title: A seven-membered cell wall related transglycosylase gene family in Aspergillus niger is relevant for cell wall integrity in cell wall mutants with reduced α-glucan or galactomannan

status: Public on Dec 21 2019

city: Leiden

first: Tim

middle: Marijn

last: van Leeuwe

address: Sylviusweg 72

institute: Leiden University

summary: Chitin is an important fungal cell wall component that is cross-linked to β-glucan for structural integrity. Acquisition of chitin to glucan cross-links has previously been shown to be performed by transglycosylation enzymes in S. cerevisiae, called Congo Red hypersensitive (Crh) enzymes. Here, we characterized the impact of deleting all seven gene members of the crh gene family (crhA-G) in Aspergillus niger on cell wall integrity, cell wall composition and genome-wide gene expression. In this study, we show that the seven-fold knockout strain shows slightly compact plate growth, but no increased sensitivity to cell wall perturbing compounds. Additionally, we found that the cell wall composition of this knockout strain was virtually identical to that of the wild type. In congruence with these data, genome-wide expression analysis revealed very limited changes in gene expression and no signs of activation of the cell wall integrity response pathway. However, deleting the entire crh gene family in cell wall mutants that are deficient in either galactofuranose (ΔugmA) or α-glucan (ΔagsE and ΔagsA, ΔagsE), resulted in a synthetic growth defect and an increased sensitivity towards Congo Red compared the parental strains. Altogether, these results indicate that loss of the crh gene family in A. niger does not trigger the cell wall integrity response in itself, but does play an important role in ensuring cell wall integrity in mutant strains with reduced galactofuranose or α-glucan.

overall_design: Expression profiles A. niger strains; wild type versus seven-fold crh deletion strain from bioreactor cultures, using RNA-sequencing, duplicate biological samples, two biomass points (70% and 90% of maximum attained biomass) per biological samples. 8 samples total

first: Jasper

last: Wattjes

first: Anna

last: Niehues

first: Gabriel

last: Forn-Cuní

first: Nicholas

last: Geoffrion

first: Hugo

last: Mélida

first: Mark

last: Arentshorst

first: Antonio

last: Molina

first: Adrian

last: Tsang

first: Annemarie

last: Meijer

first: Bruno

last: Moerschbacher

last: Punt

first: Arthur

middle: F

last: Ram


title: Single-cell CRISPR screening on mouse embryonic stem cells

city: District of Columbia

first: Lin

last: Yang

address: 111 Michigan Avenue NW

country: USA

institute: Children's National Medical Center

type: Expression profiling by high throughput sequencing

summary: We performed CROP-seq experiments to interrogate genes that are critical for mouse embryonic stem cell pluripotency and differentiation

overall_design: Examination of total 15 pluripotency-associated transcription factors and metabolic genes by perturbation

first: H

last: Huang

first: J

last: Zhang

first: Y

last: Zhu

last: Yu

last: Chu


title: Expression data of paired human neonatal thymus MSCs vs bone MSCs

status: Public on Dec 25 2019

city: Ann Arbor

first: Ming-Sing

last: Si

state: MI

address: 11-735 C.S. Mott Children's Hospital, 1540 E. Hospital Drive

department: Cardiac Surgery

institute: University of Michigan

summary:
Neonatal thymus MSCs and bone derived MSCs have differential abilities to stimulate angiogenesis and invade extracellular matrix.
We utilized microarray to identify differentially expressed genes between these two types of MSCs and analyzed this information in the context of the phenotypic differences between these two cell types.

overall_design: MSCs from the thymus and bone were isolated from six neonates and infants undergoing open heart surgery. After isolation and culture, RNA was isolated and hybridized on Affymetrix microarrays. The paired samples provided a control for other confounding factors such as age of donor, health status of donor, and sex of donor.


title: Apoptotic exosome-like vesicles regulate endothelial gene expression, inflammatory signaling, and function through the NF-κB signaling pathway.

status: Public on Dec 11 2019

city: Montreal

first: Marie-Josée

last: Hébert

state: QC

address: 900 Rue Saint-Denis

country: Canada

institute: CRCHUM

summary: Persistent endothelial injury promotes maladaptive responses by favoring the release of factors leading to perturbation in vascular homeostasis and tissue architecture. Caspase-3 dependent death of microvascular endothelial cells leads to the release of unique apoptotic exosome-like vesicles (ApoExo). Here, we evaluate the impact of ApoExo on endothelial gene expression and function in the context of a pro-apoptotic stimulus. Endothelial cells exposed to ApoExo differentially express genes involved in cell death, inflammation, differentiation, and cell movement. Endothelial cells exposed to ApoExo showed inhibition of apoptosis, improved wound closure along with reduced angiogenic activity and reduced expression of endothelial markers consistent with the first phase of endothelial-to-mesenchymal transition (endoMT). ApoExo interaction with endothelial cells also led to NF-κB activation. NF-κB is known to participate in endothelial dysfunction in numerous diseases. Silencing NF-κB reversed the anti-apoptotic effect and the pro-migratory state and prevented angiostatic properties and CD31 downregulation in endothelial cells exposed to ApoExo. This study identifies vascular injury-derived extracellular vesicles (ApoExo) as novel drivers of NF-κB activation in endothelial cells and demonstrates the pivotal role of this signaling pathway in coordinating ApoExo-induced functional changes in endothelial cells. Hence, targeting ApoExo-mediated NF-κB activation in endothelial cells opens new avenues to prevent endothelial dysfunction.

overall_design: mRNA profiles of HUVECs cells under serum-starvation +/- ApoExo treatment were generated by deep sequencing, in duplicate using Illumina Hiseq2000

first: Francis

last: Migneault


title: Effects of N-terminal truncated version of FGF2 on dissociated myelinating cultures

status: Public on Dec 09 2019

city: Glasgow

first: Chris

last: Linington

address: 120 University Avenue

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

summary: Analysis of the effects of different FGF2 variants (human FGFs-hFGF2, wild-type protein and N-terminal truncated FGF2-F2V2) on myelinating cultures generated from dissociated embryonic spinal cord after 24 hours treatment to give insights into the effects of the N-terminal region of FGF2 on FGF signalling and its implications in demyelinating diseases.

overall_design: Dissociated myelinating cultures were generated from neurosphere derived astrocytes (generated from striata of P1 Sprague-Dawley rats) and spinal cord cells from E15.5 Sprague-Dawley(SD) embryos. The effect of recombinant human FGF2 and other soluble factors on these in vitro myelinating cultures was investigated by adding them to the culture media after 18 days in vitro (DIV). The effects of each factor were analysed using four independent cultures treated for 24hrs with the different FGF2 variants.

first: Katja

last: Thuemmler

first: Christopher


title: Dosage dependent requirements of Magoh for cortical interneuron generation and survival

city: Durham

first: Debra

last: Silver

state: North Carolina

address: 224 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: We report the transcriptome of E11.5 microdissected and FAC sorted Nkx2.1-Cre;tdTomato + MGE cells from control and Magoh heterozgotes

overall_design: Examination of transcriptome differences due to Magoh haploinsufficient MGE

middle: L

first: Charles

middle: J

last: Sheehan


title: Day-night rhythm in murine retinal pigment epithelium

status: Public on Dec 01 2019

city: Nijmegen

first: Elja

last: Louer

state: Select State

address: Geert Grootplein 26, M850 route 286

department: Physiology

country: Netherlands

institute: RadboudUMC

summary: Murine RPE transcriptomes were generated for 6 time points during a 24 hour period. Our data demonstrates that genes involved in ATP generation have a high expression at night whereas genes involved in β-oxidation and cholesterol synthesis show a high expression in the morning. Additionally, genes were identified in the glycerophospholipid metabolism pathway, suggesting the generation of glycerophospholipids at night. Finally, genes involved in intracellular trafficking with different expression patterns during the day-night cycle were identified and we identified genes involved in actin cytoskeleton building, remodelling and crosslinking with a high expression in the morning.

overall_design: Murine RPE transcriptomes were generated for 6 time points during a 24 hour period (ZT0, 2, 4, 9, 14, 19). In total 30 samples were sequenced because each time point was repeated 5 times (n=5).

middle: M

first: Guoqiang

last: Yi

first: Henk

middle: G

last: Stunnenberg

first: Anneke

middle: I

last: den Hollander

first: Peter

last: Deen


title: Lineage tracing on transcriptional landscapes links state to fate during differentiation

status: Public on Nov 22 2019

city: Boston

first: Caleb

middle: D

last: Weinreb

state: MA

address: 200 Longwood avenue

department: Systems Biology

institute: Harvard Medical School

summary: A challenge in biology is to associate molecular differences among progenitor cells with their capacity to generate mature cell types. Here, we use expressed DNA barcodes to clonally trace transcriptomes over time, applied to study fate determination in hematopoiesis. We identify states of primed fate potential, and locate them on a continuous transcriptional landscape. We identify two routes of monocyte differentiation that leave an imprint on mature cells. Clonal analysis also reveals fate biases into multiple lineages that depend on stable cellular properties hidden from single-cell RNA sequencing. Finally, we benchmark computational methods of dynamic inference from single-cell snapshots, showing that fate choice occurs earlier than is detected by state-of the-art algorithms, and that cells progress steadily through pseudotime with precise and consistent dynamics.

overall_design:
Single-cell mRNA sequencing of fresh and cultured progenitors from mouse bone marrow. Cells were harvested, transduced with lineage barcodes, and then cultured or transplanted with single-cell RNA seq profiling across several time points. Sample stateFate_inVitro contains cells cultured in a broad cytokine cocktail. Sample stateFate_inVivo contains cells that were profiled before and after transplantation. Sample stateFate_cytokinePerturbation contains cells cultured in several different cytokine conditions. Sample GMP_MDP_culture contains MDPs and GMPs before after after culture.

