title: Transcriptome and ribosome profiling of XRN1-null HEK293T human cell line generated by CRISPR/Cas9 gene editing

city: Tuebingen

first: Eugene

last: Valkov

state: Baden-Wuerttemberg

address: Max-Planck-Ring 5

department: Biochemistry

institute: Max Planck Institute for Developmental Biology

summary: XRN1 is the major cytoplasmic exoribonuclease in eukaryotes, which degrades deadenylated and decapped mRNAs in the last step of the 5′–3′ mRNA decay pathway. Metazoan XRN1 interacts with decapping factors coupling the final stages of decay. Ribosome profiling revealed that XRN1 loss impacts not only on mRNA levels but also on the translational efficiency of many cellular transcripts likely as a consequence of incomplete decay. We compared differentially expressed genes derived from the analysis of the transcriptome and the translatome of HEK293T wild-type (WT) and XRN1-null cells by RNA-Seq and Ribo-Seq, respectively. Two biological replicates of each cell line were analyzed. The RNA-Seq analysis indicated that a substantial fraction of the total 10,105 genes showed significant differences between the two cell lines. 2,906 genes were significantly upregulated whilst 2,900 genes were downregulated using a fold change >0 on log2 scale with an FDR<0.005 to determine abundance. Significantly fewer genes showed differences between the WT and the XRN1-null cells at the level of translation with 433 genes showing an increase in abundance of ribosomal footprints whilst 560 genes were decreased as indicated by the Ribo-Seq analysis. Comparative analysis of translational efficiency (TE) in WT and XRN1-null cells on a genome-wide scale as a ratio of ribosomal occupancy to mRNA abundance identified an increase in TE for 102 genes but a decrease for 598 genes with most of the genes showing no evidence of change in the TE.

overall_design: Two cell types with two biological replicates analysed using two methods.

first: Ramona

last: Weber


title: The RNA-seq Parachlorella kessleri under salt stress conditions

status: Public on Jul 25 2019

city: Shanghai

first: Zaizhi

last: You

address: 800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

type: Expression profiling by high throughput sequencing

summary: To obtain differential expression of genes in Parachlorella kessleri under salt stress

overall_design: Gene expression profiles of 2-day Parachlorella kessleri under control and salt stress conditions were generated by deep sequencing, in triplicate, using Illumina

first: Xiaoling

last: Miao


title: DMSO cryopreservation: the method of choice for droplet-based single-cell RNA sequencing of preserved cells

city: Biberach

first: Christian

middle: Thaddaeus

last: Wohnhaas

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

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

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: DMSO cryopreservation: the method of choice for droplet-based single-cell RNA sequencing of preserved cells [10X Genomics]

summary: Recently, combining single-cell RNA sequencing (scRNA-seq) with upstream cell preservation procedures such as cryopreservation or methanol fixation has become more common. By separating cell handling and preparation, from downstream library generation, scRNA-seq workflows are more flexible and manageable. However, the inherent transcriptomics changes associated with cell preservation and how they may bias further downstream analysis remain unknown. Here, we present a side-by-side droplet-based scRNA-seq analysis, comparing the gold standard – fresh cells – to three different cell preservation workflows: dimethyl sulfoxide based cryopreservation, methanol fixation and CellCover reagent. Cryopreservation proved to be the most robust protocol, maximizing both cell integrity and low background ambient RNA. Importantly, gene expression profiles from fresh cells correlated most with those of cryopreserved cells. Such similarities were consistently observed across the tested cell lines (R ≥ 0.97), monocyte-derived macrophages (R = 0.97) and immune cells (R = 0.99). In contrast, both methanol fixation and CellCover preservation showed an increased ambient RNA background and an overall lower gene expression correlation to fresh cells. Thus, our results demonstrate the superiority of cryopreservation over other cell preservation methods. We expect our comparative study to provide single cell omics researchers invaluable support when integrating cell preservation into their scRNA-seq studies.

overall_design: Examination of DMSO cryopreservation in rat liver immune cells of four animals. Eight samples were analyzed represented by fresh cells and cells cryopreserved for 3 weeks per animal.

middle: T

first: Germán

middle: G

last: Leparc

first: Francesc

last: Fernandez-Albert

first: David

last: Kind

first: Florian

last: Gantner

first: Coralie

last: Viollet

first: Tobias

last: Hildebrandt

first: Patrick

last: Baum


title: DMSO cryopreservation: the method of choice for droplet-based single-cell RNA sequencing of preserved cells [Drop-Seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of 3 different cell preservation protocols in two different cell matrices and different timepoints: 11 samples


title: RNA methylation maintains hematopoietic stem cell identity and symmetric commitment

city: New York

first: Franco

last: Izzo

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: Stem cells balance cellular fates through asymmetric and symmetric divisions in order to self-renew or to generate downstream progenitors. Symmetric commitment divisions in stem cells are required for rapid regeneration during tissue damage and stress. The control of symmetric commitment remains poorly defined. N6-methyladenosine (m6A), the most abundant posttranscriptional mRNA modification controls cellular states and its abundance is dysregulated in cancer.  Here we show that mRNA methylation controls symmetric commitment and cell identity of hematopoietic stem cells (HSCs). Using single-cell RNA sequencing (scRNA-seq) in combination with transcriptomic profiling of HSPCs (hematopoietic stem and progenitor cells) from control and m6A methyltransferase Mettl3 conditional knockout mice, we found that m6A-deficient HSC fail to symmetrically differentiate. Dividing HSCs are expanded and are blocked in an intermediate state that molecularly and functionally resembles multipotent progenitors. Mechanistically, RNA methylation controls Myc mRNA abundance in differentiating HSCs.  Importantly, we identified MYC as a new marker for HSC asymmetric and symmetric commitment. Furthermore, forced expression of MYC rescued m6A’s requirement for engraftment indicating its importance in the early stage of HSC cellular fate. Overall our results indicate that RNA methylation is critical for normal blood homeostasis and may provide a general mechanism for how stem cells regulate differentiation fate choice.

overall_design: For single cell RNA sequencing, 3,000 cells were targeted for each replicate using the 10X Genomics Chromium Single Cell RNA solution, and sequenced to a depth of 50,000 reads per cell. Bulk RNA sequencing was performed in 3 replicates, for sorted hematopoietic stem cells (HSC), and the following multi potent progenitors (MPP) populations: MPP1, MPP2 and MPP4

first: Yuanming

last: Cheng

first: Hanzhi

last: Luo

first: Brian

middle: F

last: Pickering

first: Diu

last: Nguyen

first: Robert

last: Myers

first: Alexandra

last: Schurer

first: Saroj

last: Gourkanti

first: Jens

middle: C

last: Brüning

first: Ly

middle: P

last: Vu

first: Samie

middle: R

last: Jaffrey

first: Dan

last: Landau

first: Michael

last: Kharas


title: Impact of Diet Induced Obesity on Hyperoxic Lung Injury

first: Maria

last: Plataki

state: New York

address: 1300 York Ave | Box 96

department: Joan and Sanford I. Weill Department of Medicine

institute: Weill Cornell Medicine

summary:
Background: Obesity has become a worldwide concern. Acute respiratory distress syndrome (ARDS) comprises 10.4% of total intensive care unit admissions and is associated with very high mortality. ARDS incidence is increased in obese patients. Exposure of rodents to hyperoxia mimics many of the clinical and pathologic features observed in patients with ARDS. The aim of this study was to determine the impact of high fat diet-induced obesity on the susceptibility to hyperoxic acute lung injury in mice.
Methods: Male C57BL/6 mice received 60% fat versus ingredient matched 10% fat diet. Mice were exposed to >95% oxygen to induce lung damage. RNA was isolated from lung homogenates and by comparing RNA sequencing results with mouse Mitocarta, an inventory of genes encoding proteins with mitochondrial localization, we identified fatty acid synthase (FASN), an enzyme catalyzing de novo fatty acid synthesis, as one of the mitochondrial genes significantly changed with diet and with hyperoxia. We generated mice deficient in FASN in alveolar epithelial cells by using a tamoxifen inducible Cre recombinase construct (FASNflox/flox SPC Cre+/-) and subjected them to hyperoxia and high fat diet.
Results: Mice receiving 60% fat diet had significantly higher weight, serum cholesterol and fasting glucose. High fat diet mice had significantly reduced survival and increased lung damage, as assessed by BAL protein and LDH, histology and TUNEL staining. By RNA sequencing of lung homogenates we identified FASN as one of the mitochondrial genes significantly reduced in mice receiving 60% compared to 10% fat diet and further reduced with hyperoxia. We confirmed that FASN protein levels in the lung of high fat diet mice were lower by immunoblotting and immunohistochemistry. After 48 hours of hyperoxia FASNflox/flox SPC Cre+/- mice displayed increased levels of BAL protein and LDH and more severe histologic lung injury. FASNflox/flox SPC Cre+/- mice remained more prone to lung injury after hyperoxic exposure even when they received 60% fat diet.
Conclusions: These results demonstrate that obesity increases the severity of hyperoxia induced acute lung injury in mice by altering FASN levels in the lung of high fat diet fed rodents. To our knowledge, this is the first study to show that high fat diet leads to altered FASN expression in the lung and that both high fat diet and reduced FASN in alveolar epithelial cells lead to increased lung injury under hyperoxic conditions.

overall_design: Lung RNA profiles of mice that received 12 weeks of 60% fat and 10% fat diet after exposure to >95% oxygen or room air were generated

first: LiChao

last: Fan

first: Mitsuru

last: Imamura

first: Elizabeth

last: Sanchez

first: Yizhang

last: Zhu

first: Suzanne

last: Cloonan

first: Augustine

middle: M

last: Choi


title: Inactivation of Sox9 in fibroblasts reduces cardiac fibrosis and inflammation in mice after myocardial infarction

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

institute: Medizinische Fakultät Mannheim

summary: Fibrotic scarring drives the progression of heart failure after myocardial infarction (MI). Therefore, the development of specific treatment regimens to counteract fibrosis is of high clinical relevance. The transcription factor SOX9 functions as an important regulator during embryogenesis, but recent data point towards an additional causal role in organ fibrosis. We show here that SOX9 is upregulated in the scar after MI in mice. Fibroblast specific deletion of Sox9 ameliorated MI-induced left ventricular dysfunction, dilatation and myocardial scarring in vivo. Unexpectedly, deletion of Sox9 also potently eliminated persisting leukocyte infiltration of the scar in the chronic phase after MI. RNA-sequencing from the infarct scar revealed that Sox9 deletion in fibroblasts resulted in strongly downregulated expression of genes related to extracellular matrix, proteolysis and inflammation. Importantly, Sox9 deletion in isolated cardiac fibroblasts in vitro similarly affected gene expression as in the cardiac scar and prevented their activation and myofibroblast differentiation. Together, our data demonstrate that fibroblast SOX9 functions as a master regulator of cardiac fibrosis and inflammation and might constitute a novel therapeutic target during MI.

