title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and LDB2-/- skin epidermal lysates

city: Seoul

first: Jonghyo

last: Lim

address: Yonsei-ro 50

department: Biochemistry

country: South Korea

institute: Yonsei university

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived mouse back skin epidermal transcriptome profiling (RNA-seq) to evaluate protocols for optimal high-throughput data analysis
Methods: Total RNA was isolated using an RNeasy Kit (Qiagen, Germantown, MD, USA). The mRNA sequence libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit(RS-122; Illumina, San Diego, CA, USA). The protocols followed the TruSeq Stranded mRNA Sample Preparation Guide (Part 15031047 Rev. E). Sequencing was performed using an Illumina Novaseq 6000 sequencer (101 bp paired-end runs), NovaSeq 6000 System User Guide Document (#1000000019358 v02), and TruSeq Stranded mRNA LT Sample Prep Kit. After removing low-quality and adapter sequences, sequence reads were aligned to the University of California–Santa Cruz(UCSC mm10), mouse genome reference sequence Mus musculus(RefSeq_2017_06_12) using Hierarchical Indexing for Spliced Alignment of Transcripts HISAT2 version 2.1.0, Bowtie2 2.3.4.1
Results: StringTie v.1.3.4d was used to estimate gene abundance. Abundance was measured in fragments per kilobase of exon per million fragments mapped; any values of 0 were discarded. To establish log2 transformation, 1 was added to each abundance value of filtered genes, and quantile normalization was performed.
Conclusions: Our study represents detailed analysis of Skin epidermal lysates transcriptomes, with biologic replicates, generated by mRNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a tissue. We conclude that mRNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Back skin epidermal lysates mRNA profiles of 63-day old wild type (WT) and LDB2-/- mice were generated by deep sequencing, in duplicate, using Illumina Novaseq 6000.


title: DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype

status: Public on May 04 2020

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

country: USA

institute: Northwestern University Feinberg School of Medicine

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Desmoplastic small round cell tumor is dependent on EWS-WT1

city: Philadelphia

first: Patrick

last: Grohar

state: PA

address: 3501 Civic Center Blvd 4200 CTRB

department: Dept of Pediatrics, Oncology Division

institute: Children's Hospital of Philadelphia

summary: Desmoplastic small round cell tumor (DSRCT) is a rare and aggressive soft tissue malignancy. The disease is defined by the oncogenic EWS-WT1 transcription factor. However, the dependence of the tumor on this target has not been well-established and no EWS-WT1 targeted therapy has translated to the clinic.  In this report we establish the dependence of DSRCT on EWS-WT1 as well as define a gene signature and a comprehensive list of downstream targets. The selective silencing of EWS-WT1 leads to the marked suppression of proliferation of both JN-DSRCT1 and BER cells. Loss of the fusion protein results in morphologic changes in the cells and eventual cellular apoptosis. RNA sequencing demonstrates large scale gene expression changes attributable to EWS-WT1 with several hundred induced or repressed downstream targets of the fusion. We conclude DSRCT is dependent on the EWS-WT1 transcription factor for cell survival. The presence of EWS-WT1 leads to enrichment of genes involved in aberrant cell differentiation and development as well as those involved in tumor metastasis.

overall_design: Three biological replicates per treatment were sequenced; mRNA was isolated individually from each replicate.

first: Jenna

middle: M

last: Gedminas

middle: J


title: Oral tongue cancer: p53 NS+ vs. p53 NS- tumor

city: HYDERABAD

first: Murali

middle: Dharan

last: Bashyam

state: (Click to Select US State)

address: MJ MARKET

country: India

institute: CDFD

summary: Transcriptional profiling of squamous cell carcinoma of oral tongue, comparing p53 NS+ and p53 NS- tumors. Goal was to determine differentially expressed genes between them based on global gene expression.

overall_design: Two-condition experiment, p53 NS- vs. p53 NS+ oral tongue tumors. P53 NS- tumors: 17, p53 NS+ tumors: 23.

first: Raju

last: Adduri

middle: D


title: RNA sequencing reveals PNN as a predictive biomarker of clinical outcome in stage III colorectal cancer patients treated with adjuvant chemotherapy

status: Public on May 03 2020

city: Firenze

first: Stefania

last: Nobili

address: viale Pieraccini 6

department: Health Sciences

country: Italy

institute: University of Florence

summary: Five-year overall survival of stage III colorectal cancer (CRC) patients treated with standard adjuvant chemotherapy (ACHT) is highly variable. Genomic biomarkers and/or transcriptomic profiles identified lack of adequate validation. Aim of our study was to identify and validate molecular biomarkers predictive of ACHT response in stage III CRC patients by a transcriptomic approach. From a series of CRC patients who received ACHT, two stage III extreme cohorts (unfavorable vs. favorable prognosis) were selected. RNA sequencing was performed from fresh frozen explants. Tumors were characterized for somatic mutations. Validation was performed in stage III CRC patients extracted from two GEO datasets. According to disease free survival (DFS), 108 differentially expressed genes (104/4 up/downregulated in the unfavorable prognosis group) were identified. Among 104 upregulated genes, 42 belonged to olfactory signaling pathways, 62 were classified as pseudogenes (n = 17), uncharacterized noncoding RNA (n = 10), immune response genes (n = 4), microRNA (n = 1), cancer-related genes (n = 14) and cancer-unrelated genes (n = 16). Three out of four down-regulated genes were cancer-related. Mutational status (i.e., RAS, BRAF, PIK3CA) did not differ among the cohorts. In the validation cohort, multivariate analysis showed high PNN and KCNQ1OT1 expression predictive of shorter DFS in ACHT treated patients (p = 0.018 and p = 0.014, respectively); no difference was observed in untreated patients. This is the first study that identifies by a transcriptomic approach and validates PNN and KCNQ1OT1 as molecular biomarkers predictive of chemotherapy response in stage III CRC patients. After a further validation in an independent cohort, PNN and KCNQ1OT1 evaluation could be proposed to prospectively identify stage III CRC patients benefiting from ACHT.

overall_design: Two extreme cohort study according to chemotherapy outcome

first: Enrico

last: Mini

first: Andrea

last: Lapucci

first: Gabriele

last: Perrone

first: Romina

last: D’Aurizio

first: Cristina

last: Napoli

first: Marco

last: Brugia

first: Ida

last: Landini

first: Renato

last: Tassi

first: Lucia

last: Picariello

first: Lisa

last: Simi

first: Irene

last: Mancini

first: Luca

last: Messerini

first: Alberto

last: Magi

first: Pamela

last: Pinzani

first: Teresita

last: Mazzei

first: Francesco

last: Tonelli


title: Functional In vivo Recording and Single-cell Transcriptome Analysis Reveals Molecular Properties of Light-Sensitive Neurons in Mouse V1

city: Beijing

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

summary: We established a protocol of functional in vivo single-cell transcriptome (FIST) analysis

overall_design: Search for differential expressed genes defined the LS (light sensitive) and NS (non-light sensitive) neurons

first: Jianwei

last: Liu

middle: C

last: Pan

first: Le

last: Sun

first: Mengdi

last: Wang

first: Junjing

last: Zhang

first: Zhentao

last: Zuo

first: Sheng

last: He

first: Qian

last: Wu

first: Xiaoqun


title: DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [DNA methylation/RRBS]

first: Benjamin

last: Singer

summary: People with ataxia-telangiectasia (A-T) display clinical variability, yet molecular profiles associated with distinct A-T phenotypes remain undefined. We report transcriptional and DNA methylation signatures that inform the regulatory networks underlying A-T phenotypes.

overall_design:
Peripheral blood mononuclear cells from 8 participants with ataxia-telangiectasia, 4 control participants

>>>Submitter states: Raw data are not available because our IRB does not allow us to submit the raw sequence files to either GEO or dbGaP<<<

first: Sharon

middle: A

last: McGrath-Marrow


title: THE SPATIAL REGULATION OF CONDENSIN ACTIVITY IN CHROMOSOME CONDENSATION

city: Berkeley

first: lorenzo

last: costantino

state: CA

address: 16 Barker Hall # 3202

department: MCB

institute: university of california, berkeley

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Condensin mediates chromosome condensation, which is essential for proper chromosome segregation during mitosis. Prior to anaphase of budding yeast, the ribosomal DNA (RDN) condenses to a thin loop that is distinct from the rest of the chromosomes. We provide evidence that the establishment and maintenance of this RDN condensation require the regulation of condensin by Cdc5p (polo) kinase. We show that Cdc5p is recruited to the site of condensin binding in the RDN by cohesin, a complex related to condensin. Cdc5p and cohesin prevent condensin from misfolding the RDN into an irreversibly decondensed state. From these and other observations, we propose that the spatial regulation of Cdc5p by cohesin modulates condensin activity to ensure proper RDN folding into a thin loop. This mechanism may be evolutionarily conserved, promoting the thinly condensed constrictions that occur at centromeres and RDN of mitotic chromosomes in plants and animals.

overall_design: examination of genome-wide localization of 3 proteins in 3 genetic background

first: Lorenzo

last: Costantino

first: Rebecca

last: Lamothe

first: Douglas

last: Koshland


title: MicroRNA biomarkers in blood for Autism spectrum disorder

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social communication deficits and repetitive behaviors. MicroRNAs (miRNAs) have been recently recognized as potential biomarkers of ASD as they are dysregulated in various tissues of individuals with ASD. However, it remains unclear whether miRNA expression is altered in individuals with high-functioning ASD. Here, we investigated the miRNA expression profile in peripheral blood from adults with high-functioning ASD, and age and gender-matched healthy controls. Our findings may provide insights regarding the molecular clues for recognizing high-functioning ASD.

overall_design: We profiled miRNA expression using peripheral blood from 30 ASD patients and 30 controls.

first: Masatoshi

last: Hagiwara


title: Nutrient Uptake in Huanglongbing-affected Sweet Orange: Transcriptomic and Physiological Analysis

city: Lake Alfred

first: Faisal

last: Shahzad

state: FL

address: 700 Experiment Station Road, CREC

department: Horticultural Sciences

institute: University of Florida

summary: To evaluate the transcriptome response of roots towards Hoagland solution of two-year-old healthy (C) and HLB-affected (T) sweet orange (Citrus sinensis L.) cultivar Midsweet grafted on Kuharskei Carrizo rootstock at three different time points; D1 (at the start of the experiment), D2 (After 3 days of Hoagland solution), D3 (After nine days of Hoagland solution), were performed using RNA sequencing analysis. A total of 9, 19, and 2324 DEGs were expressed in HLB-affected and healthy trees feeder roots on D1, D2, and D3, respectively. Due to a small number of DEGs in HLB-affected and healthy trees roots on D1 and D2, enrichment analysis could not be performed. At D3, Gene Ontology (GO) enrichment analysis was performed using upregulated and downregulated DEGs in HLB-affected roots compared to healthy roots. For the upregulated DEGs in HLB-affected roots, the most enriched biological GO categories were related to transport, cellular amino acid metabolic process,  oxoacid metabolic process, organic acid metabolic processes, phenylpropanoid biosynthesis process, response to carbohydrate stimulus, ethylene and the jasmonic acid-mediated signaling pathway, and regulation of plant hormone. The biological GO categories based on the number of DEGs associated with downregulated DEGs were the developmental process, phosphate metabolic process, protein modification process, defense response, growth, cell cycle, cell death, and ABA-mediated signaling pathway. The results of this study strongly suggest; although, the reduced biomass limits the nutrient uptake capacity in the plants as a whole, so in order to compensate for reduced root to shoot ratio the existing root undergo anatomical and transcriptomic changes to improve nutrient uptake efficiency to meet the nutrient demand of shoot systems. It is likely that higher inputs of energy in nutrient uptake possibly results in reducing the root longevity of HLB-affected trees. Good nutrition management practices are critical for the survival of HLB-affected trees as the availability and uptake of nutrients allow HLB-affected trees in response to abiotic and biotic stress.