Raw sequencing data are available via SRA. All files are already demultiplexed. Read labels in the fastq files have format @[cell barcode]:[UMI]:[remainder]

first: Alejo

last: Rodriguez-Fraticelli

first: Fernando

last: Camargo

first: Allon

last: Klein


title: Analysis of regulatory element evolution between human and mouse reveals a lack of cis-trans compensation

status: Public on Nov 19 2019

first: Martha

middle: L.

last: Bulyk

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

summary: Gene expression differences between species are driven by both cis and trans effects. Whereas cis effects on gene expression are due to nearby genetic variants, trans effects are due to distal genetic variants that affect diffusible elements such as transcription factors. However, as previous studies have mostly assessed the impacts of cis and trans effects at the gene level, how cis and trans effects differentially impact regulatory elements such as enhancers and promoters remains poorly understood. Here, we used massively parallel reporter assays to directly measure cis and trans effects between human and mouse embryonic stem cells at thousands of individual regulatory elements, including enhancers as well as promoters of both protein-coding and long non-coding RNA genes. Our approach revealed that cis effects are widespread across regulatory elements, and the strongest cis effects are associated with the disruption of motifs recognized by strong transcriptional activators. Conversely, we found that trans effects are rare but stronger in enhancers than promoters, and can be attributed to a subset of transcription factors that are differentially expressed between human and mouse. While previous gene-based studies have found extensive co-occurrence of cis and trans effects in opposite directions that stabilize gene expression between species—or compensatory cis-trans effects—we find that cis-trans compensation is uncommon within individual regulatory elements. Moreover, regulatory elements that do show compensatory cis-trans effects are often less redundant than regulatory elements lacking compensatory cis-trans effects. Thus, our results are consistent with a model wherein compensatory cis-trans effects occur more often through crosstalk between multiple redundant regulatory elements than within a single individual regulatory element. Together, these results indicate that studying the evolution of individual regulatory elements is pivotal to understand the tempo and mode of gene expression evolution.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: We performed two experiments: (1) a massively parallel reporter assay (MPRA) to assess othologous regulatory elements in hESCs and mESCs, and (2) RNA-sequencing of hESCs and mESCs. For the MPRA data, we provide raw fastqs as well as barcode counts. For the RNA-seq data, we provide raw fastqs and gene featureCounts.

first: Kaia

last: Mattioli

first: Winona

last: Oliveros

first: Chiara

last: Gerhardinger

first: Daniel

last: Andergassen

first: Philipp

last: Maass

first: John

last: Rinn

first: Marta

last: Melé


title: Epigenetic changes of pericytes after ischemia-reperfusion renal injury

status: Public on Dec 05 2019

city: Taipei City

first: Yu Hsiang

last: Chou

state: Taiwan

address: No.7, Chung Shan S. Rd.

country: Taiwan

institute: National Taiwan University Hospital

summary: Analysis of epigenetic changes of pericytes after ischemia-reperfusion renal injury. The hypothesis tested in the present study was that epigenetic change develope in pericytes after acute kidney injury. This phenotype change would cause pericyte to be more proliferative and profibrotic. Results provide important information of the epigenetic change of pericytes, such as specific mechano-responsive genes, up-regulated specific proliferative and profibrotic functions.

overall_design: Whole genome analysis of isolated pericytes from kidney before and after acute kidney injury

first: Shuei Liong

last: Lin


title: High-Throughput Kinetic Analysis of Fractional Killing

status: Public on Nov 11 2019

city: Stanford

first: Zintis

last: Inde

state: CA

address: 327 Campus Drive

institute: Stanford University

summary: Anti-cancer drugs and other lethal agents can induce heterogeneous cell death responses in a population of cancer cells, a phenomenon referred to as fractional killing (FK). FK is often studied on a cell-by-cell basis in response to one or a limited number of stimuli. Here, we develop and validate methods to quantify FK in a high-throughput manner using population-level time-lapse measurements and mathematical modelling. Using this approach, we find that FK is highly variable over time and that the kinetics of this process can vary substantially by drug class and cell line. Focusing on FK induced by clinical candidate inhibitors of mitogen activated protein kinase kinase (MEK) 1/2, we find that MCL1 levels are be an important determinant of FK in some but not all cell lines and that generalizable molecular models of FK are rare. These studies lay the foundation for quantitative high-throughput analyses of FK.

overall_design: mRNA sequencing from two non-small cell lung cancer cell lines. Treated with vehicle control and either a cytostatic or cytotoxic dose of pimasertib, a MEK inhibitor, in duplicate

first: Giovanni

middle: C

last: Forcina

first: Kyle

last: Denton

first: Scott

last: Dixon


title: miRNome changes in the mouse kidney, LPS-administered vs. control

status: Public on Nov 06 2019

city: Budapest

first: Pál

last: Tod

state: Budapest

address: Szigony utca 43

country: Hungary

institute: Institute of Experimental Medicine

summary: Comparing control and LPS-administered with either 40 mg/kg LPS for early time points (ETP) or 10 mg/kg for late time points (LTP). In ETP, 7-7 animals were sacrificed at 1.5 and at 6 hours after LPS administration. In LTP, 7-7 animals were sacrificed at 24 and 48 hours after the endotoxin injection. In both ETP and LTP 7 mice were received equal volume of saline to use as negative control. Four animals were selected for miRNA microArray analysis based on their proinflammatory (TNF-α and IL-6) mRNA expression levels.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Two-condition design: saline and LPS administration with 2-2 endpoints, n=4 animals/dose and time point and n= 4 control

first: Gábor

last: Szénási

first: Tamás

last: Kaucsár

first: Beáta

last: Róka

first: Péter

last: Hamar


title: RNAseq of intracellular Toxoplasma gondii treated with Tartrolon E

status: Public on Nov 12 2019

city: Pullman

first: Roberta

last: O'Connor

state: WA

address: 100 Dairy Road

institute: Washington State University College of Vet Med

summary: Tartrolon E is a pan anti-apicomplexan compound derived from a symbiotic bacteria of shipworms.  The mechanism of action of the compound is unknown, and attempts to select parasite mutants resistant to the compound has been unsuccessful.  In this study, RNAseq was performed on human foreskin fibroblast cells (HFF) infected with Toxoplasma gondii RH strain and treated with Tartrolon E to identify genes targeted by the compound.

overall_design: HFF and RH strain T. gondii were cultured under standard conditions.  HFFs were infected with T. gondii for 24 hours and then treated with vehicle (DMSO), 5 or 20 ng/ml of Tartrolon E.  Total RNA was collected 4, 8 and 12 hours post treatment and RNA seq analysis was performed.   Comparisons were made between samples treated with different concentrations of TrtE or DMSO and samples treated for different lengths of time.Genes were considered deferentially expressed when both the p-value and q-value, estimated based using a negative binomial model, were below a significance value of 0.05.

first: Felix

last: Nepveux V


title: PROX1 mediates chemoresistance-associated recurrence via maintenance of quiescent colon cancer stem cells

status: Public on Nov 30 2019

city: Tokyo

first: Daichi

last: Narushima

address: 5-1-1 Tsukiji, Chuo-ku

department: Department of Bioinformatics

country: Japan

institute: National Cancer Center Research Institute

summary: Cancer stem cells (CSCs) are profoundly associated with refractory nature of cancer. A quiescent population of CSCs is responsible for tumorigenesis and chemoresistance in leukemia, whereas neither the presence nor clinical importance of the quiescent CSCs is clearly established in solid tumors. In colon cancer, LGR5 is regarded as a functional marker of CSCs, but heterogeneity among LGR5+ cells was not clearly defined. Here we stratified LGR5+ cells by single-cell gene expression analyses and revealed that a tumorigenic population of mouse LGR5+ cells resides in a quiescent state. We identified 23 signature genes that were uniquely expressed in the quiescent CSCs of mouse tumors, and found that 7 of them were also specifically expressed in a quiescent population of LGR5+ cells in human colon xenograft tumors. Among them, PROX1 was expressed in invasive fronts of colon tumors. PROX1 was induced by TCF1 (TCF7), and the TCF1-mediated PROX1 expression was responsible for not only the maintenance of quiescence but also chemoresistance of colon cancer organoids. Knockout of PROX1 in patient-derived xenograft tumors resulted in inhibition of tumor recurrence after chemotherapeutic treatment. Our data underscore the therapeutic importance of a quiescent CSC population in colon cancer.

overall_design: Three individual tumors were obtained from a DSS-administrated ApcMin/+ mouse and used in this study.  The tumors were mixed after the enzymatic digestion and DAPI-Cd31-Cd45-Epcam+Cd24+ cells were single-cell sorted into a 96-well plate containing lysis buffer [0.5 % (v/v) NonidetP-40 and 2 U/µl SUPERase-In (Ambion)] and stored frozen at -80 °C. The frozen cells were lysed and subjected for cDNA synthesis using Bead-seq method described in previous reports (DOI:10.1016/j.ab.2014.10.01, DOI:10.1038/s41598-017-04616-6). The processes from the production of cDNA libraries to their amplification and first purification were carried out automatically using a Caliper Zephyr compact liquid handler (Perkin Elmer, CA, USA) coupled with a homemade operation program. The cDNA library produced from each cell was used to examine Lgr5 expression by semi-quantitative PCR reaction for (32 cycles) using KOD polymerase (Takara), followed by Ethidium Bromide (Sigma) staining. Lgr5-positive cDNAs were then converted in to the pooled libraries for Illumina sequencing using the Nextera XT DNA preparation kit (Illumina).

first: Daisuke

last: Shiokawa

first: Hiroaki

last: Sakai

first: Hirokazu

last: Ohata

first: Toshiaki

last: Miyazaki

first: Yusuke

last: Kanda

first: Shigeki

last: Sekine

first: Masahito

last: Hosokawa

first: Mamoru

last: Kato

first: Yutaka

last: Suzuki

first: Haruko

last: Takeyama

first: Hideki

last: Kambara

first: Hitoshi

last: Nakagama

first: Koji

last: Okamoto


title: Expression data from rat vocal fold at different periods after vocal fold injury

status: Public on Oct 26 2019

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Vocal cord healing is a dynamic process, and many genes and proteins are involved, which play varying roles at different regeneration stages after injury. Previous studies have shown that inflammatory responses occur at the early stage of vocal cord injury, where the fibroblasts proliferate exuberantly with intensive secretion and deposition of ECM. These activities reach the peak at 3-7 days and their intensity begins to decline 15 days later. A study based on the dermal system has shown that ECM remodeling during the repair of injury can last for several months. However, few studies have been conducted as to the dynamic changes of gene expressions and signaling pathway during the healing process of vocal cord injury. Plotting these changes will facilitate the understanding about the physiological changes during healing and the identification of key time points and target genes in fibrosis formation.

overall_design: 20 animals were randomly divided into 4 experimental groups based on time of sacrifice: uninjured control, and 1, 4 and 8 weeks after injury. Following sacrifice, the larynx was harvested, and the bilateral vocal folds were dissected under magnification.

first: Haizhou

last: Wang

first: Wen

last: Xu


title: Effect of CTCF and Rad21 knockdown on SLK cells and KSHV gene expression

status: Public on Oct 24 2019

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

summary: CTCF and the cohesin complex modify chromatin by binding to DNA and interacting with each other and with other cellular proteins.  Both proteins regulate transcription by a variety of local effects on transcription and by long range topological effects.  CTCF and cohesin also bind to herpesvirus genomes at specific sites and regulate viral transcription during latent and lytic cycles of replication.  Kaposi’s sarcoma-associated herpesvirus (KSHV) transcription is regulated by CTCF and cohesin, with both proteins previously reported to act as restrictive factors for lytic cycle transcription and virion production.  In this study, we examined the interdependence of CTCF and cohesin binding to the KSHV genome.  ChIP-seq analyses revealed that cohesin binding to the KSHV genome is highly CTCF dependent whereas CTCF binding does not require cohesin.  Further, depletion of CTCF leads to almost complete dissociation of cohesin from sites at which they colocalize.  Thus, previous studies which examined the effects of CTCF depletion actually represent concomitant depletion of both CTCF and cohesin components.  Analysis of the effects of single and combined depletion indicate that CTCF primarily activates KSHV lytic transcription whereas cohesin has primarily inhibitory effects.  Further, CTCF or cohesin depletion was found to have regulatory effects on cellular gene expression relevant for control of viral infection, with both proteins potentially facilitating expression of multiple genes important in the innate immune response to viruses.  Thus, CTCF and cohesin have both positive and negative effects on KSHV lytic replication as well as effects on the host cell that enhance antiviral defenses.

