newly introduced PAIR-MaP correlated chemical probing strategy for detecting RNA duplexes. Multiple-hit dimethyl sulfate (DMS) probing was done using new buffer conditions that facilitate DMS modification of all four nucleotides.

sample_organism:
Escherichia coli
Vibrio vulnificus
Homo sapiens

overall_design: In vitro transcribed RNA, cell-free total RNA from E. coli and human Jurkat cells, and living E. coli and human Jurkat cells were treated with DMS in bicine (pH 8.0) probing buffer. Untreated control samples were also collected in parallel by substituting neat ethanol for DMS. MaP reverse-transcription was used to convert DMS-modified RNA into cDNA using random 9mers (16S and 23S rRNAs) or specific primers (all other RNAs). Sequencing libraries were constructed using a Nextera strategy (16S and 23S rRNAs) or two-step PCR strategy (all other RNAs) and sequenced on an Illumina MiSeq. When necessary, libraries were resequenced multiple times to obtain sufficient reads. The ShapeMapper (v2.1.4) pipeline was used to align reads and call modification-induced mutations. PairMapper (v1.0) was then used to calculate normalized DMS reactivities and detect correlated base-paired positions. Fasta files used for alignment of each sample are provided as supplementary data files. Final processed DMS reactivity files and PAIR-MaP files are provided as supplementary files for RNA and condition.

first: Nicole

last: Lama

first: Patrick

last: Irving

first: Samuel

middle: W

last: Olson

first: Kevin

last: Weeks


title: Transcriptome analysis of salivary gland epithelial cell lines derived from patients with primary Sjögren’s syndrome.

status: Public on Apr 11 2017

city: ATHENS

first: Menelaos

middle: N.

last: Manoussakis

address: 75 MIKRAS ASIAS STR

department: Pathophysiology

country: Greece

institute: National and Kapodistrian University of Athens

summary:
Primary Sjögren’s syndrome (SS or autoimmune epithelitis) is a relatively common autoimmune disorder that is primarily characterized by chronic lymphoepithelial inflammatory reactions in the exocrine glands, mainly the salivary and lachrymal glands. It may extend from disease confined to the exocrine glands (organ-specific exocrinopathy) to various extraglandular manifestations (systemic disease) and the development of B-cell lymphoma. Several studies from our laboratory had provided evidence for the strong implication of ductal salivary gland epithelial cells (SGEC) in the pathogenesis of Sjögren’s syndrome (SS), including the development of salivary gland infiltrating lesions and of adverse systemic clinical complications, such as the development of B-cell lymphoma. In fact, the comparative assessment of non-neoplastic SGEC lines derived from SS patients and disease controls had indicated that the ductal epithelia of SS patients manifest an “intrinsically activated” status that is associated with distinct aberrant phenotypic and functional features encountered in “inflamed” cells.
Herein, using microarray analysis, we sought to comparatively analyze the constitutive gene expression in long-term cultured non-neoplastic SGEC lines derived from non-SS sicca control individuals and from SS patients. The study aimed to reveal the genes that are differentially expressed between SGEC lines derived from SS patients and controls, as well as between SGEC lines derived from SS patients with moderate lymphocytic infiltrations (focus score<2; SS-Group-1) and SS patients with severe lymphocytic infiltrations (focus score ≥2; SS-Group-2). The transcriptome profiling analysis presented herein lends further support to the intrinsic activation status of patients’ ductal epithelia and its association with distinct proinflammatory and metabolism-related gene signatures, which occur primarily among patients with heavy tissue infiltrates and high risk for lymphoma development.

overall_design: Long-term cultured non-neoplastic secondary SGEC lines were established from minor salivary gland biopsies that were obtained with informed consent from patients with dryness complaints during their routine diagnostic work-up for SS. All SGEC lines studied (n=12) were of ductal type and were established and maintained under the same culture conditions in serum-free keratinocyte basal medium, as previously described (Dimitriou et al, Eur J Oral Sci, 2002, 110:21-30). The exclusive epithelial nature and ductal epithelial origin of cultured SGEC lines was verified by morphology, as well as by the uniform and consistent expression of epithelial specific markers and the absence of markers indicative of other types of cells.  Transcriptome analyses were performed in total RNA specimens isolated from the non-neoplastic SGEC lines derived from 3 non-SS sicca controls (control-SGEC lines) and from 9 SS patients (SS-SGEC lines), using the Affymetrix microarray technology (GeneChipHuGene 1.0ST arrays with 28,869 annotated genes). The SS-SGEC lines studied were selected on the basis of the intensity of lymphoepithelial infiltrates in the respective MSG biopsies (all with sialadenitis focus score ≥1), and consisted of two subgroups; SS-Group-1 (n=3) derived from biopsies with moderate mononuclear infiltrations (focus score<2) and SS-Group-2 (n=6) derived from biopsies with heavy mononuclear infiltrations (focus score ≥2). Evidence of type-1 disease (high risk for lymphoma development) was exclusively manifested by patients belonging in SS-Group-2. Microarray analysis was performed with the R statistical environment version 2.13 using the Bioconductor package. RMA normalization was performed in the microarray and identification of differentially expressed genes was conducted with Student’s t-test (p-value<0.05). Gene ontology annotation of differentially expressed genes, signal pathway analysis and network construction was performed with the use of Ingenuity Pathway Analysis (IPA) software and he Kyoto Encyclopedia of Genes and Genomes (KEGG).