overall_design: Samples (feeder root tissue) of two-year-old healthy (C) and HLB-affected (T) sweet orange (Citrus sinensis L.) cultivar Midsweet grafted on Kuharskei Carrizo rootstock treated with the Hoagland (fertilizer) solution at three different time points: D1 (at the start of the experiment), D2 (After 3 days of Hoagland solution treatment), D3 (After nine days of Hoagland solution treatment); each sample was analyzed in four biological replicates.

first: Changpin

last: Chun

first: Arnold

last: Schumann

first: Tripti

last: Vashisth


title: The asparagus genome sheds light on the origin and evolution of a young Y chromosome

status: Public on May 02 2020

city: Huntsville

first: Alex

last: Harkess

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

type: Non-coding RNA profiling by high throughput sequencing

summary: Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X and Y (or Z/W, U/V) chromosomes. Comparative and experimental analysis of a reference genome assembly for a double haploid YY male garden asparagus (Asparagus officinalis L.) individual implicates separate but linked genes as responsible for sex determination. Dioecy has evolved recently within Asparagus and sex chromosomes are cytogenetically identical with the Y, harboring a megabase segment that is missing from the X. We show that deletion of this entire region results in a male-to-female conversion, whereas loss of a single suppressor of female development drives male-to-hermaphrodite conversion. A single copy anther-specific gene with a male sterile Arabidopsis knockout phenotype is also in the Y-specific region, supporting a two-gene model for sex chromosome evolution. Additionally, we test for the presence of Y-specific small RNA loci in several XX, XY, and YY genotypes that may be acting as sex determination loci.

overall_design: Small RNA data for XX, XY, and YY genotypes


title: Genetic Basis of Alternative Polyadenylation as an Emerging Molecular Phenotype for Human Traits and Diseases

city: Irvine

first: Lei

last: Li

address: University of California, Irvine

institute: University of California, Irvine

summary: Genome-wide association studies have identified thousands of non-coding variants that are statistically associated with human traits and diseases. However, functional interpretation of these variants remains a major challenge.  Here, we describe the first atlas of human 3’-UTR alternative polyadenylation (APA) Quantitative Trait Loci (3′aQTLs), i.e. ~0.4 million genetic variants associated with APA of target genes across 46 Genotype-Tissue Expression (GTEx) tissues from 467 individuals. APA occurs in approximately 70% of human genes and substantively impacts cellular proliferation, differentiation and tumorigenesis. Mechanistically, 3′aQTLs could alter polyA motifs and RNA-binding protein binding sites, leading to thousands of APA changes. Importantly, 3′aQTLs can be used to interpret ~16.1% of trait-associated variants and are largely distinct from other QTLs such as eQTLs.  These 3′aQTLs thus represent the genetic basis of APA as a novel molecular phenotype to explain a large fraction of non-coding variants and to provide new insights into complex traits and disease etiologies.

overall_design: Examination of alternative polyadenylation and gene expression upon LARP4 KD in HEK293T cells.

first: Kai

middle: L

last: Huang

first: Nathan

last: Elrod

first: Eric

last: Wagner

first: Wei


title: HCMV-UV and SeV-UV infection of IFNAR KO and wildtype human fibroblasts

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St. West

department: Department of Pathology

country: Canada

institute: McMaster University

summary: Type 1 interferon (IFN) plays a critical role in early antiviral defense and priming of adaptive immunity by signalling upregulation of host antiviral interferon-stimulated genes (ISGs). Certain stimuli trigger strong activation of IFN regulatory factor 3 (IRF3) and direct upregulation of ISGs in addition to IFN. It remains unclear why some stimuli are stronger activators of IRF3 and how this leads to IFN-independent antiviral protection. We found that UV-inactivated human cytomegalovirus (HCMV) particles triggered an IFN-independent ISG signature that was absent in cells infected with UV-inactivated Sendai virus (SeV) particles. HCMV particles triggered mostly uniform activation of IRF3 and low-level IFN-? production within the population while SeV particles triggered a small fraction of cells producing abundant IFN-?. These findings suggest that population level activation of IRF3 and antiviral protection emerges from a diversity of responses occurring simultaneously in single cells.  Moreover, this occurs in the absence of virus replication.

overall_design: We infected wildtype or IFNAR-/- life-extended human fibroblasts with UV-inactivated HCMV or SeV to measure upregulation of antiviral ISGs

first: David

last: Hare

first: Anna

last: Dvorkin-Gheva


title: Cell-type specific gene expression profiling in heterogeneous in vitro cultures using epitope-tagged RPL22

status: Public on May 01 2020

city: New York

first: James

last: Gregory

state: NY

address: 101 Ave of the Americas

institute: New York Genome Center

summary: Here we report the use of RPL22-Flag, RPL22-V5, and RPL22-HA to co-immunoprecipitate RNA from specific cell populations

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of RPL22-HA and RPL22-V5 in HEK293 and NIH3T3 cells, respectively, in co-culture.


title: Cortical gene expression of WT, Grin1 knockdown, and Grin1 Cre rescue mice

city: Toronto

first: Amy

last: Ramsey

state: ON

address: 1 King's College Circle, Room 4302 MSB

department: Pharmacology & Toxicology

institute: University of Toronto

summary: The purpose of the study was to compare cortical transcript abundance between WT mice and Grin1 knockdown mice, and to determine whether transcript levels could be normalized in Grin1 Cre rescue mice (hemizygous for tamoxifen-inducible Rosa26 ERT2 Cre). All mice were treated with tamoxifen at 10 weeks of age until 12 weeks of age, and were euthanized at 15 weeks of age.

overall_design: Methods: WT, GluN1, and GluN1Cre mice were used (all males, 4 per group). Total RNA isolated from cortex was used for RNAseq. Raw reads were processed on Galaxy server using up-to-date Tuxedo suite of programs. Differential gene expression determined with CuffDiff.  Significant differences were determined by p<0.05, q<0.10

first: Catharine

last: Mielnik

first: Rehnuma

last: Islam

first: Ali

last: Salahpour

first: Yuxiao

last: Chen


title: Evolutionary changes in cis regulation are associated with altered chromatin activity and gene expression levels in the Drosophila eye development (RNA-Seq)

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

summary: Expression profiling by high-throughput sequencing (RNA-seq) across eight WT Drosophila species - D. melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. willistoni, D. mojavensis and D. virilis - and three tissues, namely, brain, eye-antennal and imaginal discs, at the stage of third instar larvae.

sample_organism:
Drosophila ananassae
Drosophila melanogaster
Drosophila mojavensis
Drosophila pseudoobscura
Drosophila simulans
Drosophila virilis
Drosophila yakuba
Drosophila willistoni

overall_design: By the use of Ornstein-Uhlenbeck methods, we assess the evolutionary forces acting on regulatory elements (cis-level), chromatin activity and gene expression across Drosophila eye-antennal imaginal discs at the stage of third instar larvae.

first: Marina

last: Naval-Sánchez

first: Delphine

last: Potier

first: Valerie

last: Christiaens

first: Gert

last: Hulselmans


title: Pharmacologic Inhibition of Epidermal Growth Factor Receptor Suppresses Non-alcoholic Fatty Liver Disease in Murine Fast-food Diet Model

city: Pittsburgh

first: George

middle: K

last: Michalopoulos

state: Pennsylvania

address: 411 SBST, 200 Lothrop Street

institute: University of Pittsburgh

summary:
EGFR is a critical regulator of hepatocyte proliferation and liver regeneration. Our recent work indicated EGFR can also regulate lipid metabolism during liver regeneration after partial-hepatectomy. Based on these findings, we investigated role of EGFR in a mouse model of NAFLD utilizing a pharmacological inhibition strategy. C57BL6/J mice were fed chow-diet, or fast-food diet with/without EGFR inhibitor (Canertinib) for 2-months. EGFR inhibition completely prevented development of steatosis and liver injury in this model. In order to study if EGFR inhibition can reverse NAFLD progression, mice were fed fast-food diet for 5-months, with/without Canertinib-treatment for the last 5-weeks of the study. EGFR-inhibition remarkably decreased steatosis, liver injury, fibrosis and improved glucose tolerance. Microarray analysis revealed ~40% of genes altered by fast-food diet were differentially expressed after EGFR-inhibition, and thus, are potentially regulated by EGFR. Several genes and enzymes related to lipid metabolism (particularly fatty-acid synthesis and lipolysis), which were disrupted by fast-food diet, were found to be modulated by EGFR. Several crucial transcription factors that play a central role in regulating these lipid metabolism genes during NAFLD, including PPARγ, SREBF1, ChREBP and HNF4α, were also found to be modulated by EGFR. In fact, ChIP-analysis revealed PPARγ binding to several crucial lipid metabolisms genes (Fasn, Scd1 and Plin2) was drastically reduced by EGFR inhibition. Further upstream, EGFR-inhibition suppressed AKT signaling, which is known to control these transcription factors, including PPARγ and SREBF1, in NAFLD models.  Lastly, the effect of EGFR in FFD-induced fatty-liver phenotype was not shared by receptor-tyrosine-kinase MET, as investigated using MET-KO mice. In-conclusion, our study revealed a role of EGFR in NAFLD and the potential of EGFR-inhibition as a treatment strategy for NAFLD.
We used microarrays to detail the global programme of gene expression in liver of C57BL6/J mice fed fast-food diet mice treated with EGFR inhibitor (canertinib)

overall_design: For the two months study, 6-8 weeks old male C57BL6/J mice were fed ad libitum (i) chow diet, (ii) fast-food diet [western diet - high saturated fats (21% by weight; 42% kcal from fat), high cholesterol (0.2%) and high carbohydrates (sucrose: 34% by weight)  in diet  (TD.88137, Teklad) - along with high-fructose-glucose solution (d-glucose: 18.9g/L  and d-fructose: 23.1g/L) in drinking water] or (iii) Canertinib (a highly potent and selective EGFR inhibitor/ EGFRi) added in the same fast-food diet for 2-months. Canertinib was administered to mice in diet for estimated dose of 80 mg/kg/day. For the five months study, 6-8 weeks old male C57BL6/J mice were fed ad libitum (i) chow diet, (ii) and (iii) fast-food diet for 5-months. Group (ii) and (iii) were administered vehicle (PBS) and Canertinib (80mg/kg; i.p.), respectively, 5 days/week for the last 5-weeks of 5-months period. Microarray analysis was performed on RNAs isolated from pooled liver samples (n=3-4) from the chow, FFD and FFD + EGFRi group for both 2 and 5 months studies, using the GeneChip® Mouse Genome 430 2.0 Array Set 430 (Affymetrix, Santa Clara, CA).