overall_design: Three different treatments were applied to cells: control KD, CTCF KD and Rad21 KD.  Each treatment was done in triplicate.

first: Sankar

last: Swaminathan


title: Effect of CTCF and Rad21 knockdown on cell and KSHV gene expression

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Three different treatments were applied to cells: control KD, CTCF KD and Rad21 KD.  Each treatment has three types of analyses: Input DNA, CTCF Ab IP or Rad21 IP.


title: Chronic glucocorticoid exposure in early development leads to neuroendocrine, metabolic, and immune dysregulation in adult zebrafish

status: Public on Oct 28 2019

city: Orono

first: Benjamin

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

summary: Chronic early life stress can affect development of the neuroendocrine stress system, leading to its persistent dysregulation and consequently increased disease risk in adulthood. One contributing factor is thought to be epigenetic programming in response to chronic glucocorticoid exposure during early development. We have previously shown that zebrafish embryos treated chronically with cortisol develop into adults with constitutively elevated whole body cortisol and aberrant immune gene expression. The objective of the experiments reported here was to further characterize the phenotype of those adults. We find that adult zebrafish derived from cortisol-treated embryos have aberrant cortisol tissue distribution and dynamics, which correlate with differential transcriptional activity of key glucocorticoid-responsive regulatory genes klf9 and fkbp5 in blood and brain.

overall_design: Genome-wide chromatin accessiblity was assayed from blood samples taken from 6 individual adult zebrafish. For these fish, DMSO (n = 3) or 1 micromolar cortisol (n = 3) was added to larval medium for first 5 days of development and then maintained to adulthood under normal conditions.

first: Ellen

last: Hartig

first: Ian

last: Gans

first: Shusen

last: Zhu

first: Kyle

last: Shank

first: Kathryn

middle: E

last: Patenaude

first: Melody

middle: N

last: Neely

first: James

middle: A

last: Coffman


title: Next Generation Sequencing Facilitates Quantitative Analysis of human umbilical vein endothelial cell(HUVEC) with and without treatment of CHIR99021+FGF1

status: Public on Oct 17 2019

city: Birmingham

first: Chengming

last: Fan

state: ALABAMA

address: 1670 University Blvd

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

summary: The mortality of patients suffering from acute myocardial infarction (AMI) is linearly related to the infarct size. As regeneration of cardiomyocytes from cardiac progenitor cells is minimal in the mammalian adult heart, we have explored a new therapeutic approach which leverages the capacity of nanomaterials to release chemicals over time to promote myocardial protection and infarct size reduction. Initial screening identified two chemicals, FGF1 and CHIR99021 (a Wnt1 agonist/GSK-3  antagonist) which synergistically enhance cardiomyocyte cell cycle in vitro. Poly-lactic-co-glycolic acid (PLGA) nanoparticles (NP) formulated with CHIR99021 and FGF1 (CHIR+FGF1-NPs) provided an effective slow release system for up to 4 weeks. Intramyocardial injection of CHIR+FGF1-NPs enabled myocardial protection via reducing infarct size by 20-30% in mouse or pig models of postinfarction LV remodeling.  This LV structural improvement was accompanied by a significant preservation of cardiac contractile function. Further investigation revealed that CHIR+FGF1-NPs resulted in a significant reduction of cardiomyocyte apoptosis and increase of angiogenesis. Thus, using a combination of chemicals and a NP-based prolonged release system that work synergistically, this study demonstrates a novel therapy for LV infarct size reduction in hearts with acute myocardial infarction.

overall_design:
Examination of 2 different treatment in HUVECs.
Total cellular RNA was isolated from CHIR+FGF1 (5 µM, 100 ng/ml, respectively)-treated and control HUVECs and subjected to next generation RNA sequencing (RNA-Seq). The mRNA profiles indicated that 815 genes out of 18845 genes (adjusted p < 0.05) showed significant changes in their expression levels. The relative mRNA expression profile of various representative genes related to angiogenesis, cell proliferation, cell senescence and death were examined.

first: Jianyi

last: Zhang


title: Impact of transcriptional mutagenesis on p53 transactivation

status: Public on Oct 16 2019

city: Stockholm

first: Kristian

last: Dreij

address: Nobels väg 13

department: Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary: The transcriptional error rate can be significantly increased by the presence of DNA lesions that instruct mis-insertion during transcription; a process referred to as transcriptional mutagenesis (TM). Herein, we determined the effect of O6-methylguanine (O6-meG) on transcription and subsequent transactivation activity of p53 in human lung H1299 cells.   Levels of TM and effects on transactivation were determined by RNA-seq. Results showed that 47% of all p53 transcripts contained an uridine misincorporation opposite the lesion at 6 h post transfection, which was decreased to 18% at 24 h. TM at these levels reduced DNA binding activity of p53 to 21% and 80% compared to wild type p53, respectively. Gene expression data were analyzed to identify differentially expressed genes due to TM compared to the response of wild type p53. We show a temporal repression of transactivation of >100 high confidence p53 target genes including regulators of the cell cycle, DNA damage response and apoptosis. In addition, TM repressed the transcriptional downregulation by p53 of several negative regulators of proliferation and differentiation  . Our work demonstrates that TM, even when restricting its effect to an individual transcription factor, has the potential to alter gene expression programs and diversify cellular phenotypes.

overall_design: Assessment of gene expression profiles in human lung H1299 cells following transfection with wild type, mutant (R248W) or DNA lesion-modified (at codon 248) p53 for 6 and 24 h. Biological triplicates were included for each condition including a control with GFP only expressing vector. A total of 30 samples.


title: R-loops promote antisense transcription across the mammalian genome

status: Public on Oct 22 2019

city: Oxford

first: Nicholas

last: Proudfoot

address: South Parks Road

institute: Sir William Dunn School of Pathology,  University of Oxford

summary: We report the correlation we found between R-loops and antisense trasncription initiation. Our in vitro data suggests that RNA pol II can initiate transcription off the displaced single stranded DNA from within the R-loop.  Therefore we generated Chromatin associated RNA-seq with and without over-expressing RNaseH1 and RDIP-seq (the directional RNA-seq of the RNA moeity from within the S9.6 pull down R-loop) as well as RR-ChIP-seq (the directional RNA-seq of the RNA moeity from within the catalytically dead RNaseH1-GFP GFP pull down R-loop) and confirm the correlation in vivo. We also aligned our findings with ChrCAP-seq (which is is a library enriched for RNA polymerase II capped RNA using chromatin associated RNA as the initial source) and found that capped antisense RNA were sensitive to RNase H1 overexpression.

overall_design: Examination of chromatin associated RNA of HeLa cells and capped RNA with and without over-expressing RNAseH1. Directional R-loop occupancy was conducted by 1) sequencing the RNA moeity of the R-loop fragments which were immunoprecipitated by mouse monoclonal S9.6 antibody and by 2) sequencing the RNA moeity of the RNA:DNA hybrids caught in a catalytically dead RNaseH1-GFP.

first: Sue

last: Tan-Wong

first: Somdutta

last: Dhir

first: Nick


title: Transcriptomics analysis of cortical astrocytes subjected to Rbpj-K deletion and stab-wound injury

status: Public on Nov 02 2019

first: Margherita

last: Zamboni

address: Solnavägen 9

department: Cell and Molecular Biology

summary: We performed single cell RNA-sequencing to investigate the molecular properties of Rbpj-K deleted astrocytes from the mouse somatosensory cortex. In the presence of a stab-wound injury, these cells undertake a neurogenic program, which can be analysed in the present dataset. The experiment encompassed cells from Rbpj-K-/- as well as wild type animals, and collected from injured or healthy cortices 3 wpi.

overall_design: Examination of transcriptional changes occurring in cortical astrocytes isolated from the mouse cortex subjected to Rbpj-K deletion and stab-wound injury. Four samples were analyzed: WT x healthy; WT x injured; KO x healthy; KO x injured.

first: Jonas

last: Frisén


title: Cell type-specific RNA-seq to profile transcriptional changes in sorted BLA projection neurons during conditioned taste aversion learning

status: Public on Oct 08 2019

city: WEST NEWTON

first: David

last: Levitan

address: 56 south gate park

department: Biology

institute: Brandeis University

summary: In order to identify specific transcripts that might be necessary for CTA learning within the BLA, we used cell type-specific RNA-seq to profile transcriptional changes in sorted BLA projection neurons 4 hours following training.

overall_design: RNA sequencing was performed on neurons harvested from mice undergoing CTA and from taste-only controls (n=4/group) 4 hours following training.

first: Sacha

middle: B

last: Nelson


title: Abnormalities of cellular polarity underlie the primary substrate in a genetic form of atrial fibrillation

status: Public on Dec 13 2019

city: Quechee

first: Michael

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

summary: Atrial fibrillation (AF) is the most common clinical arrhythmia and is associated with heart failure and stroke. The primary substrate for AF is poorly understood due to limited access to primary human tissue and the lack of mechanistically faithful in vitro or in vivo models. We used an MYH6:mCherry knock-in reporter line to generate and purify human pluripotent stem cell-derived cardiomyocytes displaying electrophysiological and molecular characteristics of atrial cells (hPSC-atrial cells). We modeled human MYL4 mutants, one of the few definitive genetic causes of AF. Single cell transcriptomics on hPSC-atrial cells (WT and MYL4 mutant) was performed to study changes in gene expression among the cell types that exist in atrial lineage.

overall_design: D60 hES-atrial cells derived from MYL4+/+ , MYL4+/- and MYL4-/- (two biological replicates of each) lines were dissociated with Accutase. Following centrifugation, cells were resuspended in sorting medium (RPMI with 0.5%BSA) and cells were sorted with a FACS machine into mCherry+ and mCherry- and combined in 2/3(mCherry+) and 1/3(mCherry-) ratio. Next, individual cells were captured and barcoded using the inDrop platform.