overall_design: 10 weeks old mice, LAD was performed in Sox9 fl/fl and Sox9 fl/Per_cre mice. The Per_cre allow the deletion of Sox9 only in fibroblast cells. After 6 weeks. Scar tissue from both conditions were taken. 3 replicates in the control group and 3 replicates with Sox9-deletion. Total RNA was isolated for polyA RNA-seq.

first: Gesine

last: Scharf

first: Julio

last: Cordero


title: Open chromatin landscape of rat microglia upon inflammatory or pro-invasive polarization

city: Warsaw

first: Michał

last: Dąbrowski

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Microglia are brain-resident, myeloid cells that play important roles in health and brain pathologies. While data on chromatin accessibility in activated murine microglia are available, there is no such data on rat microglia subjected to different stimuli. Herein, we report a comprehensive, replicated, FDR-controlled dataset of DNase-hypersensitive (DHS) open chromatin regions for the rat microglia. We compared open chromatin landscapes in untreated primary microglial cultures and cultures stimulated for 6h with either lipopolysaccharide (LPS) or glioma-conditioned medium (GCM). Glioma-secreted factors induce the pro-invasive and immunosuppressive activation of microglia, in which these cells promote tumor growth. The open chromatin landscape of the rat microglia consisted of 126,640 reproducible DHS regions, of which 12,357 and 2,303 significantly changed openness following the stimulation with LPS and GCM, respectively. Active genes had constitutively open promoters, but there was no direct dependence between cumulative openness of DHS regions near to a gene and its expression. LPS-regulated DHS regions were more frequent in introns, while GCM-regulated regions were more frequent away from gene bodies. GCM and LPS treatment differentially affected open chromatin regions mapped to genes in the pathways of Toll-like-receptor signaling and the Axon guidance, suggesting that the molecular machinery used by migrating microglia is similar to that of growing axons and, moreover, that modulation of these pathways is instrumental for glioma to induce a pro-invasive polarization of microglia. Our dataset of open chromatin regions active in rat microglia will constitute a useful resource for studies of the transcriptional regulation in this system.

overall_design: Microglia isolated from neonate rats was maintained in cell culture and either left untreated (control group) or stimulated for 6h with either lipopolysaccharide (LPS) or C6 glioma-conditioned medium (GCM). Two independent biological replicates (microglia cultures) were prepared for each conditions, each culture obtained from 10-15 rat pups.

first: Piotr

last: Przanowski

first: Shamba

middle: S

last: Mondal

first: Michal

last: Dabrowski


title: In the Setting of Beta Cell Stress, the Pancreatic Duct Gland Transcriptome shows Characteristics of an Activated Regenerative Response

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: The pancreatic duct gland (PDG) compartment has been proposed as a potential stem cell niche. Little is known of the molecular signature of the PDG compartment in either a quiescent state or the potentially activated state during beta cell stress characteristic of diabetes.

overall_design: We performed RNA sequencing on RNA obtained from PDGs of wild type versus pre-diabetic HIP rats, a model of type 2 diabetes.

first: Alexandra

middle: E

last: Butler

first: David

last: Kirakossian

first: Tatyana

last: Gurlo

first: Fuying

last: Gao

first: Peter


title: Fetal and trophoblast PI3K p110α have distinct roles in regulating resource supply to the growing fetus

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Using RNA-seq we identified several genes downstream of p110α in the trophoblast that are important in adapting placental phenotype to support fetal growth.

overall_design: This was achieved by comparing the transcriptomes of 5 Het-U (heterozygous deficient in p110α in both fetal and trophoblast lineages) and 4 Hom-P (heterozygous deficient in p110α in fetal lineage and homozygous deficient in p110α in trophoblast) placentas placentas at day 19 of pregnancy.

first: Jorge

last: Lopez-Tello

first: Vicente

last: Perez-Garcia

first: Jaspreet

last: Khaira

first: Laura

last: Kusinski

first: Wendy

middle: N

last: Cooper

first: Adam

last: Andreani

first: Edurne

last: FernandezdeLiger

first: Myriam

last: Hemberger

first: Ionel

last: Sandovici

first: Miguel

last: Constancia

first: Amanda

last: Sferruzzi-Perri


title: mRNA transcription profile of potato (Solanum tuberosum L.) in response to explant cutting

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

summary: The explant is likely the most essential parameter of plant tissue culture. The vast majority of tissue culture studies have focused almost exclusively on the use of explants as a tool for organogenesis or propagation, and there is limited information that documents the changes that occur in an explant in response to cutting during explant preparation just prior to culture. To better understand the molecular changes occurring during the wounding process that accompanies the preparation of an explant, this study examined the mRNA transcription profile of potato (Solanum tuberosum L. cv. Desirée) single-node segments. To achieve this, RNA-seq analysis was performed to identify significantly differentially expressed genes (DEGs) that existed between uncut in vitro plantlets and cut explants. DEGs were connected to cellular processes in the extracellular region, nucleus, and plasma membrane, and were associated with biosynthesis, carbohydrate metabolism and catabolism, cellular protein modification, growth and development, and response to stress. These results provide a novel perspective of the changes taking place within explants when they are cut and serve as a valuable basis for the study of explant-related stress in plant tissue culture in other plant species, and may provide an understanding of the success or failure of the tissue culture protocol and subsequent establishment of in vitro cultures.

overall_design: Examination of potato's mRNA transcription profile under cutting stress

first: Jaime

middle: A

last: Teixeira da Silva

first: Andrea

last: Gulyás

first: Judit

last: Dobránszki


title: Identification of HNRNPA2B1-regulated miRNA targets in breast cancer cells

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

type: Non-coding RNA profiling by high throughput sequencing

summary: Higher N(6)-methyladenosine (m6A) was identified in selected primary microRNAs (pri-miRNAs) as associated with increased levels of the corresponding mature miRNA in MDA-MB-231 triple negative breast cancer (TNBC) cells (PMID: 25799998). HNRNPA2B1 is a reader of the m6A mark in pri-miRNAs and interacts directly with DGCR8 (a component of the nuclear DROSHA complex) to promote processing of pri-miRNAs to precursor-miRNAs (pre-miRNAs) (PMID: 26321680).  We have preliminary data showing that HNRNPA2B1 is increased in TAM-resistant, ERα+ LCC9 cells derived from TAM-sensitive, ERα+ MCF-7 breast cancer cells.  We found that high HNRNPA2B1 transcript levels in primary breast tumors are associated with reduced overall survival.  We postulate that an increase in HNRNPA2B1 targets its binding to additional pri-miRNAs (not normally bound under wild type conditions), resulting in an increase in miRNAs, including those that promote TAM-resistance.

overall_design: The experimental design includes three treatment groups: MCF-7 control transfected with pcDNA 3.1 for 48 h, MCF-7  transfected with pcDNA3.1-HNRNPA2B1 for 48h, and MCF-7 stably transfected with pcDNA3.1-HNRNPA2B1 for 72h.

first: Carolyn

last: Klinge

first: Sabine

middle: J

last: Waigel

first: Mei

last: Xiang


title: Identification of a novel microRNA panel associated with metastasis following radical prostatectomy for prostate cancer

city: Toronto

first: Yutaka

last: Amemiya

state: ON

address: 2075 Bayview Ave.

country: Canada

institute: Sunnybrook Research Institute

summary: This is a case control study designed to identify microRNA sequences associated with metastasis following radical prostatectomy for clinically localized prostate cancer. Samples were obtained from patients with clinical evidence of metastatic disease following surgery (cases) and patients who showed no evidence of metastasis or biochemical recurrence at least 5 years following surgery (controls). Cases and controls were matched for tumor grade and duration of follow-up.

overall_design: Next generation whole miRNome sequencing of 19 metastatic and 19 non-metastatic prostate cancer.

first: Robert

middle: K

last: Nam

first: Christopher

last: Wallis

first: Tania

last: Benatar

first: Arun

last: Seth


title: Malus domestica cultivar: McIntosh and Husveti rozmaring

type: Methylation profiling by high throughput sequencing

summary:
Genome-wide DNA methylation analysis between long-term in vitro shoot culture and acclimatized apple plants

DNA methylation is a process of epigenetic modification that can alter the functionality of a genome. Using whole-genome bisulfite sequencing, this study quantify the level of DNA methylation in the epigenomes of two diploid apple (Malus x domestica) scion cultivars ('McIntosh' and 'Húsvéti rozmaring') derived from three environmental conditions: in vivo mother plants in an orchard, in vitro culture, and acclimatized in vitro plants. The global DNA methylation levels were not dependent on the source of plant material. Significant differences in DNA methylation were identified in 586 out of 45,116 genes, including promoter and coding sequences, and classified as differentially methylated genes (DMGs). Differential methylation was visualised by an MA plot and functional genomic maps were established for biological processes, molecular functions and cellular components. Considering the DMGs, in vitro tissue culture resulted in the highest level of methylation, which decreased after acclimatization and tended to be similar to that in the mother tree. Methylation patterns of the two scions differed, indicating cultivar-specific epigenetic regulation of gene expression during adaptation to various environments. After selecting genes that displayed differences larger than ±10% in CpG and CHG contexts, or larger than ±1.35% in the CHH context from among the DMGs, they were annotated in Blast2GO v5.1.12 for Gene Ontology. These DNA methylation results suggest that epigenetic changes may contribute to the adaptation of apple to environmental changes by modifying gene expression.

overall_design: Examination of 2 different Malus domestica scion cultivar (McIntosh and Húsvéti rozmaring) DNA methylation patterns in CpG, CHG and CHH contexts.

first: Erzsébet

last: Kiss

first: Katalin

last: Posta


title: A.thaliana seedling expression data from ASP treatment

status: Public on Jul 24 2019

city: Bei Jing

first: Xin

last: Zhao

address: West 3rd Ring Road, Haidian District

institute: Capital Normal University

summary:
ASP induces the expression of early auxin response genes by activates auxin response, and affects responses to other signals associated with the auxin signaling pathway.
We used microarrays to detail  the effect of ASP on Arabidopsis global gene expression,  and identified distinct classes of up-regulated or down genes during this process

overall_design:
Seedlings were selected at 1/2MS medium grown with or without ASP for RNA extraction and hybridization on Affymetrix microarrays.