first: Bharat

last: Bhushan


title: RNA-Seq is used to facilitate the identification of the BCR-ABL1- independent mechanism of resitance to imatinib using a human chronic myeloid leukaemia cell line model

city: London

first: Jamshid

middle: Sorouri

last: Khorashad

address: centre for haematology, Commonwealth building, Hammersmith Hospital

country: United Kingdom

institute: Imperial College London

summary: The goals of this study were to compare two human chronic myeloid leukaemia cell lines. One is sensitive to the standard treatment imatinib whereas the other is resistant to imatinib. RNA-Seq was used to identify differentially expressed genes between the two cell lines. 5282 differentially expressed genes were identified, and using gene set enrichment analysis the TNFα signalling pathway via NF-κB was identified.

overall_design: Differentially expressed genes were identified between two human chronic myeloid lukeaemia cell lines. RNA-Seq was performed using the Illumina Hiseq4000 platform at a depth of ~65 million reads per sample. Each cell line was run in triplicate.

first: J

middle: S

first: R

last: Ellwood

first: A

last: Eiring


title: Stress regulation of sustained attention and the cholinergic attention system

first: Song-Jun

last: Xu

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary:
Background: Stress exacerbates symptoms of schizophrenia and attention deficit hyperactivity disorder, which are characterized by impairments in sustained attention. Yet how stress regulates attention remains largely unexplored. Here we investigated whether a 6-day variable stressor (VS) altered sustained attention and the cholinergic attention system in male and female rats.
Methods: Sustained attention was tested with the sustained attention task (SAT). Successful performance on SAT relies on the release of acetylcholine (ACh) into the cortex from cholinergic neurons in the nucleus basalis of Meynert (NBM). Thus, we evaluated whether VS altered the morphology of these neurons with a novel approach using Cre-dependent virus in genetically modified ChAT::Cre rats, a species used for this manipulation only. Next, electrochemical recordings measured cortical ACh following VS. Finally, we used RNAseq to identify VS-induced transcriptional changes in the NBM.
Results: VS impaired attentional performance in SAT and increased the dendritic complexity of NBM cholinergic neurons in both sexes. NBM cholinergic neurons are mainly under inhibitory control, so this morphological change could increase inhibition on these neurons, reducing downstream ACh release to impair attention. Indeed, VS decreased ACh release in the prefrontal cortex of males. Quantification of global transcriptional changes revealed that, although VS induced many sex-specific changes in gene expression, it increased several signaling molecules in both sexes.

overall_design: Transcription profiles of NBM in rats undergo VS were generated by deep sequencing, in six replicates, using Hiseq 4000

first: Samantha

last: Eck

first: Debra

last: Bangasser


title: The NtrYX two-component system regulates the bacterial cell envelope

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: To investigate the R. sphaeroides NtrYX two component system on RNA transcript levels, we used global RNA sequencing (RNA-seq) to compare transcript abundance in parent and DntrYX strains grown under aerobic conditions.  Our previous studies were performed in strains deficient at synthesizing the polyhydroxybutyrate, so we used strains D0382 and DNtrYXD0382, herein referred to as parent and DntrYX, respectively. We also used ChIP-seq to identify NtrX binding sites throughout the genome.

overall_design: Comparing ∆ntrYX to parent strain for RNA-seq and using ChIP-seq to map NtrX binding sites

first: Kimberly

last: Lemmer

first: François

last: Alberge

first: Alice

last: Dohnalkova

first: Ryan

middle: E

last: Schaub

first: Jonathan

last: Lenz

first: Saheed

last: Imam

first: Joseph

middle: P

last: Dillard

first: Daniel

middle: R

last: Noguera

first: Timothy

last: Donohue


title: RNA-seq analysis of lung smooth muscle cells

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Lung smooth muscle cells are  including bronchiolar and vascular smooth muscle cells. In order to get adult lung smooth muscle cells, we use transgenic mouse line with smooth muscle actin creERT2, which is a transgenic cre recombinase in Acta2 (contractile smooth muscle cell gene). This mouse line also contains a CAG promoter-driven red fluorescent protein variant (tdTomato) - all inserted into the ROSA26 locus. This mouse line express robust tdTomato fluorescence following cre-mediated recombination after Tamoxifen injection.

overall_design: Tamoxifen (Sigma) was administered intraperitoneally with 75mg/kg body weight daily for 10 days to 8 weeks old transgenic mice. After 2 months, mice were sacrificed and lung tissue was dissected from mice and dissociated into single cells by enzyme digestion. Then, cell sorting was done with FACSAria (BD Biosciences).

first: Stefan

last: Guenther

first: Lei

last: Wang

first: Fan

last: Wu

first: Xuejun

last: Yuan


title: UTP18 as an oncogene promotes colorectal adenoma to carcinoma progression

first: Wei

last: Ge

state: State...

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

summary: To assess the possible mechanisms by which UTP18 promotes adenoma carcinogenesis, RNA-seq assay was performed to compare UTP18 overexpress A0529 adenoma with scramble.

overall_design: A total of two samples, A0529-scramble and A0529-UTP18

first: Dan

last: Luo


title: Gene expression profile of  HSPC with cell-intrinsic innate immune signaling activation after LPS treatment

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: The underlying mechanisms responsible for the competitive advantage of MDS HSPC in an inflammatory milieu remains poorly defined. Here, we show that MDS HPSC are protected from low-grade chronic inflammation, and that the adaptive response of these cells to the inflammatory milieu via the non-canonical NF-κB pathway contributes to sustained myeloid expansion and a competitive advantage. These findings uncover the mechanistic basis for the clonal dominance of functionally impaired MDS HSPC and reveal the therapeutic potential of interfering with non-canonical NF-κB signaling.

overall_design: mRNA profiles of human miR-146a deficient and WT CD34+ BM cells, Vav-TRAF6 and WT LSK murine BM cells, or Tet2F/F and Tet2F/F;VavCre murine BM cells treated with either  PBS or LPS for 90 min.

first: Tomoya

last: Muto

middle: T

last: Starczynowski


title: RNA-seq of NIH3T3 cells treated with PBS or extracellular vesicles (EV) from MCF10A or MDA-MB-231 cells

city: Duarte

first: Xiwei

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: To identify gene expression changes associated with treatment of EVs from MDA-MB-231 [231] and MCF10A [10A] cells) in NIH3T3 cells, we analyzed RNA isolated from PBS- or EV-treated NIH3T3 cells.  Gene expression in NIH3T3 cells treated with EV from MDA-MB-231 cells was compared to cells treated with PBS or EV from MCF10A cells, both of which served as controls in this experiment.

overall_design: RNA was extracted from PBS- and EV-treated cells, and subjected to library construction and RNA sequencing.

first: Shizhen


title: Expression analysis of microRNA in malignant peritoneal mesothelioma induced by intraperitoneal injections of iron saccarate in rats

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

summary: Iron plays an important role in oxidative tissue damage and subsequent carcinogenesis. Iron deposition in the peritoneum causes neoplastic changes. Here we used microRNA (miR) microarrays in a rat model by repeated intraperitoneal injections of ferric saccharate. miR microarray revealed the miR-199/214 as a distinctive feature of sarcomatoid mesothelioma.

overall_design: Carcinogenesis protocol was performed using specific pathogen-free male and female F1 hybrid rats between Fischer344 and Brown-Norway strains. A total of 8 samples were analyzed by microRNA (miR) microarray for the screening purpose. Eight samples follows; the immortalized rat peritoneal mesothelial cell and mesothelial tissue collection as non-neoplastic mesothelia;iron saccharete-Induced four cases of epithelioid mesothelioma and two cases of sarcomatoid subtypes. The six mesothelioma samples were obtained from the same tumors also analyzed in our previously submitted experiment (GSE16138).

first: Okazaki

last: Yasumasa

first: Akatsuka

last: Shinya

first: Toyokuni


title: Bulk RNA sequencing of SARS-CoV and SARS-CoV-2 infected human intestinal organoids

city: Utrecht

first: Joep

last: Beumer

address: Uppsalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Bulk RNA sequencing was performed on control and SARS-CoV and SARS-CoV-2 infected intestinal organoids.

overall_design: RNA was extracted from intestinal organoids that were either grown in expansion conditions (EXP) or differentiation conditions (DIF) and were not treated, treated with SARS-CoV (a) or SARS-CoV-2 (b) for 24 and 60 hours. After this, RNA was collected.

first: Mart

last: Lamers

first: Jelte

last: van der Vaart

first: Kèvin

last: Knoops

first: Jens

last: Puschhof

first: Tim

middle: I

last: Breugem

first: Raimond

middle: B

last: Ravelli

first: J

last: van Schayck

first: Anna

middle: Z

last: Mykytyn

first: Hans

middle: Q

last: Duimel

first: Elly

last: van Donselaar

first: Samra

last: Riesebosch

first: Helma

last: Kuijpers

first: Debby

last: Schipper

first: Willine

last: van de Wetering

first: Miranda

last: de Graaf

first: Marion

last: Koopmans

first: Edwin

last: Cuppen

first: Peter

last: Peters

first: Bart

last: Haagmans

last: Clevers


title: Identification of miRNAs in Mouse lung epithelial cells (MLE12) expression of which is altered by exposure to cigarette-smoke extracts

city: Cleveland

last: Blumental Perry

state: OH

address: 10900 Euclid Ave.

institute: Case Western Reserve University

summary: Our study aimed to identify miRNAs expression of which is affected by exposure to cigarette smoke (CS) in alveolar type-II cells. Identification and delineation of their modes of action is important for understanding CS-induced failure of repair mechanisms in COPD pathogenesis

overall_design: Cigarette smoke induced changes in miRNAs expression were measured at 2 and 10 hours post-exposure to 10% bubbled through medium cigarette smoke extract

last: Blumental-Perry

first: Naftali

last: Kaminski

first: Harshavardhan

last: Kenche

first: Kusum

last: Pandit


title: Gene expression signatures for FGFR1 Knockdown in Mantle cell lymphoma cell line (Z-138)

city: columbus

first: Lalit

last: Sehgal

department: Hematology

institute: The Ohio State University

summary: To understand the role of FGFR1 in the MCL progression.

overall_design: The gene expression profile was measured in vector control and the Knockdown of FGFR1 after puromycin selection.