first: Zaniar

last: Ghazizadeh

first: Calum

last: MacRae


title: A class I histone deacetylase is implicated in the encystation of Entamoeba invadens

status: Public on Oct 05 2019

city: MEXICO

first: ROSAURA

last: HERNANDEZ RIVAS

state: MEXICO

address: AV. IPN 2508

department: BIOMEDICINA MOLECULAR

country: Mexico

institute: CINVESTAV

summary: mRNA profiles of cysts from Entamoeba invadens treatment with ethanol and treament with 200 nM of Trichostatin A during 24h, using Illumina NextSeq 500

overall_design: 24 h cysts from Entamoeba invadens treated with ethanol or 200 nM of Trichostatin A

first: Daniela

last: Lozano-Amado

first: Rosaura

last: Hernández-Rivas


title: Characterization of novel STY1099 protein involved in the peroxide stress response of Salmonella Enteritidis

status: Public on Sep 25 2019

city: Saint Paul

first: Sinisa

last: Vidovic

state: MN

address: 1971 Commonwealth Avenue

institute: University of Minnesota

summary: We report our results of RNA-seq analysis on the wild type Salmonella Enteritidis and its yccT (i.e., yccT encodes STY1099 protein) mutant with and without H2O2 treatment

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: RNA was isolated from cultures of the wild type Salmonella Enteritidis and S. Enteritidis yccT mutant exposed to H2O2 and without exposure to H2O2. Libraries were created using standard Illumina reagents and analyzed using a HiSeq 2500 Illumina.

first: Juan

last: Abrahante


title: A reference map of cardiac transcription factor chromatin occupancy identifies dynamic and conserved transcriptional enhancers

status: Public on Sep 13 2019

first: Brynn

middle: Nicole-Yoshiko

last: Akerberg

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

summary: Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering the transcriptional programs that orchestrate organ development and homeostasis. Here we used biotinylated knockin alleles of seven key TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) that regulate heart development and homeostasis to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult heart. Our results show that these TFs have dynamic chromatin occupancy between developmental stages. We observed that multiple TFs often co-occupy the same chromatin region, exhibiting collaborative binding that overall was most consistent with indirect cooperativity. Regions with multiple TF binding were more likely to exhibit features of functional regulatory elements, including evolutionary conservation, chromatin accessibility, and activity in transcriptional enhancer assays. Although histone H3 acetylation on lysine 27 (H3K27ac) has been used to identify active enhancers, many regions occupied by multiple TFs lacked H3K27ac, and TF-bound regions with or without H3K27ac co-occupancy had similar region conservation and enhancer activity. Specific studies of TEAD1 demonstrated that it is a core component of the cardiac transcriptional network: physically interacted with NKX2-5 and MEF2C and co-occupied regulatory loci with other cardiac TFs to regulate cardiomyocyte-specific gene functions. Our study shows that co-occupancy by multiple TFs is a hallmark of a subset of functional transcriptional regulatory elements and provides a rich resource for deciphering the cardiac transcriptional regulatory network.

overall_design: Examination of cardiac TF binding in fetal (E12.5) and adult mouse heart ventricles using BioChIP-Seq. Examination of cardiac TF binding in fetal (E12.5) and adult mouse heart ventricles.

first: Fei

last: Gu

first: William

middle: T

last: Pu


title: Blood extracellular vesicle long RNA sequencing of human blood from pancreatic ductal adenocarcinoma (PDAC), chronic pancreatitis (CP) and healthy individuals

status: Public on Oct 01 2019

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Blood samples were collected from all participants in 10-mL EDTA-coated Vacutainer tubes. Plasma was separated by centrifugation at 3,000 rpm for 10 min at room temperature (25°C) within 2 h after blood collection and then centrifuged at 13,000 rpm for 10 min at 4°C to remove debris. Isolated plasma samples were stored at -80°C until use. EV RNA were isolated by affinity-based binding to spin columns using an exoRNeasy Serum/Plasma kit (Qiagen, Hilden, Germany). RNA libraries were prepared for sequencing using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian. RNA-seq was performed  by the Illumina sequencing platform on a 150-bp paired-end run.

overall_design: Blood extracellular vesicle long RNA profiles of human plasma by deep sequencing using Illumina Hiseq.

first: Peng

last: Wang


title: Transcriptional responses to IFN-alpha in human dermal fibroblasts

status: Public on Sep 30 2019

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

institute: Newcastle University

summary: We sought to examine the transcription response to IFNa in fibroblasts from three healthy controls (C1-C3) and a patient with a mutation in STAT2 (P1)

overall_design: Cells in 6 well plates were mock stimulated, or stimulated with IFNa (Intron A, 1000IU/mL) for 12h, then washed and rested for 36h, or stimulated for 6h prior to lysis and RNA isolation. Experiments were conducted in biological triplicate.

first: Christopher

last: Duncan

first: Sophie

last: Hambleton


title: Loss of ADAMTS19 causes progressive non-syndromic heart valve disease

status: Public on Sep 09 2019

city: Montreal

first: Florian

last: Wuennemann

address: 5000 Rue Bélanger

institute: Montreal Heart Institute

summary: Single-cell transcriptome sequencing of E14.5 mouse hearts from Adamts19 wild-type and Adamts19 knockout animals using Drop-seq.

overall_design: Drop-seq was performed on single-cell suspensions from whole E14.5 mouse hearts from Adamts19 wild-type (n=7) and Adamts19 homozygous knockout mice (n=8) on a C57B6/N background.

last: Wünnemann

first: Gregor

last: Andelfinger


title: Transcriptional signature of lymphoblastoid cell lines of BRCA1, BRCA2 and non-BRCA1/2 high risk breast cancer families

city: quebec

first: Francine

last: Durocher

state: quebec

address: 2705, Laurier Blvd

department: Molecular Medicine

institute: CHU de Quebec Research Centre

summary:
Approximately 25% of hereditary breast cancer cases associated with a strong familial history can be explained by mutations in BRCA1 or BRCA2 and other lower penetrance genes. The remaining high-risk families could be classified as BRCAX (non-BRCA1/2) families, in which no penetrant mutation has been found until now.
Gene expression involving alternative splicing represents a well-known mechanism regulating the expression of multiple transcripts encoded by individual genes, which could be involved in cancer development. Thus using RNA-seq methodology, the analysis of transcriptome in immortalized lymphoblastoid cell lines of high-risk breast cancer individuals could reveal transcripts implicated in breast cancer susceptibility and development.
RNA was extracted from immortalized lymphoblastoid cell lines of 117 women (affected and unaffected) coming from BRCA1, BRCA2 and BRCAX families. Anova analysis revealed a total of 95 transcripts corresponding to 85 different genes differentially expressed (Bonferroni corrected p-value <0.01) between those groups. Hierarchical clustering allowed distinctive subgrouping of BRCA1/2 subgroups from BRCAX individuals, without regard for the cancer status. We found enrichment for pathways in signaling cascades including mTOR and EIF2-related pathways. No transcripts were differentially expressed between BRCA1 and BRCA2 individuals, however out of 95 transcripts, 67 could discriminate BRCAX from combination of BRCA1 and BRCA2 individuals. On the other hand, 28 transcripts could discriminate affected from unaffected BRCAX individuals. These BRCAX-associated transcripts demonstrated enrichment in Telomere Extension by Telomerase and Double-Strand Break Repair by Non-Homologous End Joining mechanisms.
To our knowledge, this represents the first study identifying transcripts differentially expressed in immortalized lymphoblastoid cell lines coming from the major classes of mutation-related breast cancer subgroups, namely BRCA1, BRCA2 and BRCAX. Moreover, some transcripts could discriminate affected from unaffected BRCAX individuals, which could represent potential therapeutic targets for breast cancer treatment.

overall_design: Immortalised lymphocytes cell lines (LCL) were made from 117 women. Those women were classified as BRCA1, BRCA2, BRCAX unaffected and BRCAX affected individuals. Each LCLs was sequenced once except for one sample for each group. The control group is represented by BRCAX unaffected individuals.

first: Marie-Christine

last: Pouliot

first: Yvan

last: Labrie

first: Geneviève

last: Ouellette

first: Charles

last: Joly-Beauparlant


title: Expression data from uninfected and pneumococcus-infected wt and PGLYPR4-KO primary alveolar epithelial cells

status: Public on Aug 27 2019

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary:
Streptococcus pneumoniae is the most frequent cause of community-acquired pneumonia. Endogenous antimicrobial proteins such as PGLYRP4 might participate to the course of the disease. PGLYRP4 is expressed in different cell types but is downregulated in alveolar epithelial after stimulation with Streptococcus pneumoniae. Interestingly, mice lacking PGLYRP4 displayed an enhanced bacterial clearance in the lungs and less mice develop a bacteremia. This may depend on a higher proinflammatory cytokine response in PGLYRP4KO compared to wt cells, which contribute to the recruitment of more immune cells to the side of infection and an enhanced bacterial clearance by additionally stronger activation of the phagocytes.
We implemented microarray analysis of infected primary epithelial cells to identify possible regulated genes by PGLYPR4-deficency, which contribute to the seen phenotype.

overall_design: We isolated primary alveolar epithelial cells from untreated 10-16 week old BALB/c wt and PGLYRP4-deficient mice. We used three mice of each strain and performed three indipendant experiments. The extracted RNA was pooled and analyzed

first: Alexander

last: Dabrowski

first: Anshu

last: Shrivastav

first: Claudia

last: Conrad

first: Kassandra

last: Komma

first: Markus

last: Weigel

first: Stephanie

last: Plog

first: Kristina

last: Dietert

first: Achim

last: Gruber

first: Wilhelm

last: Bertrams

first: Bernd

last: Schmeck

first: Katrin

last: Reppe

first: Philippe

last: N'Guessan

first: Sahar

last: Aly

first: Norbert

last: Suttorp

first: Torsten

last: Hain

first: Janine

last: Zahlten


title: Transcriptomic profiling responses in liver and brain tissues of European eels Anguilla anguilla after a gold nanoparticle trophic exposure

status: Public on Sep 01 2019

city: Arcachon

first: Fanny

last: Perrier

address: place Peyneau

country: France

institute: Université de Bordeaux

summary: Nanometric revolution is underway, promising technical innovations in a wide range of applications, leading to a potential boost in environmental discharges. Nanoparticle propensity to be transferred throughout trophic chains and to generate toxicity was mainly assessed in primary consumers while a lack of knowledge for higher trophic levels persists. This study focused on a predatory fish, the European eel Anguilla anguilla exposed to gold nanoparticles (AuNP, 10 nm, PEG-coated) for 21 days at three concentration levels in food: 0 (NP0), 1 (NP1) and 10 (NP10) mg Au.kg-1 . Transfer was assessed by gold quantification in eel tissues and transcriptomic responses in the liver and brain were revealed by a high-throughput RNA-sequencing approach. Eels fed at NP10 presented an erratic feeding behaviour while gold quantification only indicated transfer to intestine and kidney of NP1 exposed eels. RNA-Sequencing was performed in NP0 and NP1 eels. A total of 258 genes and 156 genes were significantly differentially transcribed in response to AuNP trophic exposure in the liver and brain, respectively. Enrichment analysis highlighted modifications in the immune system-related processes in the liver. In addition, results pointed out a shared response of both organs regarding 13 genes, most of them being involved in immune functions. This finding may shed light into the mode of action and toxicity of AuNP in fish.