first: Efstathia

last: Kapsogeorgou

first: Aigli

middle: G

last: Vakrakou


title: Daphnia magna  life-stages profiling using a new custom made microarray

status: Public on Apr 01 2017

city: Barcelona

first: Bruno

last: Campos

address: jordi girona, 18, 18

department: Environmental Chemistry

country: Spain

institute: IDAEA-CSIC

summary: 7 daphnia magna life stages from embryo development till adult were profiled using a new custom made microarray on a 4*160K platform

overall_design: 3 samples eggs under 12h, 3 samples eggs under 12 to release, 2 samples 4 days old juveniles, 3 samples 14 days old females under 12 houra after ovideposition, 3 stages of 15 days old females around 36h after ovideposition, 3 stages of 16 days old females under 12 hours to embryo release and 2 samples of males

first: John

last: Colbourne

first: Carlos

last: Barata


title: Adipose tissue gene expression is differentially regulated with different rates of weight loss in overweight and obese humans

status: Public on Feb 07 2017

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Background: Moderate weight loss can ameliorate adverse health effects associated with obesity, reflected by an improved adipose tissue (AT) gene expression profile. However, the effect of rate of weight loss on the AT transcriptome is unknown.

Objective: We investigated the global AT gene expression profile before and after two different rates of weight loss that resulted in similar total weight loss, and after a subsequent weight stabilization period.

Design: In this randomized controlled trial, 25 male and 28 female individuals (BMI: 28-35 kg/m2) followed either a low-calorie diet (LCD; 1250 kcal/d) for 12 weeks or a very-low-calorie diet (VLCD; 500 kcal/d) for 5 weeks (weight loss (WL) period) and a subsequent weight stable (WS) period of four weeks. The WL period and WS period together is termed dietary intervention (DI) period. Abdominal subcutaneous AT biopsies were collected for microarray analysis, and gene expression changes were calculated for all three periods in the LCD group, VLCD group and between diets (ΔVLCD-ΔLCD).

Results: Weight loss was similar between groups during the WL period (LCD: -8.1±0.5 kg, VLCD: -8.9±0.4 kg, difference p=0.25). Overall, more genes were significantly regulated and changes in gene expression were more extreme in the VLCD group compared to the LCD group. Gene sets related to mitochondrial function, adipogenesis and immunity/inflammation were more strongly upregulated on a VLCD compared to a LCD during the DI period (positive ΔVLCD-ΔLCD). Neuronal- and olfactory-related gene sets were decreased during the WL period and DI period in the VLCD group.

Conclusions: The rate of weight loss (LCD vs. VLCD), with similar total weight loss, strongly regulates AT gene expression. Increased mitochondrial function and adipogenesis on a VLCD compared to a LCD reflect potential beneficial diet-induced changes in AT, while differential neuronal and olfactory regulation suggest functions of these genes beyond the current paradigm.

overall_design:
In this randomized controlled trial, 53 male and female individuals (BMI: 28-35 kg/m2) underwent a dietary intervention (DI) with two different rates of weight loss consisting of either a low-calorie diet (1250 kcal/d) for 12 weeks or a very-low-calorie diet (500 kcal/d) for 5 weeks (weight loss (WL) period) and a subsequent weight stable (WS) period of four weeks. Abdominal subcutaneous AT biopsies were collected for whole-genome gene expression analysis at study start, after the WL period and after the WS period.