first: Sehgal

last: Lalit


title: BCL-xL/BCL2L1 is a critical anti-apoptotic protein that suppresses BAK to promote pancreatic specification from human pluripotent stem cells

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

summary: Purpose: From qPCR and western blot analyses, we observed that BCL-xL was upregulated from D7 onwards during differentiation of human pluripotent stem cells towards pancreatic progenitors using a combination of growth factors

overall_design: Method: On D7, we treated the cells with WEHI-539 (BCL-XL inhibitor) to understand the effects of BCL-xL inhibition on the pancreatic progenitor fate. The goal of this project is to elucidate the role of BCL-XL in the generation of early pancreatic progenitors in terms of cell fate and metabolism.

first: Larry

last: Loo

first: Shawn

last: Hoon


title: p53 exon 11 mutants generated by CRISPR/Cas9 result in aberrant alternative splicing.

city: Istanbul

first: Batu

last: Erman

address: Orhanli, Tuzla

department: Biological Sciences and Bioengineering Program

country: Turkey

institute: Sabanci University

summary: The Tp53 gene encodes the famous tumor suppressor protein p53. This gene is encoded in 11 exons and various alternative spliced versions of the transcripts have been detected. Here we generated targeted mutations in human colon cancer cell line HCT116 using CRISPR/Cas9 genome editing tools. The mutations were targeted to the 5' end of Tp53 gene exon 11. CRISPR/Cas9 transfected cells were allowed to repair double stranded breaks by non-homologous end joining. Mutant cell pools were single cell cloned and analyzed by Sanger DNA sequencing. Three mutant clones, mut4, mut5 and mut9 were found to contain biallelic homozygous mutations. Poly adenylated RNA was isolated from mutant cell pools was isolated and sequenced by Illumina RNASeq in triplicate. We find that exon 11 mutations result in the alternative splicing of earlier exons and cause the expression of the p53beta alternative splice product. This C-terminally deleted protein has been associated with the induction of senescence. We thus identify an exonic splicing silencer in exon 11 of the Tp53 gene which normally suppressed alternative splicing events that encode the p53beta variant. This sequence and the factors that associate with it are prime candidates for targeting, which may induce p53beta splicing and the induction of senescence in tumors.

overall_design: RNA-seq was used to define differentially expressed genes in the HCT116 cell line and three subclones, mut4, mut5 and mut9. Each sample was represented in triplicate.

first: Bahar

last: Shamloo

first: Hakan

last: Taskiran


title: Differentiated prostate luminal cells acquire enhanced regenerative potential after androgen ablation

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: Cells in the prostate are postulated to have stem cell properties based on organ regeneration following castration. Through single cell RNA-seq (scRNA-Seq) analysis, we identify a rare luminal cell population in the mouse prostate that expresses stem-like markers (Sca1+, Psca+), as well as a larger population of more differentiated cells (Nkx3.1+, Pbsn+, CD133/Prom1+). Unexpectedly, both populations acquire enhanced organoid regeneration potential following castration and contribute equipotently to prostatic regeneration, as revealed by lineage tracing. Regeneration is mediated, in part, by androgen-driven expression of Nrg2, Igf1, Fgf10 and Rspo3 by distinct populations of mesenchymal cells acting in a paracrine fashion on luminal cells. Human prostate tissue contains similar differentiated and stem-like luminal subpopulations which also, collectively. acquire enhanced regenerative potential after androgen ablation therapy. Thus, nearly all luminal cells that persist post-castration contribute to prostate regeneration, not just rare stem cells.

overall_design: Mouse prostate 10x single cell

first: Wouter

last: Karthaus

first: Danielle

last: Choi

first: Eliot

last: Linton

first: Mesruh

last: Turkekul

first: Alborz

last: Bejnood

first: Brett

last: Carver

first: Anuradha

last: Gopalan

first: Wassim

last: Abida

first: Vincent

last: Laudone

first: Moshe

last: Biton

first: Ojasvi

last: Chaudhary

first: Tianhao

last: Xu

first: Ignas

last: Masilionis

first: Katia

last: Manova

first: Linas

last: Mazutis

first: Dana

last: Pe’er

first: Aviv

last: Regev

first: Charles

last: Sawyers


title: The effects of Arginase 2 (Arg2) knockout on chronic hypoxia-induced pulmonary hypertension

city: Chicago

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

summary: Increased arginase 2 protein expression is associated with endothelial dysfunction and pulmonary hypertension, likely by impairing NO production secondary to substrate availability. Hypoxia induces arginase 2 protein expression contributing to pulmonary vascular cell proliferation. Non-specific arginase inhibitors have been shown to prevent experimental pulmonary hypertension in animal models. RNA was isolated from whole lung tissue from adult (12-14 weeks) arginase 2 wild type and KO mice exposed to 21% O2 or 10% O2 for 28 days. Animals were sacrificed and the lungs collected and stored at -80°C .  Total RNA was  isolated with Trizol and used for RNA-seq. RNA-seq results indicate notable differentially expressed gene transcripts were evident in the Arg2 WT and Arg2 KO lungs. There were 25 unique transcripts identified (>2-fold change, p < 0.001) between the normoxia and hypoxia-exposed Arg2 WT. Interestingly, there was significantly greater differences in the Arg2 KO mice exposed to hypoxia compared to normoxia, with 188 unique transcripts (>2-fold change, p < 0.001) identified by RNA seq.

overall_design: Examination of the transcriptomal changes caused by hypoxia in the lungs of both Arg2 wildtype and knockout mice

first: Bernadette

last: Chen

first: Irina

last: Buhimschi


title: Pathway analysis of miRNA revealing immunologic alteration in lymphocyte immune response and T cell differentiation in Fontan patients with protein-losing enteropathy

city: Erlangen

first: Arif

last: Ekici

address: Schwabachanlage 10

institute: Institute of Human Genetics

summary: Protein losing enteropathy (PLE) is a severe complication of Fontan circulation with increased morbidity and mortality. The underlying pathophysiologic mechanism leading to the development of PLE in Fontan patients remain largely unknown. We performed microarray-based microRNA (miRNA) expression profiling from whole blood to generate hypotheses about relevant pathways involved in PLE pathogenesis controlled by miRNA signature.

overall_design: RNA was extracted of whole blood samples (PAXgene tubes) of 46 patients (n=10 Fontan patients with PLE, n=28 Fontan patients without PLE and n=8 patients with dextro tansposition of the great arteries (d-TGA). The miRNA microarray expression analysis was performed on GeneChip miRNA 4.1 microarray.

first: Julia

last: Moosmann


title: Genome-wide maps of chromatin state in LbetaT2 cells or in the pituitary tissues of wild-type and Foxk2 knockout mice.

city: Beijing

first: Lin

last: Shan

address: 10 You’anmen Outer West 1st Street

institute: Capital Medical University

summary: First, we report a series of ChIP-seq results in LbetaT2 cells. Briefly, we performed ChIP-seq experiments with antibodies specific for Foxk2, Sin3a, Tet1 and Uhrf1 in LbetaT2 cells. We found that a total of 343 different promoters including Nab2 that are co-targeted by Foxk2, Sin3a, Tet1 and Uhrf1. Next, hMeDIP-seq and ChIP-seq experiments with antibodies specific for 5hmC and H3K18ub in the pituitary tissues of wild-type and Foxk2 knockout mice were performed. The results showed that compared to the wild-type mice, knockout of Foxk2 reduced the enrichment of 5hmC and H3K18ub on the Foxk2 target gene.This study revealed a critical switch control of FOXK2 for GnRH pulse frequency-dependent LH production and gave us a new understanding of the role of Foxk2 in chromatin status and gene transcription.

overall_design: Examination of target genes in LbetaT2 cell line or compare the binding sites in the pituitary tissues of Wild-type and Foxk2 Knockout mice

first: Yue

last: Wang

first: Yongfeng

last: Shang


title: Analysis of metabolic enzyme expression reveals a unique progenitor cell with mast cell and erythrocyte potential

city: Newark

first: Mark

middle: C.

last: Siracusa

state: NJ

address: Cancer Center 1226, 205 South Orange Avenue

department: Medicine

institute: Rutgers New Jersey Medical School

summary: The purpose of this study was to take an unbiased look at the progenitor cell subsets that are present in the bone marrow of naïve mice.  By using single cell RNA-seq we hoped to identify marker genes of interest that could then be tracked by the generation new reporter animals.

overall_design: First, CD45+ CD3- Ly6G- cells were sort-purified from the bone marrow of 3 naïve C57BL/6 mice and pooled.  This was the input for the (Bone marrow-resident progenitor cells) sample.  Second, CD45+ Car1-GFP-expressing cells were sort-purified from the bone marrow of 3 naïve Car1-GFP reported mouse on a C57BL/6 background and pooled. This was the input for the (Car1-GFP+ bone marrow cells) sample.  10,000 sort-purified cells were then processed using the 10X Genomics ChromiumTM Controller. Cell suspensions were loaded onto the Chromium Single Cell A Chip for cell lysis and barcoding. RNA from individual cells was reverse transcribed and sequencing libraries prepared using the ChromiumTM Single Cell 3’ Library Kit v2 following the manufacturers protocol. Samples were sequenced using an Illumina NextSeq 550 with standard 10X Genomics Configuration (26bpx98bp).


title: Identification of Scrt1, a new transcriptional regulator of   beta-cell maturation using chromatin accessibility variations

city: Rehovot

first: Jonathan

middle: Aryeh

last: Sobel

address: Benoziyo Building for Biological Sciences, room 277S, Weizmann Institute of Science

department: Biomolecular Sciences

institute: Weizmann Institute of science

summary: Pancreatic beta-cells are highly specialized cells that produce and release insulin in response to nutrients, hormones and neurotransmitters. Glucose-induced insulin secretion, a unique feature of fully differentiated beta-cells, is only acquired after birth and is preceded by a phase of intense beta-cell proliferation. These events occurring in the neonatal period are critical for the establishment of an appropriate functional beta-cell mass covering the insulin needs throughout life. However, key regulators of gene expression and cis-regulatory elements involved in the cellular reprogramming along maturation remain to be elucidated. This project addresses this issue by using ATAC-seq (Assay for Transposase-Accessible Chromatin with high throughput sequencing) permitting a fine genome-wide mapping of chromatin accessibility. This approach is used to compare open chromatin regions in newborn and adult rat beta-cells. We obtained a genome-wide picture of chromatin accessible sites (100000) among which 20% were differentially accessible during maturation. Nearly 60% of these sites were in the proximity of significantly differentially expressed genes. An analysis of transcription factor binding sites revealed key known and unforeseen transcription factors which could explain these changes. We validated a transcriptional repressor named SCRT1, that depicted a significant effect on beta-cell proliferation and targeted several genes implicated in the acquisition of glucose-stimulated insulin secretion function. Thus, we were able to find several known and unforeseen key transcriptional regulators acting at cis-regulatory sites and promoters which depicted a differential accessibility and induced differential gene expression along maturation. These findings could be of interest to induce maturation of surrogate insulin-producing cells.