overall_design: 24 samples - 6 European eels were exposed to gold nanoparticles for 21 days (NP1) and 6 were kept in control conditions (NP0). Transcriptomic changes were assessed in brain and liver.

first: Anthony

last: Bertucci

first: Fabien

last: Pierron

first: Agnès

last: Feurtet-Mazel

first: Olivier

last: Simon

first: Christophe

last: Klopp

first: Frédéric

last: Candaudap

first: Oleg

last: Pokrovsky

first: Bruno

last: Etcheverria

first: Stéphane

last: Mornet

first: Magalie

last: Baudrimont


title: The role of TFEB in retinoid induced differentiation of NB4 APL leukemic cells (shTFEB)

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

summary: We report the use of RNAseq to determine the role of the TFEB transcription factor in all-trans retinoic acid induced differentiation of NB4 acute promyelocytic leukemia (APL) cells. We used lentiviral mediated shRNA approaches to functionally deplete TFEB in NB4 cells and compared the transcriptomes of wild type, scramble control shRNA and  shTFEB knockdown cells treated with ethanol (control) versus all-trans retinoic acid for 72 hours.

overall_design: Standard lentiviral approaches were used to functionally deplete TFEB mRNA in the NB4 acute promyelocytic leukemia cell line. An scrambled sequence shRNA was used as a negative control. The parental wild type NB4 cell line was used as control. Biological replicates of wildtype NB4, scrambled shRNA control and TFEB knockdown NB4 cells were treated with either ethanol (control) or all-trans retinoic acid (1microM) for 72 hours and differentiation monitored. RNA was isolated and sequenced.

first: N

last: Orfali

first: L

last: Gudas


title: Retinoid induced differentiation of NB4 APL leukemic cells

summary: We report the use of RNAseq to determine genomewide transcriptional changes induced by all-trans retinoic acid differentiation of NB4 acute promyelocytic leukemia (APL) cells.

overall_design: NB4 cells were treated with either ethanol (control) or all-trans retinoic acid (1microM) for 72 hours and differentiation monitored. RNA was isolated and sequenced.


title: DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories

status: Public on Aug 12 2019

city: Minneapolis

first: Frank

middle: Wolfgang

last: Albert

address: 6-160 Jackson Hall, 321 Church St SE

department: Department of Genetics, Cell Biology, & Development

summary: DNA variants that alter gene expression contribute to variation in many phenotypic traits. In particular, trans-acting variants, which are often located on different chromosomes from the genes they affect, are an important source of heritable gene expression variation. However, our knowledge about the identity and mechanism of causal trans-acting variants remains limited. Here, we developed a fine-mapping strategy called CRISPR-Swap and dissected three expression quantitative trait locus (eQTL) hotspots known to alter the expression of multiple genes in trans in the yeast Saccharomyces cerevisiae. Causal variants were identified by engineering recombinant alleles and quantifying the effects of these alleles on the expression of a green fluorescent protein-tagged gene affected by the given locus in trans. We validated the effect of each variant on the expression of multiple genes by RNA-sequencing. The three variants were strikingly different in their molecular mechanism, the type of genes they reside in, and their distribution in natural populations. While a missense leucine-to-serine variant at position 63 in the transcription factor Oaf1 (L63S) was almost exclusively present in the reference laboratory strain, the two other variants were frequent among S. cerevisiae isolates. A causal missense variant in the glucose receptor Rgt2 (V539I) occurred at a poorly conserved amino acid residue and its effect was strongly dependent on the concentration of glucose in the culture medium. A noncoding variant in the conserved fatty acid regulated (FAR) element of the OLE1 promoter influenced the expression of the fatty acid desaturase Ole1 in cis and, by modulating the level of this essential enzyme, other genes in trans. The OAF1 and OLE1 variants showed a non-additive genetic interaction, and affected cellular lipid metabolism. These results revealed remarkable diversity in the molecular basis of trans-regulatory variation, highlighting the challenges in predicting which natural genetic variants affect gene expression.

overall_design: Examination of the effects of three single nucleotide variants on gene expression in trans

first: Sheila

last: Lutz


title: Genome-wide transcriptional analysis of synovial tissue gene expression associated with the response to anti-TNF therapy in Rheumatoid Arthritis

status: Public on Jul 26 2019

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

summary:
Synovial biopsies of Rheumatoid Arthritis patients with active disease were obtained prior to anti-TNF therapy. Clinical response to anti-TNF treatment was measured 20 weeks later using the EULAR response criteria.
Gene expression profiles of patients responding to anti-TNF therapy were compared to non-responders and several genes were found to be differentially expressed between both groups of Rheumatoid Arthritis patients.

overall_design: Synovial samples were obtained by guided arthroscopy using a 2.7 mm arthroscope from 11 Rheumatoid Arthritis patients starting anti-TNF therapy. Samples were immediately preserved in RNALater at -80ºC until extraction. After total RNA extraction, gene expression profiles for 21,000 genes were obtained using Illumina Sentrix whole genome Beadchips WG6 version 2.

first: Sara

last: Marsal

first: Juan

last: Cañete


title: Targeted DNA methylation of the ALS/FTD gene C9orf72 via endogenous DNA damage repair pathways (II)

status: Public on Oct 11 2019

city: Philadelphia

first: Edward

last: Lee

state: PA

address: 613A Stellar Chance Laboratories; 422 Curie Blvd

institute: University of Pennsylvania

type: Methylation profiling by genome tiling array

summary: DNA methyltransferases (DNMTs) are thought to be involved in the cellular response to DNA damage, thus linking DNA repair mechanisms with DNA methylation. This study presents a novel method of targeted DNA methylation that utilizes endogenous DNA double strand break repair pathways and applies it to the neurodegenerative disease gene C9orf72. A double strand break induced by CRISPR/cas9 in the promoter of C9orf72 is sufficient to induce DNA methylation, and methylation can be precisely targeted through the process of homology directed repair (HDR) via delivery of an in vitro methylated exogenous repair template. Long methylated double stranded DNA templates induce more methylation than shorter templates and with higher efficiency than a dCas9-DNMT3a fusion protein construct.  Genome-wide methylation analysis reveals no significant off-target methylation changes when inducing methylation via HDR, whereas the dCas9-DNMT3a fusion construct causes significant off-target methylation at over 67,000 sites. This method is applied to generate a patient derived iPSC model of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD) that exhibits stable DNA methylation patterns similar to those seen in patients. Using this model, it’s shown for the first time that DNA methylation of the 5’ regulatory region directly reduces C9orf72 expression and increases histone H3K9 tri-methylation levels.

overall_design:
Measurement of off-target effects at C9orf72 using the HARDEN method
HEK293T cells were transfected with either No gRNA plasmid+Meth template or Cas9+gRNA+Meth template and puromycin selected for 2 days. Cells were collected on day 4 post transfection and bisulfite converted DNA was hybidized to Infinium MethylationEPIC

first: Christopher

last: Cali


title: Profile of new early pregnancy markers identified by transcriptomic analysis in peripheral blood immune cells in beef heifers

status: Public on Aug 22 2019

city: Fraiburgo

first: cecilia

middle: constantino

last: rocha

state: SC

address: ivan a de souza, 133

department: Animal Reproduction

country: Brazil

institute: Universidade de São Paulo

summary:
We aimed with this study through RNAseq, found diferentially expressend genes (DEGs) that can be used as a new pregnancy markers in peripheral blood mononuclear cells (PBMC) on day 18 post artificial insemination; and to assess the mRNA profile by RT-qPCR of new pregnancy markers in PBMC and peripheral blood polymorphonuclear cells (PMN) at early pregnancy
Methods: Nelore heifers (N=21) were artificially inseminated in a fixed time (D0). On Day 10, 14, 16, 18 and 20, blood was collected for isolation of PBMC and PMN, and P4 concentration assay and color Doppler ultrasonography was performed to evaluate the corpus luteum (CL) . Pregnancy diagnosis was done on Day 28 and heifers were classified in pregant (N=9) and non-pregant (N=12). Heifers (N=6/group) with different (P<0.05) plasma P4 concentration, CL area and blood perfusion on Day 18 were selected and RNAseq was done on PBMC samples. RNAseq analysis indicated 220 DEGs (200 up regulated in P). Twenty DEGs found on RNAseq of PBMC with the highest fold-changes or no overlapping between pregant  and non-pregant, were assessed by RT-qPCR from Day10 to 20 (N=6/group).
Conclusions: nine DEGs studied by RT-qPCR presented increased expression on PBMC for Pregnant group in at least one-time point from Day16 to 20; but only 4 of these DEGs retained the expression increased on PMN (IFI6, IFI44, RSAD2 and LGALS3BP). Thus, results indicate potential genes to be used as novel pregnancy predictors in immune cells in cattle at early gestation.

overall_design: The PBMC of six pregnant and six non-pregnant Nelore heifers on day 18 after artificial insemination were sequencing by RNAseq

first: Guilherme

last: Pugliesi

first: Sónia

last: da Silva Andrade


title: Targeted DNA methylation of the ALS/FTD gene C9orf72 via endogenous DNA damage repair pathways

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

overall_design: Refer to individual Series


title: Transcriptome Profile of C. Pseudotuberculosis in Response to Iron Limitation: Differential gene expression of Iron and DtxR regulated genes

status: Public on Jul 31 2019

city: belo horizonte

first: Vasco

middle: Ariston

last: Azevedo

state: MINAS GERAIS

address: 6627 AVENIDA ANTONIO CARLOS

department: Biological Sciences

institute: UFMG

summary: RNA-seq differential gene expression profiling of Corynebacterium pseudotuberculosis under iron limitation. We use two  C. pseudotuberculosis strains, a ciuA Cp13 mutant and its parental wild type T1 strain to quantify the relative gene expression of these strains in cultures with low iron availability. The ciuA Cp13 mutant is deficient for an operon which encodes a iron siderophore uptake system. The Cp13 mutant also showed reduced virulence in CLA infection models. Due to the importance of iron for many pathogenic bacteria, our primary goal was to identified the expression profile of iron regulated genes.