This trial is registered with www.clinicaltrials.gov under the accession number NCT01559415.

last: Vink

first: N

last: Roumans

first: P

last: Fazelzadeh

first: S

last: Tareen

first: M

middle: V

last: Boekschoten

first: E

last: Mariman

middle: A

last: van Baak


title: Estrogen and progesterone receptor dynamics in patient-derived luminal breast cancer xenografts

status: Public on Feb 28 2017

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

country: USA

institute: University of Colorado Denver Anschutz Medical Campus

summary: Progesterone receptors (PR) are co-expressed in over half of estrogen receptor (ER) positive breast cancers and predict positive response to endocrine therapy. PR can directly and globally modify ER action to attenuate tumor growth. However, whether this suppression occurs solely through PR-ER interactions remains unknown. We assessed tumor growth in two highly ER and PR positive breast cancer patient-derived xenografts (PDX) and found that natural and synthetic progestins potently antagonize the mitogenic effects of estrogens. Here we probed the genome-wide mechanisms by which this occurs. Chronic progestin treatment reversed expression of up to half of estrogen up- and downregulated genes at the transcript level. However, fewer than a quarter of ER DNA binding events were altered by progesterone. The PR cistrome showed an interesting bimodal distribution. In the first group, more than half of PR binding sites were co-occupied by ER, with a propensity for both receptors to coordinately gain or lose binding in the presence of progesterone. In the second group, PR, but not ER, was associated with a large fraction of RNA polymerase III (Pol III)-transcribed tRNA genes regardless of hormone treatment. Furthermore, PR formed a physical association with the Pol III holoenzyme. Select tRNAs with colocalization of PR and POLR3A at their promoters were reduced in tumors grown with estrogen plus progestin compared to estrogen alone. These data uncover a mechanism in solid tumors by which PR modulates the bioavailability of translational molecules that are necessary for robust tumor growth, which could indirectly impede ER action.

overall_design: Patient-derived luminal breast cancer xenografts from animals treated with placebo, estradiol (E2), E2+medroxyprogesterone acetate (MPA) ,E2+progesterone (P4), each in triplicate

first: Peter

last: Kabos

first: Carol

last: Sartorius


title: Cut-and-Run in situ factor profiling maps DNA binding and 3D contact sites at high resolution

status: Public on Dec 30 2016

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Unlike Chromatin Immunoprecipitation (ChIP), which fragments and solubilizes total chromatin, Cut-and-Run is performed in situ, allowing for both high-resolution chromatin mapping and probing of the local chromatin environment. When applied to yeast and human nuclei, Cut-and-Run yielded precise transcription factor profiles while avoiding cross-linking and solubilization issues. Cut-and-Run is simple to perform and at low temperatures is inherently robust, with extremely low backgrounds that make it especially cost-effective for transcription factor and chromatin profiling. When used in conjunction with native ChIP-seq and applied to human CTCF, Cut-and-Run mapped high-resolution 3D directional interactions. We conclude that Cut- and-Run is a suitable complement or replacement for ChIP-seq that can also provide 3D mapping information.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: We used Cleavage under targets and Release using nuclease (Cut-and-Run), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing.

last: Skene

first: Steven


title: Molecular Signatures Associated with Prolonged Survival In Melanoma Patients Treated with Dendritic Cell-Based Immunotherapy

status: Public on Oct 25 2017

city: Frankfurt am Main

first: Franziska

last: Matthäus

address: Ruth-Moufang-Str. 1

department: Frankfurt Institute for Advance Studies (FIAS)

institute: Goethe University of Frankfurt

summary: Analysis of gene expression dynamics in patients suffering from melanoma stage IV treated with vaccination therapy.

overall_design: Total RNA extracted from blood samples prior to first vaccination, at time points of concurrent vaccinations, and after last vaccination.

first: Tamara

last: García

first: Andrea

last: Villablanca

first: Mauricio

last: Baeza

first: Andrés

last: Tittarelli

first: Cristián

last: Pereda

first: Fernando

last: Lillo

last: Gleisner

first: Fabiola

last: Osorio

first: Fermín

last: González

first: Mercedes

middle: N

last: López

first: Jörg

middle: D

last: Hoheisel

first: Johannes

last: Norgauer

last: Gebicke-Haerter

first: Flavio

last: Salazar-Onfray


title: Thyroid progenitors are robustly derived from embryonic stem cells through transient, developmental stage-specific overexpression of Nkx2-1