overall_design: RNA-seq of FACS sorted pancreatic beta-cells of adult  rats with siSCRT1 and control (n=5).

first: Claudiane

last: Guay

first: Adriana

last: Rodriguez-Trejo

first: Lisa

last: Stoll

first: Veronique

last: Menoud

first: Sonia

last: Gattesco

first: Romano

last: Regazzi


title: Sclerostin Antibody Does Not Promote Atheroprogression, Plaque Mineralization, or Inflammation in Ovariectomized Apolipoprotein E–Deficient Mice

city: South San Francisco

first: Yudong

last: He

address: 1120 Veteran Blvd

institute: Amgen

summary: Objective—Overexpression or administration of sclerostin has been reported to have atheroprotective and anti-inflammatory effects in apolipoprotein E knockout (ApoE KO) mice infused with angiotensin II; however, effects of sclerostin inhibition on these processes are not known. This study examined the effects of sclerostin inhibition with a sclerostin antibody on transcriptional changes in the aortic arch, associated morphological changes in aortic atherosclerotic plaques, and circulating markers of inflammation in ApoE KO ovariectomized (OVX) mice fed a high-fat diet. Approach and Results—Sclerostin antibody or vehicle was administered by subcutaneous injection once weekly for 3, 8, or 16 weeks to ApoE KO-OVX and wild-type-OVX mice fed a high-fat diet. As a comparator, alendronate or saline was administered twice weekly for 16 weeks to ApoE KO-OVX mice fed a high-fat diet. Sclerostin antibody had no effect on aortic total or mineralized plaque volume, determined by microcomputed tomography. Sclerostin antibody had no meaningful effects on plaque histopathology or systemic markers of inflammation or endothelial/platelet activation. Transcriptional analysis of the aortic arch revealed significant gene expression and signaling pathway changes in ApoE KO mice compared with wild-type, consistent with the genotype and atheroprogression, that were not affected by sclerostin antibody treatment. Alendronate treatment did not alter plaque volume or histopathology. Conclusions—This study shows that inhibition of sclerostin by sclerostin antibody does not promote atheroprogression or affect systemic markers of inflammation in the high-fat diet ApoE KO-OVX mouse model and does not alter the expression of genes/pathways implicated in atherosclerosis.

overall_design: The objective of this substudy was to evaluate transcriptional changes in the aorta in response to sclerostin antibody (Scl-Ab) treatment in high fat diet-fed ovariectomized (OVX) wild-type (WT) and Apolipoprotein E (ApoE) knockout mice. The test (Scl-Ab) and reference (vehicle) items were administered to OVX female mice by subcutaneous injection (interscapular region) once weekly. The aortic arch was harvested from the satellite animals after 3, 8 and 16 weeks of treatment, RNA extracted, and the transcriptional profile assessed using RNA-seq in three batches for timely evaluation. Differential gene expression in response to sclerostin antibody treatment was examined in wild-type and ApoE knockout mice.

first: James

last: Turk

first: Aimee

middle: M

last: Deaton

first: Jun

last: Yin

first: Marina

last: Stolina

first: Melanie

last: Felx

first: Gabrielle

last: Boyd

first: Jean

middle: G

last: Bienvenu

first: Gill

last: Holdsworth

first: Charles

last: Glaus

middle: D

first: Rogely

last: Waite Boyce


title: Circular RNA Profiling of Neutrophil Transcriptome Provides Insights into Asymptomatic Moyamoya Disease

first: Li

last: Lingzhi

address: 45 Changchun Street

department: neurology

institute: Xuanwu hospital

summary: Microarray based circRNAs profiling was determined between neutrophil samples from patients with asymptomatic MMD and healthy subjects. The microarray results were followingly confirmed by quantitative reverse-transcription PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses (KEGG) were adopted for annotation and predicting the functions of differentially expressed circRNAs. Results From this comparative circRNA microarray analysis of neutrophil samples from patients with asymptomatic MMD and healthy subjects, 123 circRNAs were identified differentially expressed between the two groups. Of these, 54 were upregulated and 69 were downregulated compared to controls (fold change > 2.0 and P < 0.05).

overall_design: Between July,2014 and Novemember,2015, five patients diagnosed with asymptomatic moyamoya disease by HR-MRI in Xuanwu hospital and five matched healthy volunteers were enrolled in our microarry detection.Overall, three male patients and two female patients with MMD (age range, 45-58 years) were included in this research, which were compared with five age- and sex-matched healthy volunteers (age range, 45-58 years).

first: Yumin

last: Luo

first: Qingfeng

last: Ma

first: Lingzhi

last: Li

first: Haiping

last: Zhao

first: Ziping

last: Han


title: Exploring the var gene interactome with CRISPR/dCas9

city: Paris

first: Sebastian

last: Baumgarten

address: 25, Rue du Dr. Roux

department: Parasites and Insect Vectors

country: France

institute: Institut Pasteur

summary: Epigenetic regulation of mutually exclusive transcription within the var gene family is important for infection and pathogenesis of the malaria parasite Plasmodium falciparum.  var genes are kept transcriptionally silent via heterochromatic clusters located at the nuclear periphery; however, only a few proteins have been shown to play a direct role in var gene transcriptional regulation. Importantly, the chromatin components that contribute to var gene nuclear organization remain unknown.  Here, we adapted a CRISPR-based immunoprecipitation-mass spectrometry approach for de novo identification of factors associated with specific transcriptional regulatory sequences of var genes. Tagged, catalytically inactive Cas9 (“dCas9”) was targeted to var gene promoters or introns, cross-linked, and immunoprecipitated with all DNA, proteins, and RNA associated with the targeted locus.  Chromatin immunoprecipitation followed by sequencing demonstrated that genome-wide dCas9 binding was specific and robust.  Proteomics analysis of dCas9-immunoprecipitates identified specific proteins for each target region, including known and novel factors such as DNA binding proteins, chromatin remodelers, and structural proteins.  We also demonstrate the ability to immunoprecipitate RNA that is closely associated to the targeted locus.  Our CRISPR/dCas9 study establishes a new tool for targeted purification of specific genomic loci and advances understanding of virulence gene regulation in the human malaria parasite.

overall_design: An enzymatically "dead" Cas9 (dCas9) protein with a C-terminal 3xHA tag protein was guided by a sgRNA to either the promoter or intron of var genes. To confirm binding of dCas9 to the anticipated target sites, dCas9-ChIP sequencing was performed 14 hours post infection. As input control, DNA collected prior to dCas9 immunoprecipotation was sequenced. To identify RNAs associated with the target loci, the same dCas9-ChIP experiment was performed followed by RNA extraction and sequencing. For each sample used for dCas9-RIP, an anti-HA and anti-IgG (negative control) immunoprecipitation was performed.

first: Jessica

last: Bryant

first: Artur

last: Scherf


title: Genome-wide screen of transcription co-regulators identifies GLIS2 as a repressor for p53 target genes [ChIP-seq]

city: Wuhan City

first: Qinglan

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

summary: GLIS2, a member of the sub-family of Krüppel-like zinc finger proteins, has been linked to the development of nephronophthisis, while few studies have been conducted on the connection between tumorigenesis and GLIS2. In the current study, we identified GLIS2 as a repressor for p53 target genes, such as PUMA. GLIS2 ChIP-seq demonstrated that GLIS2 binds directly on PUMA promoter. In addition, GLIS2 inhibits the binding of p53 on PUMA promoter region and the modification of H3K27ac on PUMA enhancer. Taken together, GLIS2 is identified as an oncogene in colorectal cancer.

overall_design: ChIP-seq for p53, H3K27ac, and p300 was performed in HCT116 followed by treatment with 375µM 5-FU and 10µM Nutlin3a for 8 h. GLIS2 ChIP-seq was performed by Dynabeads MyOne streptavidin C1 (Thermo-Fisher 65001). HCT116 cells were transfected with two different siRNAs of GLIS2 followed by treatment with 5-FU, ChIP-seq for p53, H3K27ac, H3K4me1 and H3K4me3 was performed.

first: Jie

last: Yao

first: Qing-lan

first: Pin-ji

last: Lei

first: Shan-bo

last: Tang

first: Qiong

last: Xiao

first: Ji

last: Chen

first: Lian-yun

first: Min

last: Wu


title: Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation [CLASH]

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

summary: By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. We rediscovered known and identified novel sRNA seed sequences. The sRNA-mRNA interactions identified by CLASH have strong base-pairing potential and are highly enriched for complementary sequence motifs, even those supported by only a few reads. Yet, steady state levels of most mRNA targets were not significantly affected upon over-expression of the sRNA regulator. Our results reinforce the idea that the reproducibility of the interaction, not base-pairing potential, is a stronger predictor for a regulatory outcome.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Cells expressing HIS6-TEV-3xFLAG tagged Hfq were grown in LB medium from early exponential phase to stationary phase. At various optical densities, cells were UV cross-linked in the Vari-X-linker and harvested by filtration. CLASH was subsequently performed on each sample using the tagged Hfq as bait to enrich for sRNA-terget interactions. The resulting associated RNAs were sequenced on Illumina platforms. We included two biological replicates of the density series. In addition, for each density, we generated rRNA-depleted total RNA sequencing data.


title: Genome-wide screen of transcription co-regulators identifies GLIS2 as a repressor for p53 target genes

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

overall_design: Refer to individual Series


title: Genome-wide screen of transcription co-regulators identifies GLIS2 as a repressor for p53 target genes [RNA-seq]

overall_design: RNA-seq was performed with two repetitions in HCT116 followed by treatment with 375µM 5-FU and 10µM Nutlin3a for 8 h. HCT116 cells were transfected with two different siRNAs of GLIS2 for 48 h followed by treatment with 375 μM 5-FU for 8 h, the gene expression profile was studied by RNA sequencing.


title: mirRNA Expression data from Human Mammary Epithelial Cells (HMECs) transduced with shp53, HRASV12, WNT1 and CCNE1 [miRNA expression]

city: montpellier

first: stanislas

last: du manoir

address: 280 rue des apothicaires

institute: IRCM

summary:
Gene expression differences, combined with distinct patterns of genomic rearrangements and epigenetic modifications constitute the bases of molecular classification of breast cancer. Molecular subtypes may originate from different cell lineages in the mammary gland, but also from the early activation of oncogenes that may drive the establishment of these molecular subtypes. However, in the natural history of human cancer, it is difficult to discriminate between these two factors : cell lineage and initial oncogenic alterations. In this work, we designed an experimental strategy  aiming at determining whether activation of distinct oncogenic pathways in human mammary epithelial cells (HMEC) could lead to different patterns of genetic and epigenetic changes. This work suggests  that the early activation of oncogenes is an important determinant of the establishment of breast cancer molecular subtypes along with cell lineage origin.
In this work, we overexpressed by retroviral transduction three oncogenes WNT1, CCNE1 and RASv12, known to activate different oncogenic pathways, in shp53 immortalized   human HMECs and monitored epigenetic and genetic changes at different steps of cell progression.Submitted publication : Distinct Oncogenic events induces different DNA methylation and copy number changes in human mammary epithelial cells.Claire Fonti, Anne Saumet, Amanda Abi-Khalil, Béatrice Orsetti,..., J. Colinge, Michael Weber, Claude Sardet, Stanislas du Manoir, Charles Theillet.