ASP is a piperazine compound: 1-[(4-bromophenoxy) acetyl]-4-[(4-fluorophenyl) sulfonyl] piperazine.

first: Limeng

last: Deng

first: Fengyang

last: Xu


title: Mitigating antagonism between transcription and proliferation allows near-deterministic cellular reprogramming (RNAPII ChIP)

first: Kate

last: Galloway

state: MA

department: Chemical Engineering

institute: Massachusetts Institute of Technology

summary: RNA sequencing analysis of Hb9::GFP mouse embryonic fibroblasts infected with control or reprogramming transcription factors at 4 dpi, and Hb9::GFP+ mouse induced motor neurons generated using transcription factor overexpression. The goal of this study is to examine the transcriptional path of reprogramming cells to identify molecular mechanisms and populations of highly efficient reprogramming.

overall_design:
RNAPII ChIP to determine binding prolife in control infected MEFs (Puro), 6F reprogramming cells with, and without the DDRR cocktail at 4 dpi where differences in transcription rate are observed.
The 6F are Ascl1, Brn2, Myt1l, Ngn2, Isl1, Lhx3.

first: Justin

last: Ichida


title: Mitigating antagonism between transcription and proliferation allows near-deterministic cellular reprogramming (CNN)

overall_design:
Transcriptional profiling of cells during the process of direct reprogramming of mouse embryonic fibroblasts to induced motor neurons (iMNs) and at the terminal stage at 17 dpi. Samples include Hb9::GFP+ sorted iMNs generated with  six factors (6F), 6FDD (e.g. 6F with p53DD), or 6FDDRR (6F with p53DD, hRASG12V, RepSox) as well as MEFs and samples at 4 dpi in conversion for 6F and 6FDDRR for both bulk and CFSE-low populations.
The 6F are Ascl1, Brn2, Myt1l, Ngn2, Isl1, Lhx3.


title: The IL-34/CSF1R Axis is an Epigenomically Modulated Regulator of Resistance to BRAF (V600E) Inhibition in Melanoma

city: Bronx

first: Amit

last: Verma

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

type: Methylation profiling by genome tiling array

summary:
DNA methylation analysis of human melanoma samples
Melanoma samples have differentially methylated regions when compared to controls

overall_design: HELP assay used for cytosine methylation analysis

first: Kith

last: Pradhan


title: The Liquid Liver Biopsy: Detection of Circulating Epithelial Cells in Liver Disease

city: Boston

first: David

last: Ting

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

summary: Using a microfluidic device, circulating epithelial cells (CECs) were enriched from peripheral blood from patients with chronlic liver disease and hepatocellular carcinoma. Select samples were further flow sorted for WBC subsets. CEC and WBC subsets transcriptomes were sequenced.

overall_design: Examination of RNA-seq of CEC-enriched samples from patients with chronic liver disease and hepatocellular carcinoma

first: Martin

last: Aryee

first: Kelly

last: Mosesso

first: Irun

last: Bhan


title: Hyperglycemia acts in synergy with hypoxia to maintain the pro-inflammatory phenotype of macrophages

city: Paris

first: Christophe

last: Helary

address: 4, place Jussieu

department: Chemistry

country: France

institute: Sorbonne University

summary: Diabetic foot ulcers (DFUs) are characterized by a chronic inflammation state which prevents cutaneous wound healing, andDFUs eventually lead to infection and leg amputation. Macrophages located in DFUs are locked in an pro-inflammatory phenotype. In this study, the effect of hyperglycemia and hypoxia on the macrophage phenotype was analyzed. For this purpose, a microarray was performed to study the gene expression profile of macrophages cultivated in a high glucose concentration. Hyperglycemia upregulated the expression of pro-inflammatory cytokines such as TNF-α, IL-1, IL-6, chemokines and downregulatd the expression of two receptors involved in phagocytosis (CD 36 and Class B scavenger type I receptors). In addition, eleven anti-apoptotic factors were upregulated whereas three pro-apoptotic ones were downregulated. Subsequently, the contribution of hypoxia and hyperglycemia to chronic inflammation and their potential synergic effect was evaluated on activated THP-1 derived macrophages. A long term post activation effect (17 hours) was only observed on the upregulation of pro-inflammatory cytokines when hypoxia was combined with a high glucose concentration. In contrast, hyperglycemia and hypoxia did not have any effect on wound healing molecules such as TGF-β1. Taken together, the results show that hyperglycemia acts in synergy with hypoxia to maintain a chronic inflammation state in macrophages.

overall_design: THP-1 cells cultivated in hyperglycemia or normoglycemia, hypoxia and differentiated into macrophages by PMA. Macrophages activated by LPS

first: Mangesh

last: Morey

first: Peadar

middle: O

last: Gaora

first: Abhay

last: Pandit

last: Hélary


title: Gene expression data from maturing oocyte of chickens

status: Public on Jul 23 2019

city: Nagoya

first: Atsushi

last: Murai

address: Furo-cho, Chikusa-ku

department: Department of Animal Sciences

country: Japan

institute: Nagoya University

summary:
In avian species, maternal blood immunoglobulin Y (IgY) is transferred to the egg yolks of maturing oocytes, but the mechanism underlying this transfer is unknown.
IgY-deficient chickens were developed by removal of bursa of Fabricius (Bx group).  Since DIG-labeled IgY uptake into egg yolk was approximately 2-fold higher in the Bx group than that of the control, upregulated genes in oocyte of the Bx group were determined to identify IgY receptor responsible for maternal blood IgY transfer by microarray analysis.

overall_design: GeneChip® Chicken Genome Array was used for high-throughput screening of upregulated genes in oocytes of the IgY-deficient chickens. The germinal disks of F5-F7 yellow follicles of three birds were pooled, and their total RNA was used for microarray analysis.

first: Takahito

last: Hamano

first: Misako

last: Kakiuchi

first: Misato

last: Kobayashi

first: Fumihiko

last: Horio


title: Central Amygdala TRAP-Seq of Drd2 neurons

city: Belmont

first: Nikolaos

last: Daskalakis

address: Oaks Building 328, Mailstop 212, 115 Mill Street

department: Department of Psychiatry

institute: McLean Hospital/ Harvard Medical School

summary: Sequencing actively translating transcripts of Drd2 neurons using translating ribosome affinity purification (TRAP identifies differentially regulated mRNAs following fear learning. Differentially expressed transcripts with potentially targetable gene products include Npy5r, Rxrg, Adora2a, Sst5r, Fgf3, ErbB4, Fkbp14, Dlk1, and Ssh3.

overall_design: TRAP-Seq of CeA Drd2 neurons following fear conditioning

first: Kenneth

last: McCullough

first: Kerry

last: Ressler


title: Free glycans derived from O-mannosylated glycoproteins suggest the presence of an O-glycoprotein degradation pathway in yeast

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

summary: In eukaryotic cells, unconjugated oligosaccharides structurally related to N-glycans (FNGs) are generated either from misfolded N-glycoproteins destined for endoplasmic reticulum (ER)-associated degradation (ERAD), or from lipid-linked oligosaccharides, donor substrates for N-glycosylation of proteins. The mechanism responsible for the generation of FNGs is now well understood, but whether there are other type of free glycans remain unclarified. Here, we report on the accumulation of O-mannosylated free glycans in budding yeast that were cultured in media containing mannose as a carbon source. A structural analysis of these glycans revealed that their structures are identical to those of O-mannosyl glycans that are attached to glycoproteins. Deletion of the cyc8 gene, encoding a general transcription repressor, resulted in the accumulation of excessive amounts of the free O-glycans, concomitant with a severe growth defect, a reduction in the level of cellular O-mannosylated proteins, and compromised cell wall integrity. Our findings provide evidence for a regulated pathway for O-glycoprotein degradation in yeast and offer critical insights into the catabolic mechanisms that control the fate of O-glycosylated proteins.

overall_design: RNA-seq

first: Hiroto

last: Hirayama

first: Tsugiyo

last: Matsuda

first: Yae

last: Tsuchiya

first: Oka

last: Ritsuko

first: Junichi

last: Seino

first: Chengcheng

last: Huang

first: Kazuki

last: Nakajima

first: Yoichi

last: Noda

first: Yuichi

last: Shichino

first: Tadashi

last: Suzuki


title: Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinson’s Disease in Mouse Midbrain

city: Grand Rapids

first: Alison

middle: I

last: Bernstein

state: MI

address: 400 Monroe Ave NW

department: Translational Neuroscience

institute: Michigan State University

summary: Human and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson’s disease (PD). Despite previous work showing a link between developmental dieldrin exposure and increased neuronal susceptibility to MPTP toxicity in male C57BL/6 mice, the mechanism mediating this effect has not been identified. Here, we tested the hypothesis that developmental exposure to dieldrin increases neuronal susceptibility via genome-wide changes in DNA methylation. Starting at 8 weeks of age and prior to mating, female C57BL/6 mice were exposed to 0.3 mg/kg dieldrin by feeding (every 3 days) throughout breeding, gestation, and lactation. At 12 weeks of age, pups were sacrificed and midbrains were dissected. DNA was isolated and dieldrin-related changes in DNA methylation were assessed via reduced representation bisulfite sequencing (RRBS). We identified significant, sex-specific differentially methylated CpGs (DMCs) and regions (DMRs) by developmental dieldrin exposure (FDR<0.05), including DMCs at the Nr4a2 and Lmx1b genes, which are involved in dopaminergic neuron development and maintenance. Developmental dieldrin exposure had distinct effects on the male and female epigenome. Furthermore, a separate set of changes in DNA methylation was identified after adult exposure to dieldrin, suggesting that adult and developmental dieldrin toxicity may not act through a shared epigenetic mechanism. Together, our data suggest that developmental dieldrin exposure establishes sex-specific poised epigenetic states early in life. These poised epigenomes may mediate sensitivity to additional environmental stimuli and contribute to the development of late-life neurodegenerative disease, including PD.

overall_design: RRBS data for developmental exposure: control (n=12; male n=6, female n=6) vs. dieldrin treatment (0.3 mg/kg) (n=12; male n=6, female n=6). RNA-seq data for developmental exposure: control (n=12; male n=6, female n=6) vs. dieldrin treatment (0.3 mg/kg) (n=12; male n=6, female n=6). RRBS data for adult exposure: control (n=5; only male) vs. dieldrin treatment (0.3 mg/kg) (n=5; only male).

first: Joseph

last: Kochmanski

first: Sarah

last: VanOeveren


title: Dissecting the miRNome of psoriatic keratinocytes

city: Stockholm

first: Ankit

last: Srivastava

state: - Select a State -

address: CMM L8:02

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

summary:
Purpose: The purpose of this study was to identify the miRNome of keratinocytes in psoriasis
Method: We performed next-generation sequencing for small RNAs from the RNA samples obtained from keratinocytes from psoriasis lesional, non-lesional and healthy skin. Next, we removed adapters and the low quality tags from the sequencing data and clean reads were mapped and aligned to known miRNAs sequences (miRBase 21). Novel miRNA transcripts were predicted based on the length (22-25 nucleotide) and secondary structure (precursor analysis) using MIREAP and mapped to the human genome. Data were normalized (transcripts per million, TPM) and analysed using Bioconductor-EdgeR. Group comparisons (lesional vs. healthy, lesional vs. non lesional and non-lesional vs. healthy) were performed. MiRNAs with <10% FDR, fold change >1.4 (1 TPM at least in one of the groups and expressed in half of the samples in any group) were considered statistically significant.
Results: Robust expression of 411 known and 30 novel miRNAs (TPM > 1 in >50% of the samples in at least one of the groups) was detected in our samples. Using EdgeR we identified 104 miRNAs with significantly altered level (fold change > 1.4, FDR < 0.1) between healthy and psoriatic keratinocytes (P vs H). While, pair-wise comparison of miRNA expression in keratinocytes from non-lesional and lesional psoriasis skin (P vs. N) identified 87 deregulated miRNAs. Comparison of the miRNome of keratinocytes from non-lesional skin of psoriasis patients to healthy keratinocytes (N vs. H) identified 7 differentially expressed miRNAs.
Conclusion: Here, for the first time we show the keratinocyte miRNome in psoriasis which may serve as the basis for future functional studies of miRNAs deregulated in keratinocytes in psoriasis.