overall_design: Differential gene expression of two strains of C. pseudotuberculosis under iron limitation

first: Izabela

last: Ibraim

last: de Azevedo


title: DNA methylation loss coupled with mitotic cell division promotes immune evasion of tumours with high mutation load [RNA-seq]

status: Public on Aug 02 2019

city: Daejeon

first: Jeongyeon

last: Kim

address: 291 Daehakro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Mitotic cell division increases tumour mutation burden and copy number load, predictive markers of the clinical benefit of immunotherapy. Cell division correlates also with genomic demethylation involving methylation loss in late-replicating partial methylation domains. Here we find that immunomodulatory pathway genes are concentrated in these domains and transcriptionally repressed in demethylated tumours with CpG island promoter hypermethylation. Global methylation loss correlated with immune evasion signatures independently of mutation burden and aneuploidy. Methylome data of our cohort (n = 60) and a published cohort (n = 81) in lung cancer and a melanoma cohort (n = 40) consistently demonstrated that genomic methylation alterations counteract the contribution of high mutation burden and increase immunotherapeutic resistance. Higher predictive power was observed for methylation loss than mutation burden. We also found that genomic hypomethylation correlates with the immune escape signatures of aneuploid tumours. Hence, DNA methylation alterations implicate epigenetic modulation in precision immunotherapy.

overall_design: RNA-seq for a total of 27 advanced non-small cell lung carcinoma patients who were treated with anti-PD-1/PD-L1

first: HongSook


title: Molecular architecture of lineage specification and tissue organization in early mouse embryo

status: Public on Aug 08 2019

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

institute: Chinese Academy of Sciences

summary: During postimplantation development of the mouse embryo, descendants of the inner cell mass cells in the early epiblast transit from the naïve pluripotent state to the primed pluripotent state. Concurrent with the transition of the pluripotency states is the specification of cell lineages and formation of germ layers in the embryos that serves as the blueprint for embryogenesis. Fate mapping and lineage analysis studies have revealed that cells in different regions of the germ layers acquire location-specific cell fates during gastrulation. The regionalization of cell fates heralding the formation of the basic body plan is conserved in vertebrate embryos at a common phylotypic stage of development. Knowledge of the molecular regulation that underpin the lineage specification and tissue patterning is instrumental for understanding embryonic programming and stem cell-based translational study. However, a genome-wide molecular annotation of lineage segregation and tissue architecture of post-implantation embryo has yet to be undertaken. Here, we reported a spatially resolved transcriptome of cell populations at defined positions in the germ layers over the period of pre- to late gastrulation development. This spatio-temporal transcriptome provides high resolution digitized gene expression profiles and defines the molecular attribute of the genealogy of lineages and continuum of pluripotency states in time and space. The transcriptome further identifies the networks of molecular determinants that drive lineage specification and tissue patterning in the early postimplantation mouse embryo.

overall_design: By using spatial transcriptome of Geo-seq, we carried out transcriptome profiling on embryo sections at a high resolution of 20-40 cells per sample. We then constructed a comprehensive spatial transcriptome map from the pre-gastrulation to late-gastrulation embryos that are visualized in a 3D embryonic model based on the sequencing data. Please be aware that the positions for left (L) and right (R) are from mirrored images and should be considered as right and left in real embryo settings. Anterior (A) or Posterior (P) regions do not change.

first: Guizhong

last: Cui

first: Shengbao

last: Suo

first: Naihe

last: Jing

first: Jing-Dong

middle: J

last: Han


title: Derivation of authentic porcine embryonic stem cells using defined culture conditions

status: Public on Jul 08 2019

city: Seoul

first: Chang-Kyu

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

summary: Pig embryonic stem cells (ESCs) have been considered as an important candidate for preclinical researches on human therapy. However, the lack of understanding of pig pluripotent networks has hampered establishment of authentic pig ESCs. Here, we report that FGF2, ACTVIN, and WNT signaling is essential for maintaining pig pluripotency in vitro. Pig ESC lines derived by stimulating three signlaings formed colonies of flattened monolayer morphology. Newly derived ESCs were stably maintained over an extended period, and were capable of forming teratomas comprising three germ layers. Immunostaining showed that the stem cells expressed pluripotency markers including OCT4, SOX2, NANOG, SSEA1, and SSEA4. Transcriptome analysis showed that pig ESCs were developmentally similar to late epiblasts of preimplantation embryos and in terms of biological functions resembled human rather than mouse ESCs. However, the pig ESCs had distinct features such as coexpression of SSEA1 and SSEA4, two active X chromosomes, and a unique transcriptional pattern. In conclusion, we successfully derived authentic pig ESCs using novel cell culture conditions. Our findings will facilitate both the development of large animal models for human stem cell therapy and the generation of pluripotent stem cells from other domestic animals for agricultural use.

overall_design: Expression profiling of two pig parthenogenetic embryonic stem cell (ESC) lines, an IVF-derived ESC line and fetal fibroblasts, in triplicates.

first: Kwang-Hwan

last: Choi

first: Dong-Kyung

first: Sung

middle: W


title: Enhanced Myocardial Repair with CardioClusters

status: Public on Jul 05 2019

city: San Diego

first: Oscar

last: Echeagaray

address: 5500 Campanile Drive

institute: San Diego State University

summary: Single-cell RNA-seq (10X Genomics Chromium) to profile of mesenchymal stem cells (MSCs), cardiac and endothelial progenitor cells (CPC and EPC) and CardioCluster

overall_design: Transcriptional profiling of CPC, MSC, EPC and CardioCluster by scRNA-Seq approaches using 10X Genomics Chromium

first: Mark

last: Sussman

first: Megan

last: Monsanto


title: siRNA knockdown in neonatal rat cardiac myocytes

status: Public on Jul 04 2019

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

summary: Primary neonatal rat cardiac myocytes were isolated and subjected to siRNA mediated Yap knockdown

overall_design: Primary cardiac myocytes were isolated from two-day old rats via neonatal heart dissociation kit (Miltenyi Biotec) according to the manufacturer’s protocol followed by percoll gradient separation. Cells were transfected with siRNAs designed against a combination of Llgl1 and Llgl2, Yap, or universal negative control siRNAs. Transfected cells were collected 48 hours post transfection for RNAseq.

first: Caitlin

last: O'meara

first: Brian

last: Link


title: Ikaros prevents autoimmunity by promoting anergy induction and restraining Toll-like receptor signaling in B cells

status: Public on Jul 01 2019

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Establishment of a diverse B-cell receptor (BCR) repertoire by V(D)J recombination generates autoreactive B-cells that are eliminated by central tolerance in the bone marrow or down-regulate their BCR responsiveness to self-antigen during anergy induction in peripheral B-cells. The loss of anergy combined with hyperactivation of nucleic acid-sensing Toll-like receptors (TLRs) is thought to break B-cell tolerance leading to autoimmunity, although the transcriptional factors controlling these processes are still unknown. Here, we describe a critical role of Ikaros in promoting B-cell anergy and restraining TLR signaling by analyzing mice with specific deletion of Ikaros in mature B-cells, which resulted in systemic autoimmunity. While regulating many anergy-associated genes, Ikaros also activated the Zfp318 gene, implicated in down-tuning of the BCR responsiveness by shifting expression from IgM to IgD in anergic B-cells. TLR signaling was hyperactive in Ikaros-deficient B-cells, which failed to up-regulate feedback inhibitors of the MyD88-NF-?B signaling pathway. Systemic inflammation was lost upon expression of a non-self-reactive BCR or loss of MyD88 in Ikaros-deficient B-cells, which identified Ikaros as a guardian preventing autoimmunity by coordinately regulating anergy induction and TLR signaling.

overall_design: 28 RNA-Seq samples: 8 different genotypes with at least 2 replicates, 6 ATAC-Seq samples: 2 different genotypes, 2 cell types, 2 replicates, 4 ChIP-Seq samples

first: Tanja

last: Schwickert

first: Hiromi

last: Tagoh

first: Karina

last: Schindler

first: Maria

last: Fischer

first: Markus

last: Jaritz

first: Meinrad

last: Busslinger


title: Targeted DNA methylation of the ALS/FTD gene C9orf72 via endogenous DNA damage repair pathways (I)

first: Edward

last: Lee

overall_design:
Measurement of off-target effects at C9orf72 using dCas9-DNMT3a Fusion protein
HEK293T cells were transfected with either dCas9-DNMT3a-ANV or dCas9-DNMT3a plasmid and puromycin selected for 2 days. Cells were collected on day 4 post transfection and bisulfite converted DNA was hybidized to Infinium MethylationEPIC

first: Christopher

last: Cali


title: Targeting HuH7 cells with JumonjiC Lysine Demethylase Inhibitors and RAC1 inhibitors (RNA-Seq)

city: Derqui

first: Juan

last: Bayo

state: Buenos Aires

address: Av Peron 1500

department: IIMT

country: Argentina

institute: Universidad Austral-Conciet

summary: Characterization of gene expression changes in HuH7 HCC cells upon treatment with the Jumonji KDM inhibitor, JIB-04, GSK-J4 and SD-70 and the RAC1 inhibitor 1D-142.

overall_design: Comparison of gene expression changes between HuH7 cells treated with JIB-04, GSK-J4, SD-70 or 1D-142 vs. DMSO

first: Guillermo

last: Mazzolini


title: Profiling of 18 - 40 nt small RNAs and transcriptomes in the testis and epididymis of WT and Gpx5 KO mice.

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

country: USA

institute: Dana-Farber Cancer Institute

summary: Total RNAs were extracted from the Testis and Epididymal Caput, Corpus and Cauda tissues of 2-month and 13-month-old WT and Gpx5 KO mice (C57BL/6). The 18 - 40 nt fraction small RNAs and transcriptomes were subjected to library construction and deep sequencing, using Illumina GAIIx or Hiseq 2000.

overall_design: Deep sequencing profiling of 18 - 40 nt small RNAs and transcriptomes in the Testis and Epididymal Caput, Corpus and Cauda tissues of 2-month and 13-month-old WT and Gpx5 KO mice (C57BL/6) by Illumina GAIIx or Hiseq 2000.

first: Yonglian

last: Zhang

first: Joël

last: Drevet


title: RNA-Seq of Breast and Ovarian Cancer Cell Lines

status: Public on Jun 30 2019

city: Los Angeles

first: Michelle

middle: Renee

last: Jones

state: CA

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

summary: A panel of 20 commonly used cell lines were used for RNA-Seq in order to measure gene expression.

overall_design: RNA-Seq in 20 cell lines

middle: R

first: Simon

last: Gayther


title: Human umbilical cord mesenchymal cells from 4 donors cultured from P1 or P2 to replicative senescence

status: Public on Sep 03 2019

city: Medicine Hat

first: Lorena

last: Braid

state: Alberta

address: PO Box 21053, Crescent Heights PO

country: Canada

institute: Aurora BioSolutions Inc.

summary: To characterize the growth kinetics and transcriptome drift of human umbilical cord perivascular cells (HUCPVCs), cells were recovered from cryopreservation and cultured in chemically defined xeno- and serum-free media until replicative senescence. Growth kinetics and transcriptome profiles were analyzed at each passage.