overall_design: For miR profiling total RNA were extracted uzing Trizol (Invitrogen/Thermo-Fisher, Illkirch-Graffenstaden, France ) according to manufacturer’s instructions from 18 samples. All samples are in duplicates. samples corresponding to HMEC cell just after   cell culture establishement are named R2. Two samples correspond to HMEC samples shortly after shP53 transduction (R2shP53early) and several weeks after shP53 transduction(R2shP53late). HMEC was then transduced with oncogene construct (either HRASV12, WNT1 or CCNE1), samples are called R2shp53-ONCOGENE.Late. Finaly,R2shp53-ONCOGENE samples were grown in soft agar. Samples are named R2shp53-ONCOGENE.SA after selection in soft agar.  For exact timing see the associated publication.

first: C

last: Theillet

first: S

last: du Manoir

last: Sardet

first: M

last: Weber

first: B

last: Orsetti

last: Fonti

first: A

last: Saumet


title: mRNA Expression data from Human Mammary Epithelial Cells (HMECs) transduced with shp53, HRASV12, WNT1 and CCNE1 [mRNA expression]

summary: Gene expression differences, combined with distinct patterns of genomic rearrangements and epigenetic modifications constitute the bases of molecular classification of breast cancer. Molecular subtypes may originate from different cell lineages in the mammary gland, but also from the early activation of oncogenes that may drive the establishment of these molecular subtypes. However, in the natural history of human cancer, it is difficult to discriminate between these two factors : cell lineage and initial oncogenic alterations. In this work, we designed an experimental strategy  aiming at determining whether activation of distinct oncogenic pathways in human mammary epithelial cells (HMEC) could lead to different patterns of genetic and epigenetic changes. This work suggests  that the early activation of oncogenes is an important determinant of the establishment of breast cancer molecular subtypes along with cell lineage origin.

overall_design:
In this work, we overexpressed by retroviral transduction three oncogenes WNT1, CCNE1 and RASv12, known to activate different oncogenic pathways, in shp53 immortalized human HMECs and monitored epigenetic and genetic changes at different steps of cell progression.
All samples are in biological duplicates. Primary HMECs are named R2. Two samples correspond to HMECs shortly after shP53 transduction (R2shP53_Early) and several weeks after shP53 transduction (R2shP53_Late). HMECs transduced with oncogenes (either HRASV12, WNT1 or CCNE1) are named R2shp53-ONCOGENE_Late. Finaly, HMECs transduced with oncogenes were also grown in soft agar and are named R2shp53-ONCOGENE_SA after selection in soft agar.


title: A Functional Role for REST Co-Repressor 2 (Rcor2) in Callosal Development

city: Bronx

first: Mark

middle: F

last: Mehler

address: 1300 Morris Park Ave.

department: Neuroscience

institute: Albert Einstein College of Medicine

summary: Pallial functional organization is mediated by the dynamic interplay of a broad spectrum of cellular and molecular cues that promote midline patterning, neurogenesis, axon guidance and neural connectivity. The regulators that orchestrate these seminal processes are still poorly understood. By employing a pallial conditional ablation model, we report that the transcriptional and epigenetic modulator, REST corepressor 2 (Rcor2) plays key roles in organizing the developing corticoseptal boundary.  ChIP-seq and RNA-seq analyses reveal that Rcor2 modulates a diverse repertoire of classes of genes with essential roles in CC development, including pallial/subpallial patterning, cell fate specification and axon guidance.

overall_design: ChIP-sequencing performed on embryonic day 14.5 midline cortex of C57/Bl6 strain mice.  Immunoprecipitation was carried out using an Rcor2 specific antibody, or a rabbit IgG non specific mock antibody.  2 replicates of each immunoprecipitation were multiplexed using the NEBnext II library prep kit and sequenced through Cornell epigenomcs core facility using a Hiseq2500 platform.  RNA-seq was performed on E14.5 cortical midline comparing Rcor2f/f used as controls versus Rcor2f/f/EMX1-iCRE conditional knockouts. 2 Replicates per genotype were used.  Multiplexed libraries were generated with the TRUseq Total RNA library prep kit, and sequenced on a Hiseq2500 platform by the Cornell epigenomics core facility.

first: Christopher

last: DeJesus

first: Aldrin

last: Molero

first: Ping

last: Wang

first: Deyou

last: Zheng

first: Solen

last: Gokhan


title: Drop-Seq analysis of rTg4510 mouse hippocampus and control at young and old age

city: Santa Barbara

first: Veronique

last: Lisi

state: California

address: Neuroscience Research Institute, Bldg 571, room6131

department: Neuroscience Research Institute

institute: University of California Santa Barbara

summary: Single cell suspension of hippocampus was generated and single cell mRNAseq libraries were prepared using Drop-seq.

overall_design: Dropseq was performed on the hippocampus of old (>30 weeks) rTg4510 animals, rTTa, P301L and double negative (WT) littermates and on young (2-4 weeks) rTg4510 and double negative (WT) littermate controls.


title: DNA methylation data from Human Mammary Epithelial Cells (HMECs) transduced with shp53, HRASV12, WNT1 and CCNE1 [RRBS-seq]


title: DNA methylation and mirRNA/mRNA Expression data from Human Mammary Epithelial Cells (HMECs) transduced with shp53, HRASV12, WNT1 and CCNE1

platform_organism:
Homo sapiens
synthetic construct


title: Deficient LRRC8A-dependent Volume-Regulated Anion Channel (VRAC) activity is associated with male infertility in mouse and humans

city: Smithville

first: Jianqiang

last: Bao

state: Texas

address: 1808 Park Road 1C (P.O. Box 389), Smithville  TX 78957

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: We reported the essential function of Lrrc8a on germline development

overall_design: Examination of differentially expressed genes between WT and lrrc8a MUT testis

first: Jiangqiang

first: Fernando

middle: J

last: Benavides

first: Yue

last: Lu


title: Effect of very low concentrations (< 10 μM) of glucose on T. brucei gene expression

city: Clemson

first: Rooksana

middle: Elizabeth

last: Noorai

state: South Carolina

address: 105 Collings St, BRC 157

department: Clemson University Genomics and Bioinformatics Facility

institute: Clemson University

summary: The ability to adapt to varying nutrient availability in changing environments is critical for successful parasitism.  The lifecycle stages of the African trypanosome, Trypanosoma brucei, that infect the host mammalian bloodstream utilize glucose exclusively for ATP production.  The finding that trypanosomes also inhabit other tissues that frequently contain lower glucose concentrations suggests blood stage parasites may have to respond to a dynamic environment with changing nutrient availability in order to survive.  However, little is known about how the parasites coordinate gene expression with nutrient availability.  Through transcriptome analysis, we have found blood stage parasites deprived of glucose alter gene expression in a pattern similar to transcriptome changes triggered by other stresses.  A surprisingly low concentration of glucose (<10 μM) was required to initiate the response.  To further understand the dynamic regulation of gene expression that occurs in response to altered glucose availability in the environment, we have interrogated the 3’UTR of cytochrome c oxidase subunit VI, a known lifecycle stage regulated gene, and have identified a stem-loop structure that confers glucose-responsive regulation at the translational level.

overall_design: Six samples types, with 2-3 replicates each, which consist of 2 forms of T. brucei parasites (long slender and bloodstream) in varying concentrations of glucose at 0hrs and 12hrs. Three samples (LS_+glc replicates) were previously submitted in BioProject PRJNA438967 and SRA Study accession SRP142743. All 17 samples are included in BioProject PRJNA454021.  All LS_-glc and BF* samples are in SRA Study accession SRP145483.

first: Yijian

last: Qiu

first: Vijay

last: Shankar

first: Nelson

last: Yeung

first: Sarah

last: McAlpine

first: James

last: Morris


title: Genome-wide expression in asymmetric histone H3 mutants in Saccharomyces cerevisiae

city: Worcester

first: Caitlin

last: Connelly

state: MA

address: 364 Plantation Street, LRB

department: Biochemistry & Molecular Pharmacology

institute: University of Massachusetts Medical School

summary: Using histone H3 mutants designed so that they can only form a heterodimer, we studied the gene expression in a collection of mutants, comparing mutations to one histone H3 tail of a nucleosome compared to two histone H3 tails of a nucleosome.

overall_design: RNA-Seq on 13 different histone H3 mutants present in asymmetric or symmetric form, as well as 8 additional histone H3 mutants present in asymmetric form (symmetric form was presumed lethal in these remaining).

first: Oliver

last: Rando


title: Transcriptome analysis of light-utilizing Strain IMCC1322, a member of SAR116 group bacteria

city: Busan

first: Hyun-Myung

last: Oh

state: South Korea

address: Yongdang Campus, Sinseonro 365 Namgu

department: Marine Bio-Cnvergence Science

institute: Pukyong National University

summary: The purpose of this study is to elucidate the proteorhodopsin function based on the genome of strain IMCC1322 which was cultivated species of SAR116 from East Sea of Korea. Light-enhanced photoheterotrophy of strain IMCC1322 is interrogated by the transcriptomics of IMCC1322 once the appropriate phenotypic characteristics are revealed by cultivation and polyphasic studies. Transcriptome revealed that green light (max. wavelength =522nm) drives metabolism and cessation of bacterial aging of IMCC1322. Here we report the mRNA profiling of IMCC1322 which is the first effort to the biogeochemistry of light-utilizing SAR116 group in the ocean.