overall_design: Keratinocytes were sorted from epidermal cell population of healthy, psoriasis lesional and non-lesional skin and small RNA sequencing was performed.

first: Florian

last: Meisgen

first: Andor

last: Pivarcsi

first: Enikö

last: Sonkoly


title: ChIP-seq of MOZ (Flag-V5-BIO tagged) in mouse mouse craniofacial development

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Carboxy-terminally tagged MOZ (Flag-V5-BIO tagged) was detected by ChIP-seq using anti-V5 antibody (Sigma, A7345) to precipitate chromatin associated with MOZ

overall_design: A Flag-V5-BIO triple tag was added in frame to the carboxy-terminus of the Moz locus by BAC by recombineering in E. coli. The construct was used to generate homologously recombined mouse embryonic stem cells, chimeras and mice that carry the Flag-V5-BIO tag in the Moz locus. Mice homozygous for a null mutation of Moz die between embryonic day 14.5 (E14.5) and birth. Mice homozygous fo the Moz-Flag-V5-BIO allele are viable, healthy and fertile showing that the MOZ-Flag-V5-BIO protein functions normally. The first the second pharyngeal arches of E10.5 embryos homozygous for the Moz-Flag-V5-BIO allele as well as wild-type control pharyngeal arches (negative control) were used for anti-V5 chromatin immunoprecipitation to detect the distribution of tagged MOZ in the mouse genome.

first: Hannah

last: Vanyai

first: Anne

last: Voss

middle: L

first: Gordon

last: Smyth


title: RNA Seq of Fmr1 NPC nuclear fractions

city: Pasadena

first: Brittany

middle: Megan

last: Edens

address: 1200 E California Blvd

institute: Caltech

summary: N6-methyladenosine (m6A) modification of mRNA is emerging as a vital mechanism regulating RNA function.  Here, we show that fragile X mental retardation protein (FMRP), an RNA-binding protein, reads m6A to regulate nuclear export of methylated mRNA targets during neural stem cell differentiation.  In Fmr1 KO mice neural progenitors show delayed cell cycle exit and differentiation, resulting in their progressive accumulation in the ventricular and subventricular zones.  RNA-seq of neural precursor cells (NPCs) from Fmr1 KO mice and m6A-seq uncovered nuclear retention of m6A-modified FMRP target mRNAs involved in regulating neural differentiation, including components of Notch and Hedgehog signaling pathways.  Analysis of NPCs from Mettl14 cKO mice, which are devoid of m6A, revealed that methylation of RNAs promotes their nuclear export through CRM1.  Altogether, our findings suggest that FMRP reads and facilitates nuclear export of m6A-modified mRNAs to regulate neural stem cell differentiation, contributing to Fragile X syndrome.

overall_design: Comparison of nuclear RNAs from WT and Fmr1 KO NPCs from three independent lines

first: Yongchao

last: Ma


title: Genome-wide maps of chromatin state in murine Müller glia

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

institute: University of Miami Miller School of Medicine

summary: We investigated the epigenetic plasticity of adult (postnatal day (P) 28) murine Müller glia using ChIP-seq analysis.

overall_design: To characterize the epigenetic states of the adult Müller glia, we isolated Glast+ cells from P28 retinas (Glast/Slc1a3 is a marker of Müller glia precursors and Müller glia in the retina). To study genome-wide histone modifications in Müller glia, we chose four histone marks: H3K4me3, H3K4me1, H3K27me3, and H3K9me3.


title: Inhibition of LINC00052  in MCF-7

city: México

first: Vilma

middle: Araceli

last: Maldonado

state: Distrito Federal

address: Periferico  4809

department: Investigacion

country: Mexico

institute: INMEGEN

summary: Changes in the transcriptome due to the inhibition of linc00052 in mcf7 cells stably transfected with a sihRNA

overall_design: MCF-7 were stably transfected with a shlinc00052, the selection was made using puromycin por 14 days at concentration 0.6 ug/ml. MCF-7 transfected with shRNALUC were used as control cell.

first: José

last: Sánchez-López

first: Floria

last: Lizarraga


title: Development and epigenetic plasticity of murine Müller glia

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

overall_design: Refer to individual Series


title: RNA-seq analysis of the effects of single and compound deletion of Moz (Kat6a) and/or Dlx5 during mouse craniofacial development

summary: The purpose of these data is to investigate the genetic perturbations which underlie the cleft palate phenotype in Kat6a and Dlx5 mutant mouse embryos. The palate develops from the maxillary portion of the first pharyngeal arches, commencing between E10.5 and E11.5 of mouse gestation.

overall_design: The pharyngeal arches were taken from E10.5 female mouse embryos for each of the following genotypes: wild type (WT), Kat6a heterozygous knockout (KO), Dlx5 heterozygous KO, Kat6a and Dlx5 heterozygous KO, Dlx5 homozygous KO, Kat6a homozygous KO. There are four biological replicates for each genotype, giving a total of 24 samples. Batch effects, which were corrected for, arose from samples being derived from two different mouse facilities.


title: Smoking-associated DNA methylation features link to HIV outcomes [HumanMethylation450 BeadChip]

city: New Haven

first: Ke

last: Xu

state: CT

institute: Yale University

summary: Smoking is common in people who live with HIV infection and has significant adverse effects on HIV outcomes. The impacts of smoking on methylome has been well established in non-HIV populations. However, the smoking’s effects on host methylome in HIV-positive population has not been investigated and it is unknown if smoking-associated DNA methylation link to HIV outcomes. In this study, we applied machine learning methods selected smoking-associated DNA methylation features to predict HIV related frailty and mortality.

overall_design:
We have collected blood samples from the Veteran Aging Cohort Study (VACS). Smoking status was based on self -report. HIV frailty was measured by VACS index. All DNA samples were extracted from whole blood in HIV-positive men. Epigenome-wide DNA methylation of each sample was profiled using the Illumina Infinium HumanMethylation450 BeadChip array. Data were normalized and controlled for quality using standard techniques.

Please note that the 'readme.txt' contains a brief description for each sample characteristics.
The following data is included in each sample records (as characteristics) and in the 'PCA_analysis_results.txt' file:
Cont_Pr_850k_PC1-PC30 PCA analysis results (PC1 to PC30) on positive control intensities
resi_850k_PC1-PC5 PCA analysis results (PC1 to PC5) on residual values of the first regression model

first: Xinyu

last: Zhang

first: Amy

last: Justice


title: Smoking-associated DNA methylation features link to HIV outcomes [Infinium MethylationEPIC]


title: Targeting NSD2 in mouse prostate cancer cells

city: Hospitalet de Llobregat

first: Alvaro

last: Aytes

state: Catalonia

address: Granvia 199

department: ProCURE

country: Spain

institute: IDIBELL

summary: Transcriptome analysis of mouse prostate cancer cell line (NPK) silenced for Nsd2 using shRNA or treated with MCTP--39. NPK prostatre cancer cells are derived Nkx3.1CreERT2/+ ;Ptenflox/flox;KrasLSL-G12D/+ mice, and were used to silence the histone methyltransferase NSD2 or treat them with the NSD2 inhibitor MCTP39 for subsequent gene expression profiling by RNAseq

overall_design: Total RNA obtained from NPK mouse prostate cancer cells. Prostate cells were harvested and processed for RNA isolation and transcriptome analysis using the MagMAX RNA isolation kit (Ambion).

first: Katia

last: Ruggero


title: Smoking-associated DNA methylation features link to HIV outcomes


title: Distribution of MOZ (KAT6A) in the genome and effects of MOZ on gene expression during mouse craniofacial development

status: Public on Jul 22 2019


title: Evidence That Three Classes of Methylomes Specific for Stem, Somatic and Transformed Cells Are Set by Three Independent Mechanisms

first: Boris

last: Bartholdy

department: Cell Biology


title: Age and Sex Influence the Hippocampal Response and Recovery Following Sepsis

city: Gainesville

first: Tom

last: Foster

address: 1149 Newell Drive

institute: University of Florida

summary: Although in-hospital mortality rates for sepsis have decreased, survivors often experience lasting physical and cognitive deficits. Moreover, older adults are more vulnerable to long-term complications associated with sepsis. We employed a murine model to examine the influence of age and sex on the brain’s response and recovery following sepsis. Young (~4 months) and old (~20 months) mice (C57BL/6) of both sexes underwent cecal ligation and puncture (CLP) with restraint stress. The hippocampal transcriptome was examined in age and sex-matched controls at 1 and 4 days post-CLP. In general, immune and stress-related genes increased while neuronal, synaptic, and glial genes decreased one day after CLP-induced sepsis. However, specific age and sex differences were observed for the initial responsiveness to sepsis as well as the rate of recovery examined on day 4. Young females exhibited a muted transcriptional response relative to young males and old females. Old females exhibited a robust shift in gene transcription on day 1 and, while most genes recovered, genes linked to neurogenesis and myelination continued to be downregulated by day 4. In contrast, old males exhibited a more delayed or prolonged response to sepsis, such that neuronal and synaptic genes continued to decrease while immune response genes continued to increase on day 4. These results suggest that aging is associated with delayed recovery from sepsis, which is particularly evident in males.

overall_design: This study was conducted on 47 mice either 24 hours or 4 days after sepsis [young male control (n = 4), young male 24 hours post-sepsis (n = 4), young male 4 days post-sepsis (n = 4), old male control (n = 4), old male 24 hours post-sepsis (n = 4), old male 4 days post-sepsis (n = 4), young female control (n = 4), young female 24 hours post-sepsis (n = 4), young female 4 days post-sepsis (n = 4), old female control (n = 4), old female 24 hours post-sepsis (n = 4), and old female 4 days post-sepsis (n = 3)]. Hippocampal mRNA was used to investigate how sepsis altered the response in the brain within different age and sex groups.