status: Public on Dec 20 2016

city: Boston

first: Laertis

last: Ikonomou

address: 670 Albany St

department: Center for Regenerative Medicine

summary: The clinical importance of anterior foregut endoderm (AFE) derivatives, such as thyrocytes, has led to intense research efforts for their derivation through directed differentiation of pluripotent stem cells (PSCs). Here we identify transient overexpression of the transcription factor (TF) NKX2-1 as a powerful inductive signal for the robust derivation of thyrocyte-like cells from mouse PSC-derived AFE. This effect is highly developmental stage-specific and dependent upon FOXA2 expression levels and precise modulation of BMP and FGF signaling. The majority of the resulting cells express thyroid TFs (Nkx2-1, Pax8, Foxe1, Hhex) and thyroid hormone synthesis-related genes (Tg, Tpo, Nis, Iyd) at levels similar to adult mouse thyroid and give rise to functional follicle-like epithelial structures in Matrigel culture. Our findings demonstrate that NKX2-1 overexpression converts AFE to thyroid epithelium in a developmental time-sensitive manner and suggest a general methodology for manipulation of cell fate decisions of developmental intermediates.

overall_design: We analyzed RNA-seq from cells collected from three developmental stages after Dox-mediated induction of Nkx2-1

first: Keri

last: Dame


title: HCT116 cells N-BLR shRNA vs. empty vector control

status: Public on Dec 27 2016

first: Simone

last: Anfossi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Therapeutics

institute: UT MD Anderson Cancer Center

summary: HCT116 cells transfected with lentiviral vectors expressing two different N-BLR shRNAs (clones #3-1 and #4-7) and empty vector control

overall_design: Two HCT116 stable clones expressing N-BLR shRNAs (named clones #3-1 and #4-7) compared to empty vector control. Biological replicate: two stable clones vs empty vector controls

first: Isidore

last: Rigoutsos

first: George

last: Calin

first: Hu

last: Limei


title: Transcriptomic Profiles of Xylose-utilizing Zymomonas mobilis 8b to Pretreatment Inhibitor Furfural

status: Public on Nov 18 2016

city: Golden

first: Shihui

last: YANG

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

type: Expression profiling by genome tiling array

summary:
Background: Lignocellulosic biomass is a promising renewable feedstock for the microbial production of fuels. To release the major fermentable sugars such as glucose and xylose, pretreatment, hydrolysis, and subsequent conditioning of biomass feedstock are needed. During this process, many toxic compounds are produced or introduced which subsequently inhibit microbial growth and in many cases the production titer and rate. An understanding of the toxic effects of compounds found in hydrolysate on the fermentation microorganism is critical to improving biofuel yields in the process. One of the inhibitory compounds is furfural, liberated from hemicelluloses, which strongly inhibits the cell growth and ethanol production especially from xylose. Zymomonas mobilis is a capable ethanologenic bacterium with high ethanol productivity and high levels of ethanol tolerance. The development of robust biocatalyst to tolerate the lignocellulosic pretreatment inhibitors is one of the key elements for economic biofuel production.

Results: In this study, the molecular responses of Z. mobilis to furfural, one major pretreatment inhibitor, were investigated using transcriptomic approaches of chip-based microarray. Furfural shock time course experiment with 3 g/L furfural supplemented when cells reach exponential phase and stress response experiment in the presence of 2 g/L furfural from the beginning of fermentation were carried out to study the short and long-term effect of furfural on 8b physiological and transcriptional profiles. The presence and supplementation of furfural negatively affect 8b growth in terms of final biomass and the fermentation time. Transcriptomic studies indicated that the response of 8b to furfural is dynamic, complex and differences exist between short-term shock response and long-term stress response. However, the gene function categories are similar with most downregulated genes related to translation and biosynthesis, while the furfural-upregulated genes were mostly related to cellular processes of general stress response and energy metabolism.

Conclusions: Similar to previous report that acetate inhibited the growth of Z. mobilis 8b in RM using glucose or xylose as carbon source, the existence or supplementation of another major hydrolysate inhibitor furfural also inhibited 8b growth with slowing the substrate utilization and ethanol production. The difference between carbon sources is more dramatic than that of the major hydrolysate inhibitors of both NH4OAc (GSE57553) and furfural (this study). Several gene targets have been selected for genetic studies with promising preliminary results.

overall_design: In this study, the molecular responses of Z. mobilis to furfural, one major pretreatment inhibitor, were investigated using transcriptomic approaches of chip-based microarray. Furfural shock time course experiment with 3 g/L furfural supplemented when cells reach exponential phase (0min before furfural shock, 15min and 60min post-furfural shock) and stress response experiment in the presence of 2 g/L furfural from the beginning of fermentation were carried out to study the short and long-term effect of furfural on 8b physiological and transcriptional profiles. Three biological replicates were used for each condition.

first: Steven

middle: B

last: Brown

first: Mary

last: Franden

first: Yat-Chen

last: Chou

first: Philip

middle: T

last: Pienkos

first: Min

last: Zhang