sample_organism: Candidatus Puniceispirillum marinum IMCC1322

overall_design: Examination of 6 different mRNA sampled from dark/light/diel cultures of IMCC1322 from 3 and 6 days post inoculation

first: Wang-Rim

last: Jung

first: Hyung-Jin

last: Yu

first: Yong-Hak

last: Kim

first: Jang-Cheon

last: Cho


title: Gene expression data from CITED4 knockout and control mouse hearts after transverse aortic constriction

status: Public on Apr 30 2020

city: Charlestown

first: Robert

last: Kitchen

institute: MGH / HMS

summary:
Rationale:
Cardiac CITED4 is induced by exercise and is sufficient to cause physiological hypertrophy and mitigate adverse ventricular remodeling after ischemic injury. However, the role of endogenous CITED4 in response to physiological or pathological stress is unknown.
Objective:
To investigate the role of CITED4 in murine models of exercise and pressure overload.
Methods and Results:
We generated cardiomyocyte-specific CITED4 knockout mice (C4KO) and subjected them to an intensive swim exercise protocol as well as transverse aortic constriction (TAC). Echocardiography, western blotting, qPCR, immunohistochemistry, immunofluorescence, and transcriptional profiling for mRNA and miRNA expression were performed. Cellular crosstalk was investigated in vitro.
CITED4 deletion in cardiomyocytes did not affect baseline cardiac size or function in young adult mice. C4KO mice developed modest cardiac dysfunction and dilation in response to exercise. After TAC, C4KOs developed severe heart failure with left ventricular dilation, impaired cardiomyocyte growth accompanied by reduced mammalian target of rapamycin (mTOR) activity and maladaptive cardiac remodeling with increased apoptosis, autophagy, and impaired mitochondrial signaling. Interstitial fibrosis was markedly increased in C4KO hearts after TAC. RNAseq revealed induction of a pro-fibrotic miRNA network. miR30d was decreased in C4KO hearts after TAC and mediated crosstalk between cardiomyocytes and fibroblasts to modulate fibrosis. miR30d inhibition was sufficient to increase cardiac dysfunction and fibrosis after TAC.
Conclusions:
CITED4 protects against pathological cardiac remodeling by regulating mTOR activity and a network of miRNAs mediating cardiomyocyte to fibroblast crosstalk. Our findings highlight the importance of CITED4 in response to both physiological and pathological stimuli.

overall_design: Eight samples were analyzed over all, four samples from CITED4 knockout hearts and four samples from floxed control hearts

first: Carolin

last: Lerchenmueller


title: Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms

city: irvine

first: Sorena

last: Rahmanian

state: ca

address: 2134 verano pl

department: Center for Complex Biological Systems

institute: University of California Irvine

summary: The steady state expression of each gene is the result of transcriptional rate, dynamic processing, and degradation of RNA. While regular RNA-seq methods only measure steady state expression levels, RNA-seq of metabolically labeled RNA identifies transcripts that were transcribed during the window of metabolic labeling. Whereas short-read RNA sequencing can identify metabolically labeled RNA at the gene level, long-read sequencing results in dramatically improved resolution of isoform-level transcription. Here we combine thiouridine-to-cytosine conversion (TUC) with PacBio long-read sequencing to study the dynamics of mRNA transcription in the GM12878 cell line. We show that using long-TUC-seq, we can detect metabolically labeled mRNA of distinct isoforms more reliably than using short reads. Long-TUC-seq holds the promise of capturing isoform dynamics robustly and without the need for enrichment.

overall_design: PacBio and Illumina sequencing of  TUC-seq treated GM128278 replicates with their corresponding controls

first: Ali

last: Mortazavi


title: Unique genomic and neoepitope landscapes across tumors: a study across time, tissues, and space within a single Lynch Syndrome patient

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

summary: To investigate the longitudinal mutational patterns arising in Lynch Syndrome associated tumors we interrogated the genomes of five different cancers that arose over a period of 10 years in a patient who underwent resection in the absence of chemotherapy and radiation for each cancer. These included a papillary transitional cell carcinoma (PTCC) in the renal pelvis, a duodenal carcinoma, two separate CRCs that arose 3 years apart, and multiple regions of a triple negative breast cancer (TNBC).  In each case we flow sorted tumor fractions from archived formalin fixed paraffin embedded (FFPE) tissue and profiled the tumor genomes with whole genome copy number variant (CNV) arrays and whole exome sequencing. These data were then used to identify the pathogenic variant underlying the diagnosis of LS, and to compare and contrast the CNV, mutational and neoepitope patterns across these divergent tumors that arose over a 10 year period. These results provide a unique analysis of distinct MSI+ tumors arising in a single LS patient.

overall_design: We applied DNA content based flow sorting to isolate the nuclei from biopsies of five distinct tumors that arose in a patient with Lynch Syndrome over a 10 year period. We coupled this strategy with oligonucleotide array CGH (aCGH) and whole exome sequencing (WES), thereby obtaining high definition genomic profiles of from each tumor. The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2). Reads from the WES BAM files were stripped using XYalign version 1.1.5 then mapped to the 1000 genomes version of GRCh38 using bwa-mem version 0.7.17. We applied EpitopeHunter to predict neoepitopes.

first: Tanya

last: Phung

first: Elizabeth

last: Lenkiewicz

first: Smriti

last: Malasi

first: Amit

last: Sharma

first: Karen

middle: S

last: Anderson

first: Melissa

middle: A

last: Wilson

first: Barbara

last: Pockaj


title: A Study of the Gene Expression of Colorectal Liver Metastases: Tumour, ‘Halo’ and Liver Parenchyma

city: Guildford

first: Emma

last: Laing

address: Stag Hill

institute: University of Surrey

summary: This was a study comparing the gene expression of liver parenchyma, metastatic colorectal cancer within the liver, and the halo, which is an artifactual area which contained metastatic colorectal cancer before neo-adjuvant chemotherapy reduced the cancer.

overall_design: Three-condition experiment, Normal liver vs. Metasis and Metasis halo.

first: Jeff

last: Lordan

first: Giselda

last: Bucca

first: Colin

middle: P

last: Smith


title: Expression profiling of Cellvibrio japonicus using either glucose, crab shell,  or N-acetylglucosamine

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Chitin utilization by microbes plays a significant role in cycling of carbon and nitrogen in the biosphere, and the study of the microbial approaches used to degrade chitin will facilitate our understanding of bacterial strategies to degrade this recalcitrant polysaccharide. The early stages of chitin depolymerization by the bacterium Cellvibrio japonicus have been characterized and are dependent on one chitin-specific lytic polysaccharide monooxygenase and non-redundant glycoside hydrolases from the family GH18 to generate chito-oligosaccharides for entry into metabolism. Here, we describe the mechanisms for the latter stages of chitin utilization by C. japonicus with an emphasis on the fate of chito-oligosaccharides. Our systems biology approach combined transcriptomics, bacterial genetics, and complex environmental substrates to determine the essential mechanisms for chito-oligosaccharide transport and catabolism in Cellvibrio japonicus. Using RNAseq analysis we found not only the up-regulation of genes that encode CAZymes specific for chitin metabolism but also a coordinated expression of non-chitin specific CAZyme genes. Furthermore, we used mutational analysis to characterize the hex20B gene product, predicted to encode a hexosaminidase, and found that it is required for efficient utilization of chito-oligosaccharides. Surprisingly, two additional gene loci (CJA_0353 and CJA_1157), which encode putative TonB-dependent transporters, were essential for shuttling chito-oligosaccharides into the periplasmic space. Here we propose naming these loci cttA (chito-oligosaccharides transporter A) and cttB respectively. This study further develops our model of how C. japonicus can derive nutrients from recalcitrant chitin-containing substrates and may be potentially useful for other environmentally or industrially important bacteria.

overall_design: Three carbon conditions (Crab Shell, glucose, N-acetylglucosamine); Two sample points (exponential phase, stationary phase); Data collected in biological triplicate; Total of 18 samples


title: scRNA-seq of E15.5 epicardium and epicardium-derived cells

city: Oxford

first: Irina-Elena

last: Lupu

address: Sherrigton Building

department: DPAG

institute: University of Oxford

summary: The embryonic epicardium provides a source of multipotent progenitors for cardiac lineages, including pericytes, fibroblasts and smooth muscle cells. However, it remains unclear if the epicardium comprises of heterogeneous progenitors or if epicardial cells are multipotent. Using scRNA-seq, we analysed the expression profile of epicardial  and epicardial-derived cells at E15.5 and found no evidence of discrete epicardial sub-compartments. Our findings also support the notion that epicardial fate is specified after epithelial-mesenchymal transition, not pre-determined.

overall_design:
E15.5 heart tdTOM+ sorted cells labelled with Wt1CreERT2;
SMART-Seq2 sequencing of E15.5 heart tdTomato positive sorted cells labelled with tamoxifen induction at E9.5 (1mg) and E11.5 (1mg) of Wt1CreERT2 from 6 pooled C57BL/6 embryos

The following additional sample information is provided in the 'associated_metadata15_updated.csv':
nGene: number of genes/cell
nUMI: number of unique molecular identifiers/cell
percent.mito: percentage of mitochondrial genes/cell
S.Score:
S phase score calculated using Cell Cycle Regression vignette in Seurat
G2M.Score:
G2M phase score calculated using Cell Cycle Regression vignette in Seurat
Phase:
cell cycle phase determined by Cell Cycle Regression Vignette in Seurat
CC.differences:
score calculated using the Alternative Cell Cycle Regression Vignette in Seurat
res 0.6/0.8/1/1.2/1.4:
Different cluster allocation calculated via  FindClusters in Seurat

first: Nicola

last: Smart


title: Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism [CRISPR]

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

institute: University of Toronto

summary: The de novo synthesis of fatty acids has emerged as a therapeutic target for various diseases including cancer. Since cancer cells are intrinsically buffered to combat metabolic stress, it is important to understand how cells may adapt to loss of de novo fatty acid biosynthesis. Here we use pooled genome-wide CRISPR screens to systematically map genetic interactions (GIs) in human HAP1 cells carrying a loss-of-function mutation in FASN, which catalyzes the formation of long-chain fatty acids. FASN mutant cells show a strong dependence on lipid uptake that is reflected by negative GIs with genes involved in the LDL receptor pathway, vesicle trafficking, and protein glycosylation. Further support for these functional relationships is derived from additional GI screens in query cell lines deficient for other genes involved in lipid metabolism, including LDLR, SREBF1, SREBF2, ACACA. Our GI profiles also identify a potential role for the previously uncharacterized gene LUR1/C12orf49 in exogenous lipid uptake regulation through modulation of SREBF2 signalling in response to lipid starvation. Overall, our data highlight the genetic determinants underlying the cellular adaptation associated with loss of de novo fatty acid synthesis and demonstrate the power of systematic GI mapping for uncovering metabolic buffering mechanisms in human cells.

overall_design: Genome-wide CRISPR gene knockout screens were performed in human HAP1 cells across 6 gene knockout queries implicated in lipid metabolism. Genetic interactions were identified by comparison of each query's fitness  profile to screens in HAP1 WT cells. The FASN screen was performed as three biologically independent replicates.

last: Aregger

first: Keith

last: Lawson

first: Maximillian

last: Billmann

last: Costanzo

first: Amy

middle: H

last: Tong

first: Katherine

last: Chan

first: Mahfuzur

last: Rahman

first: Kevin

middle: R

last: Brown

first: Catherine

last: Ross

first: Matej

last: Usaj

first: Lucy

last: Nedyalkova

first: Olga

last: Sizova

first: Andrea

last: Habsid

first: Judy

last: Pawling

first: Zhen-Yuan

last: Lin

first: Hala

last: Abdouni

first: Cassandra

last: Wong

first: Alexander

last: Weiss

first: Patricia

last: Mero

first: James

middle: W

last: Dennis

first: Anne-Claude

last: Gingras

first: Chad

middle: L

last: Myers

first: Brenda

last: Andrews

first: Charles

last: Boone


title: A hybrid signal/sequence model to detect RNA polymerase activity in ATAC-seq

city: Boulder

first: Ignacio

middle: Javier

last: Tripodi

state: Colorado

address: 3415 Colorado Avenue

department: Computer Science

institute: University of Colorado, Boulder

summary: We explore different uses of machine learning classifiers, including neural networks, to combine the “signal” from ATAC-seq with its underlying genome sequence in order to classify ATAC-seq peaks on the presence or absence of transcription. We show how a hybrid signal/sequence representation, classified using recurrent neural networks (RNNs), yields the best performance across different cell types.