first: Jolie

last: Barter

first: Ashok

last: Kumar

first: Julie

last: Stortz

first: McKenzie

last: Hollen

first: Dina

last: Nacionales

first: Philip

last: Efron

first: Lyle

last: Moldawer

first: Thomas

middle: C


title: Evidence That Three Classes of Methylomes Specific for Stem, Somatic and Transformed Cells Are Set by Three Independent Mechanisms (RNA-Seq)

summary: Whole genome-bisulfite sequencing has revealed that methylomes differ dramatically in a cell type-specific manner. However, the global mechanisms of maintenance of DNA methylation patterns and their functional consequences are not clear. Using a combination of novel haplotype-resolved methylomes and publicly available data, we show that three distinct classes of methylomes that differ by the proportion of partially and highly methylated domains are characteristic of stem and progenitor, somatic and transformed cells. We provide evidence that three mechanisms can account for most of the differences between these three classes of methylomes. The first, protection of promoters and cis-acting regulatory elements from DNA methylation by DNA-binding proteins, keeps regulatory elements unmethylated. The second, DNA replication-associated maintenance of DNA methylation, is highly efficient in stem cells, moderately efficient in somatic cells, and very inefficient in transformed cells, and sets variable basal levels of methylation characteristic of the partially methylated domains of each cell type. The third, transcriptional elongation-associated gene-body DNA methylation is responsible for the formation of highly methylated domains in somatic and transformed cells. We show that partitioning of the genome into partially and highly methylated domains is associated with different mechanisms of gene silencing.

overall_design: A transcriptome analysis was performed  on self-generated data from basophilic erythroblasts (“BasoE”, as described in detail below, with raw data files included), as well as from previously published cell lines and primary tissues (only processed data included here): IMR90, H1 hESC, HepG2, K562, hematopoietic stem/progenitor cells (HSPC), and pancreas. ENCODE raw sequencing data was retrieved from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/ for replicates of paired-end data, i.e. for IMR90 cells: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqImr90CellPapFastqRd1Rep1.fastq.gz, http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqImr90CellPapFastqRd1Rep2.fastq.gz, http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqImr90CellPapFastqRd2Rep1.fastq.gz, http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqImr90CellPapFastqRd2Rep2.fastq.gz, for H1 hESC: wgEncodeCshlLongRnaSeqH1hescCellPapFastqRd1Rep1.fastq.gz, wgEncodeCshlLongRnaSeqH1hescCellPapFastqRd1Rep2.fastq.gz, wgEncodeCshlLongRnaSeqH1hescCellPapFastqRd2Rep1.fastq.gz, wgEncodeCshlLongRnaSeqH1hescCellPapFastqRd2Rep2.fastq.gz, for HepG2: wgEncodeCshlLongRnaSeqHepg2CellPapFastqRd1Rep1.fastq.gz, wgEncodeCshlLongRnaSeqHepg2CellPapFastqRd1Rep2.fastq.gz, wgEncodeCshlLongRnaSeqHepg2CellPapFastqRd2Rep1.fastq.gz, wgEncodeCshlLongRnaSeqHepg2CellPapFastqRd2Rep2.fastq.gz, for K562: wgEncodeCshlLongRnaSeqK562CellPapFastqRd1Rep1.fastq.gz, wgEncodeCshlLongRnaSeqK562CellPapFastqRd1Rep2.fastq.gz, wgEncodeCshlLongRnaSeqK562CellPapFastqRd2Rep1.fastq.gz, wgEncodeCshlLongRnaSeqK562CellPapFastqRd2Rep2.fastq.gz. RNA-seq from HSPC was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM909310 (SRX135562), and RNA-seq from pancreas was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1120309 (SRX263865).

first: Julien

last: Lajugie

first: Rituparna

last: Mukhopadhyay

first: John

last: Greally

first: Masako

last: Suzuki

first: Eric

last: Bouhassira


title: Transcriptional characterization of LV of Nppb KO

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: Expression analysis of LV in Nppb KO

overall_design: RNA-seq on left ventricle of 8-12 wks old mice

first: Joyce

last: Man


title: A cell-free system to study the damage response at unprotected DNA ends in Drosophila

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: We discovered that the cell-free chromatin assembly system senses free DNA ends and mounts a DNA double-strand break response. DNA ends are first recognized by the Ku complex and later resected. The phosphorylation of H2A.V (homologous to gH2A.X) initiates at DNA breaks and spreads over ten thousands of base pairs of DNA within a few minutes. The phosphorylation of gH2A.V remains tightly associated with the damaged DNA in cis and does not transfer to intact DNA circles in the same reaction. Our descriptions of the damage-related proteome and phospho-proteome provide a rich resource for in-depth mechanistic analyses of the DNA chromosome break response in this model system.

overall_design: ChIP-seq experiments on cell-free chromatin assembly system under DNA damage conditions comparing 3 different restriction enzymes in 5 time points.

first: Lisa

last: Harpprecht

first: Sandro

last: Baldi

first: Peter

middle: B

last: Becker


title: Evidence That Three Classes of Methylomes Specific for Stem, Somatic and Transformed Cells Are Set by Three Independent Mechanisms (Methyl-Seq)

city: Bronx

first: Boris

last: Bartholdy

institute: Albert Einstein College of Medicine

overall_design: A methylome analysis was performed on self-generated data from basophilic erythroblasts (“BasoE”, as described in detail below, with raw data files included), as well as from previously published cell lines and primary tissues (only processed data included here): Processed methylation calls were downloaded and filtered to include only CpG dinucleotides with at least 10x read coverage on the autosomes for the following cell lines: H1 hESC (from ftp://ftpuser3:s3qu3nc3@neomorph.salk.edu/mc/h1_c_basecalls.tar.gz, based on GSE16256), IMR90 (from ftp://ftpuser3:s3qu3nc3@neomorph.salk.edu/mc/imr90_c_basecalls.tar.gz, based on GSE16256), HepG2 (from https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM1204463&format=file&file=GSM1204463_BiSeq_cpgMethylation_BioSam_1500_HepG2_304072.BiSeq.bed, based on GSM1204463), hematopoietic stem/progenitor cells (HSPC; from http://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/E050_WGBS_FractionalMethylation.bigwig and http://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/ReadCoverage_bigwig/E050_WGBS_ReadCoverage.bigwig, based on GSM916052), ganglionic neurospheres (GNeurosphere, from http://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/E054_WGBS_FractionalMethylation.bigwig and http://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/ReadCoverage_bigwig/E054_WGBS_ReadCoverage.bigwig, based on GSM1127055), pancreas (from http://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/E098_WGBS_FractionalMethylation.bigwig and http://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/ReadCoverage_bigwig/E098_WGBS_ReadCoverage.bigwig, based on GSM983651), and adult liver from http://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/E066_WGBS_FractionalMethylation.bigwig and http://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/ReadCoverage_bigwig/E066_WGBS_ReadCoverage.bigwig, based on GSM1058027). For K562 cells, raw data was retrieved from ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX840/SRX840166/SRR1754892/SRR1754892.sra (GSM1583563) and processed using Bismarck, followed by filtering on HCG loci with at least 10x coverage.

middle: M


title: Gene expression profiling comparing myeloma cell line MM1.144 transduced with a scramble shRNA or an shRNA targeting the non-canonical WNT receptor ROR2

city: Milan

first: Giovanni

last: Tonon

address: Via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

summary: We examined the gene expression profiles resulting from the depletion of the non-canonical WNT receptor ROR2 in myeloma cells

overall_design: Total RNA obtained from MM1.144 cells transduced with a scramble shRNA or an shRNA targeting the non-canonical WNT receptor ROR2, stimulated with WNT3A or WNT5A for 45 minutes or 8 hours.

first: Michela

last: Frenquelli

first: Filippo

last: Martinelli-Boneschi

first: Paola

last: Brambilla


title: Periprostatic fat gene expression in male mouse diet induced obesity and calorie restriction study

city: New York

first: Akanksha

last: Verma

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

summary:
Obesity is associated with an increased incidence of high grade prostate cancer (PC) and worse prognosis for PC patients. Recently, we showed in men that obesity-related periprostatic white adipose tissue (WAT) inflammation, characterized by macrophages surrounding dead or dying adipocytes forming crown-like structures, was associated with high grade PC.  Possibly, interventions that suppress periprostatic WAT inflammation will improve outcomes for men with PC. We found that supplemental 17β-estradiol (E2) could decrease periprostatic WAT inflammation in obese male mice in association with reduction in weight and calorie consumption. Here, we tested the hypothesis that calorie restriction alone would have similar effects on periprostatic WAT inflammation in obese male mice.
To test this hypothesis, male mice were fed high fat diet to induce obesity and then switched to a 30% caloric restriction diet for an addition 7 weeks until sacrifice. LFD fed mice and mice fed HFD ad libitum serve as controls.

overall_design: Male C57BL/6J mice were obtained from The Jackson Laboratory and fed low fat diet (LFD, 10 kcal% fat, 12450Bi; Research Diets) or high fat diet (HFD, 60 kcal% fat, D12492i) beginning at 6 weeks of age. The mice were continued on these diets for a total of 12 weeks. After 12 weeks of feeding, the HFD fed mice were divided into two groups. One group was fed ad libitum for an additional 7 weeks until sacrifice while the other group was switched to a 30% CR feeding regimen for 7 weeks until sacrifice. Each day for 7 weeks the CR group received 70% of the amount consumed by the HFD group that was fed ad libitum. The LFD group was fed ad libitum for an additional 7 weeks until sacrifice. All mice were sacrificed at 25 weeks of age and periprostatic fat was harvested and snap frozen. Total RNA was isolated and analyzed from 6 LFD, 6 HFD ad libitum, and 5 HFD calorie restricted mice and analyzed by microarray.

first: Andrew

last: Dannenberg


title: In utero exposure to diesel exhaust and its effect on placental transcriptional response in rabbit F2 generation

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary:
Atmospheric pollution is a rising concern in urban areas and a major contributor to people’s mortality, with potential intergenerational consequences. Our aim was to evaluate the effects of exposure of pregnant F0 females to diluted diesel exhaust (DE) on feto-placental development in the second generation (F2). These rabbits were exposed to diluted and filtered DE (E: exposed group) or clean air (C: Control group) for 2h/day, 5days/week by nose-only exposure from 3rd to 27th days post-conception (dpc). Not exposed anymore after birth, female offspring (F1) were mated with control males at adulthood. F2 feto-placental units were collected at 28dpc. Fatty acid profiles were determined from fetal and maternal plasma, maternal liver and placenta by gas chromatography. Placental structure was explored by stereology while placental gene expression was analyzed using a dedicated microarray. At 28dpc, maternal F1 biochemistry was not different between groups, although F1 E females exhibited increased content of hepatic neutral lipid. Similarly the content of lipid was higher in F2 E placentas, mostly by monounsaturated fatty acids while arachidonic acid was reduced. The proportion of n-3 polyunsaturated fatty acids (n-3 PUFA) was increased whereas AA decreased in F2 E fetal plasma compared to Controls. No structural change was observed in placentas between groups. GSEA analysis of transcriptomic data revealed that gene involved in proteasome complex and ubiquitin pathways were up-regulated in E placentas when compared to C placentas, whereas those involved in ion channel or inflammation regulations were down-regulated. In conclusion, in utero exposure of F1 females to DE can affect both placental function and fetal metabolism in the second generation (F2). Placental FA profiles suggest adaptive protective mechanisms against inflammation, through placental storage of non-essential FA and the favored transplacental transfer of n-3 PUFA. The fetal physiological consequences of observed alterations in placental genes involved in protein metabolism and intracellular signaling remain to be determined.
In order to evaluate the intergenerational effects to the F2 generation of in utero F1 exposure to DE, we chose the rabbit model because of its hemochorial placenta closer to the human one (Fischer et al 2012; Furukawa, 2014) than those of rodents. The present study follows our recent publication related to the effects of diesel exhaust exposure of rabbit female F0 during gestation on feto-placental development in F1 and F2 generations (Valentino et al., 2016) where we have shown that F2 feto-placental biometry was not disturbed consecutively to the in utero exposure of the F1 generation  (Valentino et al., 2016). Nevertheless, these macroscopically normal fetuses had reduced plasma total cholesterol (-25.9%) and non-HDL cholesterol (-26%) associated with an increase in plasma triglycerides concentrations (+25.9%) compared to F2 control group (Valentino et al., 2016). In the present study, placental function in the second generation was explored at a biochemical and molecular levels in order to understand how the placenta contributed to the fetal dyslipidemia without affecting the biometry.