overall_design: Aliquots of 1 million cells from 4 donor populations of HUCPVCs, provided by Tissue Regeneration Therapeutics (TRT), Inc. (Toronto, Canada), were thawed from cryopreservation and subject to independent, continuous in vitro culture in serum- and xeno-free media until they reached replicative senescence. Senescence was defined as sub-confluence 4 or more weeks after seeding in the current culture vessel. Cells were lifted at 70-80% confluence in culture vessels, denoting the end of each passage, and re-seeded. RNA was extracted from the remaining cell collection and analyzed by Affymetrix Human Genome U133A 2.0 Array. Information on batches of experimental culture and GeneChip processing time frames, encompassing variability of laboratory conditions and reagent lots, is included.

first: Danielle

last: Wiese

first: Cindy

middle: C

last: Ruttan

first: Catherine

last: Wood

first: Barry

last: Ford


title: Effect of the twelve isoforms of Hepatocyte nuclear factor 4 alpha on HCT116 cell line transcriptome

status: Public on Jun 28 2019

city: Sherbrooke

first: Francois

last: Boudreau

state: Quebec

address: 3201 rue Jean-Mignault

department: Anatomie et biologie cellulaire

institute: Université de Sherbrooke

summary: The nuclear receptor HNF4alpha is regulating a wide set of genes associated with development, cell differentiation, inflammation and metabolism. In human, 12 variants of HNF4α  can be expressed by the use of two promoters and by alternative splicing. Until now, the characterization of this transcription factor has ignored this diversity and has remained confined to the study of a fraction of the isoforms. We therefore wanted to clarify the situation by specifically characterizing the transcriptional functions of the 12 isoforms of HNF4α. We have generated for this purpose stable lines expressing each isoform of HNF4α in HCT 116 cells. The expression of each isoform was then induced for 48 hours and the whole transcriptome was analyzed by RNA sequencing. The transcriptome associated with each specific isoform was then compared to empty control cells to determine the specific transcriptional functions of HNF4alpha's isoforms.

overall_design: Stable HCT116 cell lines containing a single insertion of the different human HNF4alpha isoforms (1 to 12) fused to GFP at its C-terminal were generated through the Flp-In T-REx system. Expression of HNF4alpha isoforms was induced for 48 hours with 2.5 ug/ml of doxycycline before analyzing the transcriptome by RNA sequencing on Illumina NovaSeq 6000 system. Experiments were realized in triplicate for all isoforms of HNF4alpha and transcripts expression was compared to the one of the parental empty HCT116 cell line.

first: Élie

last: Lambert

first: Jean-Philippe

last: Babeu

last: Simoneau

first: Dominique

last: Lévesque

first: Émilie

last: Jolibois

last: Scott

first: François

first: François-Michel

last: Boisvert


title: Identification of AtGBF3-regulated targets in Arabidopsis thaliana under combined stress of drought and Pseudomonas syringae infection

status: Public on Jun 12 2019

city: New Delhi

first: Senthil-Kumar

last: Muthappa

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Plant Genome Research

summary:
Crop plants are often exposed to the combination of drought and pathogen stress. Transcriptome studies on Arabidopsis thaliana and other plants unveiled activation of shared molecular defense mechanisms between under individual and combined stresses. These shared plant responses are characterized by commonly regulated genes under individual and combined stresses. Based on the previous studies, G-box binding factor 3 (GBF3) is one of the regulatory components of such shared responses. However, the mechanistic understanding on the role of GBF3 under combined drought and pathogen stress is not yet decoded. Using genetic approaches, we demonstrated Atgbf3 mutant plants are more susceptible under individual and combined drought and Pseudomonas syringae pv. tomato DC3000 stresses as compared to the wild-type plants. We further analyzed the global transcriptome of Atgbf3 mutant under combined stress to identify its downstream targets to further validate the role of AtGBF3 in combined stress.
We used microarrays to detail the global transcriptome reprogramming during AtGBF3-mediated regulation of combined stress.

overall_design: Leaves of mock treated and combined drought and P. syringae stressed Col-0 and Atgbf3 mutant plants for RNA extraction and hybridization on Affymetrix microarrays.

first: Aarti

last: Gupta

first: Sandeep

middle: K

last: Dixit

first: Muthappa

last: Senthil-Kumar


title: Sirt6 Oncogene Mediates PI3K/Akt Signaling Activation in Diffuse Large B-Cell Lymphoma

status: Public on Aug 17 2019

city: Jinan

first: Juan

last: Yang

address: No. 324 Jingwu Road

institute: Shandong Provincial Hospital Affiliated to Shandong University

summary:
Purpose:Sirtuin 6 (Sirt6) is a highly conserved ADP-ribosylase and NAD+ dependent deacylase, involved in broad cellular processes. This molecule possesses contradictory roles in carcinogenesis, as it has been documented to both suppress and augment tumor growth. This experiment aimed to document the Sirt6 expression and functions in diffuse large B-cell lymphoma (DLBCL).
Methods:Immunohistochemistry was conducted to assess the expression of Sirt6 on paraffin-embedded tissues from 70 DLBCL patients and 35 reactive hyperplasia patients with informed contents. Lentivirus vectors either encoding shSirt6, lvSirt6 or empty lentiviral vector were stably transfected into DLBCL cells. shSirt6 transfected or shControl transfected LY1 cell samples were performed RNA sequencing (RNA-seq) analysis, functional enrichment analyses of gene ontology (GO) and gene set enrichment analysis (GSEA). DLBCL cells were subcutaneously injected to SCID-Beige mice to establish xenograft models.
Results:Sirt6 is found to be highly expressed and predictive of negative prognoses in DLBCL. Sirt6-deprived DLBCL cells demonstrated augmented sensitivity towards chemotherapy, higher rates of apoptosis, dysfunctional cell proliferation and were noted to have arrested cell cycle progression between the G2 and M phases. In accordance with the gene set enrichment analysis (GSEA) according to RNA-sequencing, PI3K signaling along with phosphorylation of its downstream targets (including mTOR and AKT) was reduced upon Sirt6 downregulation. Xenograft models that were infected with Sirt6-knockdown vectors demonstrated suppressed tumor growth and lower rates of c-Myc/Ki-67 staining.
Conclusion: These findings provide mechanistic insights into the oncogenic activity of Sirt6 for the first time.

overall_design: RNA profiles of three test and three control samples were generated by deep sequencing, using Illumina HiSeq 4000.

first: Xiangxiang

last: Zhou

first: Ying

last: Li

first: Ya

last: Zhang

first: Xiaosheng

last: Fang

last: Chen

first: Xin

last: Wang


title: RNA-seq data of canine mammary tumors and normal samples

status: Public on Jul 22 2019

first: Sangwoo

last: Kim

state: State...

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Biomedical Systems Informatics

institute: Yonsei University College of Medicine

summary:
Canine mammary gland tumors (CMTs) have been suggested as promising cancer models to human breast cancer due to their many biological and clinical similarities. Here, we collected 222 samples consist of 158 tumor samples and 64 matched normal samples of CMTs. Fresh tissue samples were transferred in to RNAlater, and refrigerated overnight at 4°C and then stored at -80°C. Total RNA was extracted from tissues using RNeasy mini kit. We aligned RNA-Seq raw data from 222 samples to canine reference genome CanFam3.1 using Tophat. We assembled transcript and calculated FPKM values using Cufflinks. All tumor samples were evaluated by histopathological characteristics including histopathological subtype, grade, and lymphatic invasion, and annotated with corresponding sequencing data. The histopathological classification and the histological grading system of CMTs were adopted from those of human breast cancer. In addition, immunohistochemical evaluation was performed in samples for estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2) status.

DISCLAIMER: Using this dataset became freely available on Jul 22, 2019. On the other hand, we are now preparing a key paper about comparative analysis of canine and human breast cancer based on this dataset. If you plan to submit a similar paper using this dataset before the main paper is published, please feel free to contact the submitter (swkim@yuhs.ac) to coordinate submission.

overall_design: RNA-seq of 158 canine mammary gland tumors and 64 matched normal samples.

first: Ka

first: Byung

last: Seung

first: Dohyun

first: Hee

last: Park

first: Doo

last: Song

first: Jae

middle: H

last: Cheong

first: Hojung

last: Nam

first: Jung

last: Sur


title: Genome-wide analysis identifies Nr4a1 as a key mediator of T cell tolerance (ChIP-seq)

status: Public on Jun 10 2019

city: Seattle

first: Raymond

last: Doty

state: WA

department: Division of Hematology

institute: University of Washington

summary: T cells become dysfunctional when they encounter self antigens or are exposed to chronic infection or to the tumour microenvironment1. The function of T cells is tightly regulated by a combinational co-stimulatory signal, and dominance of negative co-stimulation results in T cell dysfunction2. However, the molecular mechanisms that underlie this dysfunction remain unclear. Here, using an in vitro T cell tolerance induction system in mice, we characterize genome-wide epigenetic and gene expression features in tolerant T cells, and show that they are distinct from effector and regulatory T cells. Notably, the transcription factor NR4A1 is stably expressed at high levels in tolerant T cells. Overexpression of NR4A1 inhibits effector T cell differentiation, whereas deletion of NR4A1 overcomes T cell tolerance and exaggerates effector function, as well as enhancing immunity against tumour and chronic virus. Mechanistically, NR4A1 is preferentially recruited to binding sites of the transcription factor AP-1, where it represses effector-gene expression by inhibiting AP-1 function. NR4A1 binding also promotes acetylation of histone 3 at lysine 27 (H3K27ac), leading to activation of tolerance-related genes. This study thus identifies NR4A1 as a key general regulator in the induction of T cell dysfunction, and a potential target for tumour immunotherapy.

overall_design: Genome-wide examination of H3K4me3 and H3K27me3 histone modifications across in vitro-generated CD4+ T cell subsets including naive, Th1, Th2, Th17, nTreg, and tolerant T cell. Genome-wide examination of Nr4a1, C-Jun, and Batf bindings, as well as H3k27ac  peaks across chromain in Nr4a1-overexpressed T cell, Naive T cell, TCR/co-stimulation-activated T cell, as well as Nr4a1-deficient T cells.

first: Xindong

last: Liu

first: Huiping

last: Lu

first: Xiaowei

last: Yan


title: mRNA-seq of C. elegans starved L1 progeny of parents fed empty vector, daf-2, or pitr-1 RNAi

status: Public on May 01 2019

city: Eugene

first: Amy

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

summary: hrde-1(tm1200) animals were bleached and embryos were plated on empty vector, daf-2, or pitr-1 RNAi (HT115). Animals were allowed to develop for 72 hr, after which embryos were released via bleaching and allowed to hatch in the absence of food. Arrested L1 larvae were snap frozen in liquid nitrogen ~24 hr after bleaching.

overall_design: Starved L1 progeny of worms grown on empty vector RNAi were compared to starved L1 progeny of worms grown on daf-2 RNAi or pitr-1 RNAi

first: J

last: Jordan

first: A

first: R

last: Chitrakar

first: L

last: Baugh


title: MCF-7 as a model for functional analysis of breast cancer risk variants

status: Public on May 09 2019

city: Grand Rapids

first: Gerry

middle: A.