overall_design: HCT116 treated with 10 ul DMSO (control) or 10 μM Nutlin-3A (inhibitor of p53) in DMSO [Sigma SML0580]

first: Mary

last: Allen

first: Robin

last: Dowell


title: ChIP-seq analysis of H3K9ac and H4K16ac

status: Public on Apr 29 2020

city: Beijing

first: Qianhong

last: Ye

address: Malianwa

institute: China Agricultural University

summary: We report the application of H3K9ac- and H4K16ac-based sequencing technology for high-throughput profiling of histone modifications in human granulosa KGN cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of KGN cells. We find that H3K9ac effectively discriminates genes that are influenced by butyrate treatment. H4K16ac described less influence of genes by butyrate treatment. Finally, we show that butyrate could mediate the H3K9ac to effectively influence genes that related to biological functions ang signalings. This study provides a framework for the application of comprehensive gene profile towards H3K9ac regulation by butyrate in human granulosa KGN cells.

overall_design: Examination of 2 different histone modifications in KGN cells by butyrate treatment.

first: Xiangfang

last: Zeng


title: Gene Expression Patterns of Quiescent and Activated  Mouse Primary Hepatic Stellate Cell (HSC)

city: Guangzhou

first: Chen

last: Qu

state: Guangdong

address: #601 West Huangpu Road

institute: Jinan University

summary: Liver fibrosis is a manifestation of chronic liver injury. It leads to hepatic dysfunction and is a critical element in the pathogenesis of cirrhosis and hepatocellular carcinoma. The activation of hepatic stellate cells (HSC) plays a central role in liver fibrogenesis of different etiologies. To elucidate the molecular mechanism of this phenomenon, it is important to analyze the changes in gene expression that accompany the HSC activation process. In this study, we isolated quiescent and activated HSCs from control mice and mice with CCl4-induced liver fibrosis, respectively, and performed RNA sequencing to compare the differences in gene expression patterns between the two types of HSCs.

overall_design: Quiescent and activated hepatic stellate cells (qHSCs and aHSCs) were isolated from three control mice (0.1mL olive oil gavage, thrice a week for eight weeks)  and three mice with CCl4-induced liver fibrosis (0.1 mL of a 40% CCl4-olive oil solution gavage, thrice a week for eight weeks) respectively. And transcriptome profiles of qHSCs and aHSCs were generated by RNA sequencing using Illumina HiSeq 4000.


title: Whole transcriptome profiles and ribosome profiling of thapsigargin- and tunicamycin-treated LN308 cells

city: Heidelberg

first: Grischa

last: Toedt

address: Meyerhofstr. 1

department: Computational Biology

institute: EMBL

summary: Accumulation of unfolded proteins in the endoplasmic reticulum triggers the unfolded protein response (UPR), an adaptive signal transduction pathway aimed at reinstating cellular homeostasis, or, if that fails, at triggering of apoptosis. To gain a comprehensive and systems-wide understanding of the UPR, we have pursued a multi-omics approach that, upon chemical induction of the UPR with two different compounds, monitors in parallel several parameters in the astrocytoma cell line LN-308. Changes to the cellular transcriptome (by high throughput sequencing) and altered translation status (by ribosome profiling) were measured after 2h and 6h of treatment.

overall_design: Whole transcriptome profiles and ribosome profiling libraries were generated for thapsigargin- and tunicamycin-treated LN308 cell lines by next generation sequencing (Illumina Next Seq 500). Samples were taken after 0, 2 and 6 hours of pharmacological treatment.

first: Stefan

last: Reich

first: Jan

last: Medenbach


title: miRNA profiles on wild caught mosquitoes in Grenada West Indies

city: MILTON

first: Maria

middle: Eugenia

last: Ramos-Nino

state: VT

address: 257 LAKE RD

department: Microbiology

institute: SGU

summary:
Determination of miRNA profiles in most prominent mosquitoes will determine the potential targets for mosquito control
Some of the most medically important viruses, such as dengue virus, West Nile virus, Zika virus, and yellow fever virus, are transmitted by mosquitoes. These aptly named arboviruses impose a tremendous cost to the health of populations around the world. As a result, much effort has gone into the study of the impact of these viruses in human infections. Comparatively less efforts, however, have been made to study the way these viruses interact with mosquitos themselves. It has long been held that these viruses are introduced into the midgut of mosquitoes upon ingestion of a blood meal before being transmitted within the saliva upon subsequent feeding. This sequence requires that the mosquito be able to defend itself from infection every step along the way-from ingesting bloodmeal to subsequent feeding. The main defense mechanisms employed by the mosquitoes to control viruses is RNA interference (RNAi). Modulation of this facet of the mosquito’s immune system would thereby suggest a practical strategy for vector control. This paper will provide an up to date overview of the mosquito’s immune system along with novel data describing miRNA profiles for Aedes aegypti and Culex quinquefasiatus in Grenada, West Indies.

sample_organism:
Aedes aegypti
Culex quinquefasciatus

overall_design: Pools of RNA from mosquitoes trapped in 2018 (12 months) were analyzed

middle: E

first: Daniel

last: Fitzpatrick

first: Sonia

last: Cheetham

first: Julie

last: Dragon


title: Gene expression changes in response to UV-B and low R:FR vs low R:FR in wild-type,uvr8 and hfr1 mutants

city: Geneva

first: Roman

last: Ulm

address: 30 Quai E. Ansermet

department: Department of Botany and Plant Biology

country: Switzerland

institute: University of Geneva

summary: We analysed global gene expression changes in Arabidopsis thaliana in response to 3h low R:FR or UV-B or both , in order to elucidate the transcriptional reprogramming elicited by UV-B antagonism of shade avoidance response.

overall_design: mRNA profiles generated by deep sequencing from triplicate replicate Arabidopsis thaliana 7day old seedlings samples sourced from independent seedling plates either exposed for 3h to low R:FR, or white light supplemented with UV-B, or both.

first: E

last: Tavridou

first: R


title: Genome-wide gene expression profiling of anti-tuberculosis drugs-treated macrophages

city: Paris

first: Alexandre

last: Giraud-Gatineau

address: 25-28 rue du docteur roux

institute: Institut Pasteur

summary:
Background: Tuberculosis (TB) remains a major public health problem, especially in developing countries, with 1.5 million deaths annually worldwide. Antibiotics are commonly used in the treatment of bacterial infections. As with most drugs, antibiotic treatment can also alter host metabolism, leading to adverse side-effects. Antibiotics can also interfere with the immune system, indirectly through the disturbance of the body’s microbiota or directly by modulating the functions of immune cells. It is therefore important to understand how antibiotic treatment modulates immune cell  functions. Here we aim to evaluate the impact of first-line anti-TB drugs on the response of human macrophages infected with Mycobacterium tuberculosis (MTB).
Results: Human macrophages  were stimulated with heat-killed Mycobacterium tuberculosis (hk-MTB) and treated with isoniazid (INH), rifampicin (RIF), ethambutol, pyrazinamide (PZA) or amikacin (AMK). After 24h of treatment, RNA was collected and we characterized the genome-wide gene expression profiles of drug-treated cells by RNAseq. 556, 752 and 7  genes were differentially expressed in hk-MTB-stimulated macrophages upon RIF, PZA and EMB treatment respectively, whereas in uninfected macrophages, 448 and 11 genes were differentially expressed upon RIF and PZA treatment respectively. No genes were differentially expressed upon INH and AMK treatment. We classified all modulated genes by performing gene-set enrichment analysis. The gene set regulated by PZA in infected macrophages  was significantly enriched for genes involved in Integral to lumenal side of endoplasmic reticulum membrane, Cytokine-mediated signaling pathway or Interferon-gamma-mediated signaling pathway. In hk-MTB-stimulated macrophages treated by RIF, we found an enrichment in Endoplasmic reticulum unfolded protein response, NADP binding or Lipid metabolic process.
Conclusions: Our results highlight the importance to understand how antibiotic treatment modulates macrophage (Mφ) functions, and more generally, how it impacts the host immune response.

overall_design: mRNA sequencing of human monocytes-derived macrophages treated with RIF, PZA, EMB or AMK. The cells were either infected with Mycobacterium tuberculosis resistant to the drug, or were uninfected.

first: Ludovic

last: Tailleux


title: The secretion regulation mechanisms of pollination drop in Ginkgo biloba L.

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

summary: High-throughput RNA, sRNA and degradome sequencing were conducted to identify a large number of mRNA, miRNAs and their targets in G. biloba ovules at two different developmental stage, which provided useful information for uncovering the secretion regulatory mechanisms of G. biloba pollination drop.

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

first: Bei

last: Jiang


title: Transgenerational effects of paternal restraint stress in Drosophila

city: Tsukuba

first: Ki-Hyeon

last: Seong

state: Ibaraki

address: 3-1-1 Koyadai

institute: RIKEN

summary: At present, the experimental evidences of epigenetic inheritance caused by stresses are beginning to accumulate in some animal models. However, molecular mechanism and biological meaning underlying these phenomena has not been clearly understood yet. Previously, we showed that Drosophila transcription factor-2 (dATF-2) is involved in heterochromatin formation and that phosphorylation of dATF-2 by various stresses, such as heat shock and osmotic stresses, induces heterochromatin disruption. We also revealed these stress dependent epigenome changes mediated by dATF-2 can be inherited to next generations (Seong et al., 2011). In this study, we established a drosophila model of restraint stress (RS) to analyze the transgenerational effects of strong psychological stress. We observed that Drosophila F1 progenies, derived from RS exposed fathers, showed significant disruption of heterochromatin state and that such effect was not observed in the dATF-2 and MEKK1 mutant background. To reveal trangenerational effects and role of paternal restraint stress, we analyzed gene expression profiles of F1 progenies derived from either RS exposed or control fathers of wild-type and dATF-2 KO father.

overall_design: w[1118] females were crossed to w[1118] or dATF-2[KO] males treated with/without restraint stress (RS) (10 hours, 3 times). After that, 6-7-days old F1 progenies were frozen by nitrogen liquid and separated to head and other parts, and then prepared mRNA.  RNA-seq dataset include 5-6 biological replicates.

first: Shunsuke

last: Ishii

first: Yuki

last: Katou

first: Naoko

last: Yokota

first: Ryuichiro

last: Nakato

first: Katsuhiko

last: Shirahige