overall_design: For microarray experiments, total RNAs were extracted from pieces of labyrinthine area randomly collected from each of the litters of the control (n=8 CC) and the exposed (n=8 EC, eight replicates per condition). The microarray analyses were performed using Agilent-042421 Rabbit BDR version 2 [Probe Name Version], custom-commercial with Agilent, using the technology in situ oligonucleotide, for Oryctolagus cuniculus organism, and registered in GEO as Platform GPL18913

first: Sarah

last: Valentino

first: Catherine

last: Archilla

first: Jérôme

last: Lecardonnel

first: Luc

last: Jouneau

first: Anaïs

middle: V

last: Carvalho


title: Mouse Estrogen Treatment Study Analysis of Peri-prostatic Fat

summary: Obesity is associated with an increased incidence of high grade prostate cancer (PC) and worse prognosis for PC patients. Recently, we showed in men that obesity-related periprostatic white adipose tissue (WAT) inflammation, characterized by macrophages surrounding dead or dying adipocytes forming crown-like structures, was associated with high grade PC.  Possibly, interventions that suppress periprostatic WAT inflammation will improve outcomes for men with PC.  Here, we tested the hypothesis that supplemental 17β-estradiol (E2) could decrease periprostatic WAT inflammation in obese male mice.

overall_design: Male C57BL/6J mice were obtained from The Jackson Laboratory and fed low fat diet (LFD, 10 kcal% fat, 12450Bi; Research Diets) or high fat diet (HFD, 60 kcal% fat, D12492i) beginning at 6 weeks of age. The mice were continued on these diets for a total of 12 weeks. After 12 weeks of feeding, the HFD fed mice were divided into two groups. One group of HFD-fed mice received a 0.25mg E2 pellet (60-day continuous release). A second group of HFD-fed mice received a placebo pellet. Pellets were subcutaneously implanted using a 10 gauge trocar. The LFD mice did not receive any implantation and is a control group in this study. All mice continued on their respective diets for an additional 8 weeks until sacrifice at 26 weeks of age. At sacrifice, periprostatic fat was harvested from each mouse and snap frozen. n=5/group from each of 3 groups (total of 15 samples). Total RNA was extracted and quality and concentration were measured. RNA integrity values were >7 in all 15 samples.

first: Priya

last: Bhardwaj

first: Kathy

middle: X

last: Zhou

first: Olivier

last: Elemento


title: Periprostatic fat gene expression in male mouse diet induced obesity study

summary:
Obesity is associated with an increased incidence of high grade prostate cancer (PC) and worse prognosis for PC patients. Recently, we showed in men that obesity-related periprostatic white adipose tissue (WAT) inflammation, characterized by macrophages surrounding dead or dying adipocytes forming crown-like structures, was associated with high grade PC.  Possibly, interventions that suppress periprostatic WAT inflammation will improve outcomes for men with PC. Prior to testing interventions we conducted this study to identify transcriptomic differences in periprostatic fat from lean and obese mice. We hypothesized that periprostatic fat from obese mice would have a proinflammatory signature in gene expression pattern.
To test our hypothesis that obese mice would develop molecular signatures of inflammation in periprostatic fat, we fed mice low fat diet or high fat diet for 12 weeks and then harvested periprostatic fat at sacrifice. RNA was isolated and analyzed from 5 lean and 5 obese mice and analyzed by microarray.

overall_design: Male C57BL/6J mice were obtained from The Jackson Laboratory and fed low fat diet  (10 kcal% fat, 12450Bi; Research Diets), n=4 or high fat diet (60 kcal% fat, D12492i), n=5 beginning at 6 weeks of age. The mice were continued on these diets for a total of 12 weeks before being sacrificed by CO2 asphyxiation at 18 weeks of age.


title: Next Generation Sequencing Facilitates Quantitative Analysis of s.c. tumors from nude mouse allografted by R728T1 (non-SMCs derived from Rb/P53 mouse model) with and without Taz knockdown

city: Shanghai

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

summary: The goals of this study are to compare the different transcriptome signiture between s.c. tumors from nude mouse allografted by R728T1 (non-SMCs derived from Rb/P53 mouse model)with and without Taz knockdown with NGS-derived retinal transcriptome profiling (RNA-seq).

overall_design: Total mRNA profiles of s.c. tumors from nude mouse allografted by R728T1 (non-SMCs derived from Rb/P53 mouse model) with and without Taz knockdown were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000.

first: Yujuan

last: Jin

first: Hongbin

last: Ji


title: Expression Data from Ets1/2 WT, Ets1KO, Ets2KO and Ets1/2 DKO endothelial cells

city: Columbus

first: Michael

last: Ostrowski

state: Ohio

address: 460 W. 12th Avenue, Room - 598

department: Department of Molecular & Cellular Biochemistry

institute: The Ohio State University

summary: Angiogenesis is a highly orchestrated process involving complex crosstalk between several endothelial cell (EC) processes including cell cycle, cell survival and migration. Transcription factors ETS1 and ETS2 are required for EC functions necessary for embryonic angiogenesis. However owing to the lethal nature of the double mutant embryo, the specific gene targets of these factors are yet to be identified. In the current study, we try to elucidate the effect of endothelial cell specific deletion of Ets1 and Ets2 on post natal angiogenesis and characterize the downstream regulatory pathways. Deletion of Ets1 and Ets2, restricted to endothelial cells in new born mice (P1-P3), reduced retinal angiogenesis. Similarly, EC infiltration and invasion into matrigel plugs subsided when matrigel admixed with mouse mammary tumor cells was injected into adult mice with inactivated Ets1 and Ets2 specifically in ECs. Expression of key cell cycle and cell survival regulators were diminished in double mutant cells as compared to controls. In addition, both these factors were found to occupy the enhancer regions of the target genes. Deletion of Ets1 and Ets2 in cultured aortic EC resulted in altered cell cycle phases with a G2/M phase arrest and increased sensitivity to apoptosis in vitro. These results demonstrate that deletion of Ets1 and Ets2 in endothelial cells inhibits angiogenesis by altering cell cycle progression and decreasing cell survival.

overall_design: Endothelial cells were infected with lentiviral-egfp to generate Ets1/2 WT, Ets1KO, Ets2KO and Ets1/2 DKO endothelial cells, cultured, RNA was extracted and Affymetrix gene expression arrays were performed.

first: Sankha

last: Ghosh


title: Spatiotemporal pattern of the transcriptional regulatory landscape of the mouse ventricle after myocardial infarction

first: Vincent

last: Christoffels

summary: Stress-response gene activity replaces cardiomyocyte lineage-specific program in a transcriptionally discrete infarct border zone

overall_design: RNA-seq & ATAC-seq on left ventricular remote and border zone tissues at 3, 7 and 14 days after myocardial infarction

first: Karel

last: van Duijvenboden

first: Rob

last: Janssen


title: Heterozygous p53-R280T mutation promotes proliferation of NPC cells through activating PI3K/Akt signaling pathway

status: Public on Jul 21 2019

city: Changsha

first: zhenqi

last: qin

address: 87 Xiangya Road

institute: Xiangya Hospital, Central South University

summary: Heterozygous p53-R280T mutations frequently occur in many nasopharyngeal carcinoma cell lines and nasopharyngeal carcinoma patients. However, the role of this mutation in the progression of nasopharyngeal carcinoma remains unclear. In this study, we successfully generated the tp53 knockout nasopharyngeal carcinoma (NPC) cells by CRISPR/Cas9-mediated genome editing and found that knockout of heterozygous tp53-R280T inhibited the proliferation of NPC cells significantly in vivo and in vitro. Mechanistic analyses indicated that heterozygous p53-R280T can activate the PI3K/Akt Signaling pathway in NPC cells. In conclusion, our findings provide a mechanistic insight into the role of heterozygous p53-R280T in NPC progression.

overall_design: mRNA profiles of  CNE2 (control) and KO CNE2 cells.

first: Zhenqi

last: Qin

first: Qiguang

last: Li

first: Zhiqiang

last: Xiao


title: Effects of hydroquinone on whole-genome scale transcription of human epidermal keratinocytes.

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

summary: Hydroquinone (HQ) is a well-known phenolic compound that causes chemical leukoderma. Hydroquinone was once used as photographic developers for films and papers, and it is widely used as a topical application in skin whitening to reduce the color of skin. Recently, the United States Food and Drug Administration (US FDA) banned all over-the-counter products with hydroquinone due to its potential toxicity. Topical cream with hydroquinone up to 4% should be prescribed and used with specific caution. In this study, to elucidate the toxicological role of keratinocyte in the pathogenesis of chemical leukoderma, we analyzed genome-wide transcriptional data of cultured human epidermal keratinocytes (HEKs) treated with sub-cytotoxic hydroquinone concentration.

overall_design: Human Epidermal Keratinocytes (HEKs) were treated with 10 microM of hydroquinone for 24 hours and harvested for total RNA extraction and hybridization on Affymetrix Human GeneChip 133 2.0 microarrays.


title: Circular RNA Expression Profiles in the Plasma from Patients with Heart Failure

status: Public on Jul 20 2019

city: Yantai

first: yeying

last: sun

address: No.346 Guanhai road

institute: Binzhou Medical Univeristy

summary: To identify the circRNA expression profiles in HF patients’ plasma and to evaluate the potential application of circRNAs for HF diagnosis, circRNA microarrays were performed on plasma samples obtained from HF patients and healthy controls. The RNAs of the plasma from the HF and control groups were extracted for microarray analysis. The purified RNAs were hybridized to a microarray (Agilent human circRNA Array V2.0) containing 170,340 human circRNA probes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to validate the results.

overall_design: Peripheral blood samples were collected from three HF patients and three control groups into blood collection tubes containing 85 mM trisodium citrate, 78 mM citric acid, and 111 mM glucose. The whole blood was centrifuged at 2000 × g for 10 min at 22 °C to obtain plasma. Plasma was transferred to a new tube and stored at –80 °C in aliquots.