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

summary: Here we report how the ER+ cell line MCF-7 can be used to inform risk mechanisms for BCa. We identified active regulatory elements (enhancers, promoters, and chromatin organizing elements) by histone H3K27 acetylation and CTCF occupancy and determined the enrichment of risk variants at these sites. We measured gene expression via RNA-seq. After intersection with GWAS risk variants we found 39 enhancers and 15 CTCF occupancy sites that, between them, overlapped 96 BCa credible risk variants at 42 loci. These risk enhancers likely regulate the expression of dozens of genes, which are enriched for GO categories including estrogen and prolactin signaling.

overall_design: Two WT MCF-7 samples were used for CTCF ChIP-seq and two for H3k27Ac ChIP-Seq. 8 samples in 2 separate batches, were used for RNA-Seq. These data were compared with publically available data for MCF-7 and HMEC.

first: Gerhard

middle: A

first: Steven

middle: E

last: Pierce

first: Alix

last: Booms


title: miRNA Expression data from CD133+CD15+ chordoma cells (Chordoma Cance Stem Cells) and CD133-CD15- chordoma cells

status: Public on Apr 15 2019

city: Istanbul

first: Emre Can

last: Tüysüz

address: Ibrahimaga Mah.

country: Turkey

institute: Yeditepe University

summary:
Chordoma is a rare, resistant bone tumor thought to be arised from remnants of embryonic notochord. Cancer stem cells (CSCs) are associated with tumorigenesis, recurrence and resistance in cancers.
Here, we used miRNA and mRNA transcriptome analysis to discover novel genes and networks in chordoma CSCs

overall_design: CD133+CD15+ and CD133-CD15- chordoma cells were sorted in duplicate

first: Emre

last: Tuysuz

first: Sukru

last: Gulluoglu

first: Ömer Faruk

last: Bayrak


title: RNA-Seq of CD4+ T cells treated with AS1842856 or DMSO

status: Public on Apr 10 2019

city: San Francisco

first: Albert

last: Vallejo-Gracia

address: 1650 Owens Street

department: GIVI

institute: Gladstone Institutes

summary: Quiescence is a hallmark of CD4+ T cells latently infected with HIV-1. While reversing this quiescence is an effective approach to reactivate latent HIV from T cells in culture, it can cause deleterious cytokine dysregulation in patients. Here we report that FOXO1, a key regulator of T-cell quiescence, promotes latency and suppresses productive HIV infection. In resting T cells, FOXO1 inhibition induces ER stress and activates two associated transcription factors: activating transcription factor 4 (ATF4) and nuclear factor of activated T cells (NFAT). Thus, our studies uncover a novel link between FOXO1, ER stress, and HIV infection that could be therapeutically exploited to selectively reverse T-cell quiescence and reduce the size of the latent viral reservoir.

overall_design: RNA-Seq of CD4+ T cells from 3 donors treated with AS1842856 or DMSO for 12h and 48h


title: Theiler’s Virus-Mediated Immunopathology in the CNS and Heart: Roles of Organ-Specific Cytokine and Lymphatic Responses

status: Public on Apr 23 2019

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

institute: Kindai University Faculty of Medicine

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

overall_design: Refer to individual Series


title: Mice heart: wild-type mice vs. alpha MHC/mir-143/145 transgenic mice

status: Public on Apr 01 2019

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Transcriptional profilings of the mouse heart obtained from control (wild-type) and alpha MHC/mir-143/145 transgenic mouse line 9 and 19.

overall_design: Each array demonstrates one control mouse (three month) and one transgenic mouse (three month). One replicate per array.

first: Takashi

last: Iwamoto

first: Jun

last: Ueda


title: Early responses of Brassica oleracea roots to zinc supply under sufficient and sub-optimal phosphorus supply

status: Public on Mar 01 2019

city: Loughborough

first: Sina

last: Fischer

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

summary: Shoot zinc (Zn) in Brassica oleracea is affected by soil Zn and phosphorus (P) concentrations. Most problematic is the negative impact of P fertilizers on Zn concentrations in crops, which makes balancing yield and mineral quality challenging. To evaluate molecular mechanisms involved in the accumulation of large shoot Zn concentrations regardless of the P supply, two B. oleracea accessions were grown hydroponically for two weeks with different combination of P and Zn supply. Ionome profiling and deep RNA sequencing of roots revealed interactions of P and Zn in planta, without apparent phenotypic effects. In addition, increasing P supply did not reduce tissue Zn concentration. Substantial changes in gene expression in roots of both accessions ensured nutritionally sufficient P and Zn uptake. Numerous genes were differentially expressed after changing Zn or P supply and most of them were unique to only one accession, highlighting different strategies in achieving nutrient sufficiency. Thus, different gene networks responded to the changing P and Zn supply in the two accessions. Additionally, enrichment analysis of gene ontology classes revealed that genes involved in lipid metabolism, response to starvation, and anion transport mechanisms were most responsive to the contrasting P and Zn supply in both accessions. The results agreed with previously studies demonstrating alterations in P transport and phospholipid metabolism in response to reduced P supply. Knowledge of genes responsive to P or Zn supply will help illuminate the interactions between these elements in their uptake and accumulation by plants and might highlight candidate genes for breeding high-yield-high-Zn crops.

overall_design: Analysis of root material of two different Brassica oleracea accessions grown hydroponically with four different combinations of phosphorus and zinc supply.

first: Paula

last: Pongrac

first: Jacqueline

last: Thompson

first: Gladys

last: Wright

first: Philip

last: White


title: Insulin/IGF signaling and vitellogenin provisioning mediate intergenerational adaptation to nutrient stress

status: Public on Apr 09 2019

first: Amy

last: Webster


title: Transcriptome profiling of H1-iCas9 cells grown on laminin and on MEFs

status: Public on Feb 28 2019

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

institute: University of Toronto

summary: This experiment is part of a study of differentially essential genes in H1 hPSCs grown on different substrates ("Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies", Mair et al., Cell Reports 2018). The cells used stably express DOX-inducible Cas9 in the AAVS1 locus and were profiled together with unmodified H1 wt hPCS on both substrates to asses transcriptional changes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human pluripotent stem cells (hPSCs) provide an invaluable tool for modeling diseases and hold therapeutic promise for regenerative medicine. Hence, there is great interest in understanding the genetic wiring that governs pluripotency and lineage differentiation. A critical first step involves a systematic understanding and cataloging of genes that are indispensable for hPSC maintenance and proliferation. In order to map core and context-specific genetic determinants of hPSC fitness, we generated an inducible Cas9 H1 hPSC line and performed genome-scale loss-of-function screens using a highly optimized CRISPR-Cas9 library to identify essential genes in hPSCs cultured on feeder cells and in feeder-free conditions. Dependencies that were predictable in hPSCs were identified such as FOXH1 and VENTX, genes that encode transcription factors that have been implicated in stem cell biology and differentiation, as well as genes not previously associated with stem cells, including an uncharacterized gene encoding a potential hPSC regulator, C22orf43/DRICH1. Genes found to be essential in hPSCs are substantially different from essential gene sets derived from a broad set of cell lines, and gene essentiality in hPSCs is highly context-dependent, i.e. essential gene sets vary with different substrates. We present condition-specific CRISPR screens in hPSCs, and establish parameters for genome-wide screens in this cell type. Ultimately, these data will facilitate the investigation of essential genes in hPSCs in different contexts and the characterization of unappreciated regulators of hPSC biology to understand the genetic wiring of hPSC fitness and pluripotency.

first: Barbara

last: Mair

first: Kevin

last: Brown


title: Neural cell adhesion molecule 1 (NCAM1; CD56) promotes leukemogenesis and confers drug resistance in acute myeloid leukemia.

status: Public on Feb 22 2019

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

summary: Neural cell adhesion molecule 1 (NCAM1; also known as CD56) is expressed in up to 20% of acute myeloid leukemia (AML) patients. Expression of NCAM1 is widely used as a marker of minimal residual disease; however, the biological function of this cell surface protein in AML remains elusive. In this study we investigated the impact of aberrant NCAM1 expression on leukemogenesis, drug resistance and its role as a biomarker to guide therapy.Gene expression profiling was performed with RNA-seq in three cell lines (SKM-1, NOMO-1, MOLM-14) after doxycycline-mediated induction of scrambled shRNA or shNCAM1 at timepoint 72 hours.

overall_design: mRNA profiles of cell lines SKM-1, NOMO-1, MOLM-14 transfected either with scrambled shRNA or shRNA-NCAM1 were generated using TruSeq RNA Library Prep Kit v2 (Illumina) followed by sequencing with 100 bp paired-end reads on HiSeq 2000.

first: Daniel

last: Sasca

first: Lars

last: Bullinger

first: Thomas

last: Kindler


title: Identification of tumor suppressor microRNAs by integrative miRNA and mRNA sequencing of matched tumor normal pairs in lung adenocarcinoma

status: Public on Feb 20 2019

city: Seoul

first: Jihae

last: Seo

address: 52 Ewhayeodae-gil, Seodaemun-Gu

department: Ewha Research Center for Systems BIology

institute: Ewha Womans University

summary: Roles of microRNAs (miRNAs) have not yet been explored systematically at the genome scale in lung cancer biology despite their important regulatory functions. Here, we report an integrative analysis of microRNA and mRNA sequencing data for the matched tumor and normal samples from 109 Korean female patients with non-small-cell lung adenocarcinoma. We produced miRNA-Seq and RNA-Seq data for 48 patients and RNA-Seq data only for additional 61 patients. Differential expression analysis with stringent criteria yielded 44 miRNAs and 2,322 genes. Integrative gene set analysis of differentially expressed miRNAs and genes using miRNA-target information yielded several processes related to cell cycle regulation that were targeted by tumor suppressor miRNAs. We performed the colony formation assay in A549 and NCI-H460 cell lines to test the tumor suppressive activity of down-regulated miRNAs in cancer and identified 7 novel tumor suppressor miRNAs. Two miRNAs showed differential survival characteristics in the TCGA LUAD patient cohort, suggesting their prognostic value. Our study not only provides a massive dataset of miRNA and mRNA sequencing from the matched tumor-normal samples but also reports several novel tumor suppressor miRNAs that could be further developed into prognostic biomarkers or RNA therapeutic targets.

overall_design: We produced miRNA-Seq in 48 patient-matched lung adenocarcinoma and non-malignant lung tissue pairs from current and never smokers.

first: Namhee

last: Yu

first: Seunghui

last: Yong

first: YeonJoo

last: Jung

first: Ye

last: Lee

first: Jaesang

last: Kim

first: Jhingook

first: Sanghyuk