first: Yeying

last: Sun

first: Xiaoli

last: Jiang


title: Characterization of the DNA methylome in murine Müller glia

first: Dmitry

last: Ivanov

summary: We investigated the epigenetic plasticity of adult (postnatal day (P) 28) murine Müller glia using whole-genome bisulfite sequencing (WGBS)

overall_design: To study DNA methylation in the adult Müller glia, we isolated Glast+ cells from P28 retinas (Glast/Slc1a3 is a marker of Müller glia precursors and Müller glia in the retina). Two WGBS libraries were prepared using DNA from two independent samples containing 150,000–200,000 cells. The WGBS libraries were sequenced and bisulfite sequence reads were aligned using the Bismark software package. Global methylation level in adult mouse Müller glia was measured and percentages of methylation of CpG, CHG, and CHH contexts (where H is A, C or T) were identified.


title: Characterization of Human Pegivirus Infection in Liver Transplantation Recipients

status: Public on Jul 28 2019

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Approximately 2% of heathy persons are infected with human pegivirus (HPgV). HPgV is transmitted via vertical, sexual, and blood-borne routes. Recently, the association of HPgV infection with the risk of lymphoma was reported. We examined the prevalence of chronic HPgV infection in liver transplantation (LT) recipients and hepatectomy patients and the influence of HPgV infection after LT on clinical and perioperative factors. We enrolled 313 LT recipients and 187 hepatectomy patients who received care at the Kyusyu University Hospital between May 1997 and September 2017. Total RNA was extracted from peripheral blood samples of patients/recipients collected postoperatively. HPgV RNA was measured using real-time polymerase chain reaction (RT-PCR). Of the 313 recipients and 187 patients enrolled in this study, 44 recipients (14.1%) and two patients (1.1%) had HPgV viremia. There was no significant association between HPgV infection and LT outcomes. Interestingly, one recipient was infected with HPgV during the peritransplant period, which was likely transmitted via blood transfusion as HPgV RNA was detected from the blood bag transfused to the recipient during LT. Additionally, HPgV infection induced the upregulation of interferon stimulated gene (ISG) expression in peripheral blood mononuclear cells (PBMCs). LT recipients had higher HPgV viremia compared to hepatectomy patients. Although HPgV infection was not associated with LT-related outcomes, it induced ISG expression in recipients.

overall_design: We examined interferon stimulated gene (ISG) expression in HPgV-positive or negative peripheral blood mononuclear cells (PBMCs) via RNA sequencing analysis.

first: Takuma

last: Izumi

first: Takasuke

last: Fukuhara


title: Quantitative analysis of bi-modal binding of BET proteins at promoters predicts I-BET sensitivity

city: Beirut

first: Pierre

last: Khoueiry

address: Bliss street

department: Biochemistry and Molecular Genetics

country: Lebanon

institute: American University of Beirut

summary: We identified a chromatin displacement signature for the bromodomain proteins BRD2, BRD3 and BRD4 at TSS following treatment with I-BET152, an inhibitor of BET proteins. By integrating ChIP-seq, RNA-seq and Chem-seq data, we correlated alteration of the BRD4 signature at TSS with strong downregulation of gene expression which will facilitate identification of markers of sensitivity and resistance to drug.

overall_design: Examination of drug effect on chromatin bound proteins of sensitive and resitant cell lines

first: Paola

last: Grandi

first: Aoife

last: Gahlawat


title: Mitigating antagonism between transcription and proliferation allows near-deterministic cellular reprogramming (iMN)

city: Cambridge

first: Kate

middle: E

last: Galloway

department: Chemical Engineering

institute: Massachusetts Institute of Technology

summary: RNA sequencing analysis of Hb9::GFP mouse embryonic fibroblasts infected with control or reprogramming transcription factors at 4 dpi, and Hb9::GFP+ mouse induced motor neurons generated using transcription factor overexpression. The goal of this study is to examine the transcriptional path of reprogramming cells to identify molecular mechanisms and populations of highly efficient reprogramming.

overall_design:
Transcriptional profiling of cells during the process of direct reprogramming of mouse embryonic fibroblasts to induced motor neurons (iMNs) and at the terminal stage at 17 dpi. Samples include Hb9::GFP+ sorted iMNs generated with  six factors (6F), 6FDD (e.g. 6F with p53DD), or 6FDDRR (6F with p53DD, hRASG12V, RepSox) as well as MEFs and samples at 4 dpi in conversion for 6F and 6FDDRR for both bulk and CFSE-low populations.
The 6F are Ascl1, Brn2, Myt1l, Ngn2, Isl1, Lhx3.

first: Justin

last: Ichida


title: Functional role and interactions of a recalcitrant to cultivation Sphingomonas degrading the persistent thiabendazole in the context of a microbial enrichment

city: Larissa

first: Sotirios

last: Vasileiadis

email: vasiliad@gmail.com, sovaileiadis@uth.gr

address: Viopolis

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

summary: Thiabendazole (TBZ), a benzimidazole used against postharvest fungal growth and as anthelmintic in livestock farming, is highly persistent in soil (DT50> 1-2 years) and therefore challenging concerning its environmental management. In our recent copious attempts to isolate organisms that degrade TBZ, at best, we ended up with a soil microbial enrichment capable of accelerated TBZ degradation. Here, we employed a multi-omic approach combined with DNA stable isotope probing (SIP) for elucidating the underlying system complexity. We obtained 18 high-quality metagenome-assembled genomes, with six being dominant and versatile concerning their putative xenobiotics degradation ability. SIP combined with microbiome analysis verified our previous results about the key role of a Sphingomonas strain in TBZ degradation. Next to this, metabolomics suggested minimal/no cross-feeding events, and Sphingomonas being the sole TBZ degrader. RNA sequencing and proteomics analysis of the consortium using TBZ or succinate as sole carbon sources showed the enhanced expression in Sphingomonas of a carbazole dioxygenase locus with putative role in the TBZ degradation. Gene expression networking analysis suggested the interaction of Sphingomonas with a Hydrogenophaga strain that possibly contributes to the overall cobalamin balance. Our study depicts the need for integrated omic approaches for understanding complex interactions frequently occurring in bioremediation.

overall_design: Two different carbon sources (thiabendazole vs succinate) in otherwise minimal salts medium cultures, in three different timepoints along the thiabendazole degradation

first: Dimitrios

middle: G

last: Karpouzas

first: Chiara

last: Perruchon


title: WISP2/CCN5 is  a prognostic biomarker influenced by tumour purity and fibroblast infiltration in hepatocellular carcinoma

city: Xi 'an

first: Xia

last: Liao

state: Shaanxi

address: 277# West Yanta Road

country: China

institute: Department of nutrition

summary: Background Hepatocellular carcinoma (HCC) is the second leading cause of cancer death worldwide. The dismal outcome is attributable to high frequency of recurrence and metastasis. Therefore, identification of effective biomarkers is a key strategy to inform prognosis and improve survival of HCC patients  Methods We analysed expression of WNT-1-induced signalling protein-2 (WISP2) and the prognostic correlation in HCC patients using Oncomine, Kaplan Meier plotter, and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) . We explored the role of WISP2 in HCC using the Cancer Cell Line Encyclopedia (CCLE) and gene microarrays and then assessed the correlation between WISP2 and stromal cells in tumour tissues using the Tumor IMmune Estimation Resource (TIMER). Finally, the role of WISP2 and its relationship with tumour purity and fibroblast infiltration were examined both in vitro and in vivo.  Results WISP2 was downregulated in HCC tissues, and high expression of WISP2 was associated with better prognosis in patients with certain clinicopathologic  characteristics. Upregulation of WISP2 in HCC was related to inhibition of the malignant phenotype in vitro, but these alterations were not observed in vivo . WISP2 also negatively correlated with tumour purity, and increased infiltration of fibroblasts promoted malignant progression in HCC tissues. The enhanced infiltration ability of fibroblasts was related to upregulated high-mobility group protein 1 (HMGB1) after overexpression of WISP2 in HCC.  Conclusions The findings shed light on the anticancer role of WISP2 in HCC, suggest that WISP2 overexpression may serve as a biomarker for better prognosis, and indicate that WISP2 expression is influenced by tumour purity and fibroblast infiltration.

overall_design: In the present study, we comprehensively analysed WISP2 expression in various cancer types and explored the correlation between expression and prognosis in HCC patients, using available databases. We also explored the role of WISP2 in HCC and examined the correlation between WISP2 and stromal cells in tumour tissues using the Tumor IMmune Estimation Resource (TIMER). Moreover, the relationship between WISP2 and fibroblasts was verified in vitro and in vivo. Our studies revealed an anticancer role for WISP2 in HCC and suggested that WISP2 expression serves as a prognostic biomarker influenced by tumour purity and fibroblast infiltration.

first: Yang

last: Bu

first: Fengan

last: Jia

first: Fan

last: Chang

first: Xuelian

last: Xiao

first: Mei

last: Zhang

first: Pengbo

last: Ning

first: Qingan


title: RNA-Seq profiling of BIN1 knock-out mouse microglia cells

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

country: USA

institute: BiogenIdec, Inc.

summary: Experimental Questions:  Does knocking out BIN1 have an effect on gene expression in microglia cells?   Does BIN1 expression have a different effect in males vs. females?

overall_design: Thirty samples were analyzed, with 4 to 6 replicates per group. Male and Females for BIN1_WT, BIN1_Het, and BIN1_Homo mice.

first: Andrea

last: Crotti

first: Hameetha

middle: R

last: Sait

first: Kathleen

last: McAvoy

first: Karol

last: Estrada

first: Ayla

last: Ergun

first: Galina

last: Marsh

first: Luke

last: Jandreski

first: Michael

last: Peterson

first: Taylor

last: Reynolds

first: Isin

last: Dalkilic-Liddle

first: Andrew

last: Cameron

first: Ellen

last: Cahir-McFarland

first: Richard

last: Ransohoff


title: Hes1 is Associated with Long Non-Coding RNAs in Colorectal Cancer

city: Rochester

first: Fei

last: Gao

address: 200 1st St SW

institute: Mayo Clinic

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

overall_design: Refer to individual Series


title: RNA-binding protein immunoprecipitation (RIP)and RNA sequencing

summary: We report the result of lncRNAs binding to Hes1 in colon cancer SW480 cells using Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore, MD, USA) following the manufacturer's instructions, the RNAs were analyzed by Illumina HiSeq 2500 Sequencing.

overall_design: Examination of RNAs/lncRNAs binding to Hes1 in human colon cancer SW480 cells

first: Yuqin

last: Zhang


title: High Throughput, Efficacious Gene Editing & Genome Surveillance in Chinese Hamster Ovary Cells

city: Kenilworth

first: Amit

last: Kumar

state: NJ

address: 2000 Galloping Hill Rd

institute: Merck & Co., Inc.

summary:
Purpose: Chinese hamster ovary (CHO) cells are a common tool utilized in bioproduction and directed genome engineering of CHO cells is of great interest to enhance recombinant cell lines. Until recently, this focus has been challenged by a lack of efficacious, high throughput, and low-cost gene editing modalities and screening methods. In this work, we demonstrate an improved method for gene editing in CHO cells using CRISPR RNPs and characterize the endpoints of Cas9 and ZFN mediated genetic engineering.
Methods: Amplicons were first assayed for quality using an Invitrogen Quant-iT dsDNA (Thermo, Cat Q33120) assay and gel electrophoresis to determine DNA concentration and DNA quality. Samples were then used for Sanger sequence based decomposition or processed downstream using NGS. For NGS,  libraries were generated using the Illumina TruSeq Nano DNA kit (Illumina, Cat: 20015964). The libraries were sequenced using the Illumina MiSeq platform, with read length of 2x150bp. 4.5Gb of sequencing data was generated per DNA sample.
Results: There was a tendency for decomposition to underestimate editing as compared to NGS as the indel size became larger. Despite these results, sequence decomposition was able to reproduce next-generation data in the context of gene editing efficiency across a short amplicon.
Conclusions: We took advantage of the differential Indel spectrums induced by both ZFN and CRISPR to validate metrics for assess gene editing and show how deconvolution-based methods, can be utilized in the context of cell line development.

overall_design: Amplicons from ZFN or CRISPR modified cell pools were analyzed 48-72 hours after transfection. The cells were lysed, amplified by PCR, and the amplicons were sequenced. For clones, cells were FACs sorted and allowed to grow for approximately 14 days. The clones were then analyzed using the method described above.

first: Steven

last: Huhn


title: Effects of small molecules targeting the androgen receptor DNA-binding domain on prostate cancer cell transcriptome

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

summary: Prostate cancer is a leading cause of cancer related death among men. Current Androgen Receptor (AR) antagonists often target the ligand binding domain (LBD). However, occurrence of resistance to drugs targeting the LBD is common due to emergence of mutations in the LBD or constitutively active variants that lack the LBD itself.  Two novel small molecules, VPC-17005 and VPC-14449 targeting the DNA-binding domain have been developed and published previously. In this study, LNCaP cells were treated with one of these drugs or the well-established AR antagonist Enzalutamide, and the transcriptomic changes have been determined using RNA-seq analysis.

overall_design: Polyadenylated RNA profiles of LNCaP cells treated with treated with dihydrotestosterone (DHT) plus either DMSO (Control), Enzalutamide, VPC-17005, or VPC-14449, in three biological replicates, obtained using BGISeq500 platform.

first: Ayse

middle: D

first: Nathan

middle: A

last: Lack


title: Using RNAseq for identifying hepatic genes involved in the response to chronic endocrine disruptor exposure in Xenopus tropicalis.

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

institute: Grenoble-Alpes University

summary: Xenopus tropicallis were exposed from seven-days-aged tadpoles to adult stage (one year) to benzo[a]pyrene, triclosan or a mixture of the two compounds at a weekly average concentration of 50 ng.L-1. After 12 months of exposure, 4 females by exposure conditions were used for studying liver transcriptome by RNAseq. RNA-seq libraries were sequenced on an illumina GAIIx sequencer as 75bp single reads

last: Reynaud


title: CRC lncRNA/mRNA expression

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

summary: ArrayStar Human LncRNA/mRNA Expression Microarray Version 3.0 was used to detect lncRNA expression in CRC tissues compared with their matched non-tumoral tissues. Here we report significantly up-regulated as well as down-regulated lncRNAs in CRC tissues compared with their matched non-tumoral tissues.

overall_design: Examination of  LncRNA/mRNA Expression difference between 3 pairs of colorectal tumor tissues and normal tissues


title: Transcriptomic analysis of gene-knockouts in M. tuberuclosis H37Rv

city: College Station

first: Thomas

last: Ioerger

state: TX

address: 3112 TAMUS

department: Department of Computer Science

institute: Texas A&M University

summary: Analysis of changes in gene expression in 9 gene-knockout strains.

overall_design:
RNA-seq of knockout strains and parental strain (H37Rv) for comparison, grown in-vitro (7H9 medium).

contributor: FLUTE project (NIH U19 AI107774)

SRA Study accession: SRP174545, BioProject accession: PRJNA511742


title: Comparative analysis of the Trichoderma reesei transcriptome during ethanol fermentation under anaerobic and aerobic condition

city: nanning

first: jun

last: huang

institute: guangxi sciences academy

summary: In this study, the recombinant Trichoderma reesei strain HJ48 was employed to investigate the differences between anaerobic and aerobic fermentation of glucose, through genome-wide transcription analysis.Analysis of the genes induced under fermentation condition has revealed novel features in T. reesei. Our results how that many genes related to ribosome were expressed more highly under aerobic condition in HJ48.

overall_design: mRNA profiles of 4-day old of Trichoderma_reesei during ethanol fermentation under anaerobic and aerobic condition were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Ribo

last: Huang

first: Jun


title: Downregulation of the histone methyltransferase SETD2 promotes imatinib resistance in chronic myeloid leukemia cells

status: Public on Jul 19 2019

first: Sheng

last: Yaru

address: Stem Cell Research Center, Ren Ji Hospital, 160 Pujian Road

institute: State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center

summary: Epigenetic modifiers were important players in the development of hematological malignancies and sensitivity to therapy. Mutations of SET domain-containing 2 (SETD2), a methyltransferase that catalyzes the trimethylation of histone 3 on lysine 36 (H3K36me3), were found in various myeloid malignancies. However, the detailed mechanisms through which SETD2 confers chronic myeloid leukemia progression and resistance to therapy targeting on BCR-ABL remain unclear. Here we found SETD2 acted as a tumor suppressor in CML. The novel oncogenic targets MYCN and ERG were shown to be the direct downstream targets of SETD2, where their overexpression induced by SETD2 knockdown caused imatinib insensitivity and leukemic stem cell enrichment in CML cell lines. Treatment with JIB-04, an inhibitor that restores H3K36me3 levels through blockade of its demethylation, successfully improved the cell’s imatinib sensitivity and enhanced the chemotherapeutic effect.

overall_design: RNA Sequencing Analysis between Imatinib Sensitive and Resistant TF1-BCR-ABL Cells.

first: Yaru

last: Sheng


title: Gene expression in Krt16 null paw lesions relative to WT paw skin

city: Ann Arbor

first: Pierre

middle: A.

last: Coulombe Ph.D..

address: 109 Zina Pitcher Place

department: Cell & Developmental Biology

institute: University of Michigan

summary:
The type I intermediate filament keratin 16 (Krt16 gene; K16 protein) is constitutively expressed in ectoderm-derived appendages and volar palmar/plantar epidermis, and is otherwise inducibly expressed in non-volar epidermis when skin epithelia are under stress. Mutations at the (human) KRT16 locus can cause pachyonychia congenita (PC) and focal non-epidermolytic palmoplantar keratoderma (PPK), which each entail painful calluses on palmar and/or plantar skin. Krt16 null mice develop footpad lesions that mimic several aspects of PC-associated PPK and FNEPPK, including hypoactive Keap1-Nrf2 signaling and elevated expression of skin barrier homeostasis genes and Danger Associated Molecular Patterns (DAMPs). This provides a unique opportunity to understand the intricacies of PPK and devise effective therapies (see Lessard and Coulombe, J. Invest. Dermatol. 2012; Lessard et al. PNAS (USA) 2013; Kerns et al.  J. Clin. Invest. 2016; Kerns et al., J. Invest. Dermatol. 2018; Zieman and Coulombe Exp. Dermatol. 2018). Here, we report on insight gained from a genome-wide analysis of gene expression in PPK-like lesions of Krt16 null mice.
In this dataset, we include expression data obtained from Krt16 null paw skin lesions and WT littermate controls (C57Bl/6 strain background) at two months of age.

overall_design: Paw skin was dissected from murine forepaws of Krt16 null and Krt16 WT littermates (C57Bl/6 strain background). A total of 8 mice were used, 4 Krt16 null (2 male, 2 female) and 4 Krt16 WT (2 male, 2 female). Mice were aged to two months before RNA isolation.

first: Abigail

last: Zieman

last: Coulombe


title: Foxn1 compound het mice have a different transcriptome in the fetal thymii

city: Dallas

first: Igor

last: Dozmorov

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary:
RNA was isolated from fetal mice thymus. This was used for gene comparisons with an affymatrix Clariom S array
We compared the differences in transcripts expressed in the fetal thymus in control mice and those with compound het mutations in Foxn1, which revealed significant differences in transcripts

overall_design: RNA was isolated from e13.5 fetal thymii . This was used for gene comparisons with an affymetrix Clariom S array

first: Nicolai

last: van Oers


title: Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment.

city: DAVIS

first: PEROT

last: SAELAO

state: CA

address: One Shields Ave, 3307 Meyer Hall

institute: UC DAVIS

summary:
Whole transcriptome analysis of two genetically distinctinct inbred chicken lines during NDV infection and heat stress.
Background:
Newcastle disease virus, in its most pathogenic form, threatens the livelihood of rural poultry farmers where there is a limited infrastructure and service for vaccinations to prevent outbreaks of the virus. Previously reported studies on the host response to Newcastle disease in chickens have not examined the disease under abiotic stressors, such as heat, which commonly experienced by chickens in regions such as Africa. The objective of this study was to elucidate the underlying biological mechanisms that contribute to disease resistance in chickens to the Newcastle disease virus while under the effects of heat stress.
Results:
Differential gene expression analysis identified genes differentially expressed between treated and non-treated birds across three time points (2, 6, and 10 days post-infection) in Fayoumi and Leghorn birds. Across the three time points, Fayoumi had very few genes differentially expressed between treated and non-treated groups at 2 and 6 days post-infection. However, 202 genes were differentially expressed at 10 days post-infection. Alternatively, Leghorn had very few genes differentially expressed at 2 and 10 days post-infection but had 167 differentially expressed genes at 6 days post-infection. Very few differentially expressed genes were shared between the two genetic lines, and pathway analysis found unique signaling pathways specific to each genetic line.
Conclusions:
The findings in this study confirmed our hypothesis that the Fayoumi line was more resistant to Newcastle disease virus infection compared to the Leghorn line. Fayoumi had significantly lower viral load, higher viral clearance, higher anti-NDV antibody levels, and fewer viral transcripts detected compared to Leghorns. Fayoumis activated immune related pathways including SAPK/JNK and p38 MAPK signaling pathways at earlier time points, while Leghorn would activate these same pathways at a later time. Further analysis revealed activation of the GP6 signaling pathway that may be responsible for the susceptible Leghorn response. Interaction analysis demonstrated substantial differences in response patterns between the two genetic lines that was not observed from the within line contrasts. This study has provided novel insights into the transcriptome response of the Harderian gland tissue during Newcastle disease virus infection while under heat stress utilizing a unique resistant and susceptible model.

overall_design: Examination of two genetic lines response Newcastle disease virus and heat stress in chickens

first: Perot

last: Saelao

first: Huaijun

last: Zhou