title: Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast

city: New Haven

first: Yinuo

last: Wang

address: 333 Cedar St C129

department: Molecular Biophysics and Biochemistry

institute: Yale University

summary: Ribosome binding proteins function broadly in protein synthesis, gene regulation and cellular homeostasis but the complete complement of functional ribosome-bound proteins remains unknown. Using quantitative mass spectrometry we identified Late-annotated short open reading frame 2 (Lso2) as a ribosome-associated protein that is broadly conserved in eukaryotes. Genome-wide crosslinking and immunoprecipitation of Lso2 and its human ortholog CCDC124 recovered 25S rRNA in a region near the A site that overlaps the GTPase activating center. Consistent with this location, Lso2 also crosslinked to most tRNAs. Ribosome profiling of yeast lacking LSO2 (lso2Δ) revealed global translation defects during recovery from stationary phase with translation of most genes reduced more than 4-fold. Ribosomes accumulated at start codons, were depleted from stop codons, and showed codon-specific changes in occupancy in lso2Δ. These defects, and the conservation of the specific ribosome-binding activity of Lso2/CCDC124, indicate broadly important functions in translation and physiology.

overall_design: Enhanced crosslinking and immunoprecipitation (IP) followed by deep sequencing: 5 IP samples of Lso2 and CCDC124, 6 controls of size-matched input and untagged IP. Ribosome footprint profiling: 7 samples of wild-type and 7 samples of lso2 null mutants.

first: Wendy

last: Gilbert


title: Rat IUGR islet transcriptome sequencing at 2 time points

status: Public on Sep 11 2018

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: Intrauterine growth restriction (IUGR) increases the risk of developing type 2 diabetes during adulthood.  At day 18 of gestation, we used bilatual uterine artery ligation (BUAL) to restrict nutrient supply to developing rat fetuses to produce IUGR pups. At 2 and 10 weeks of age pancreatic islets were isolated and total RNA extracted using Trizol. Samples with RNA integrity numbers greater than 7 were used to generate libraries

overall_design: 2 experimental conditions (IUGR and Control) and 2 time points (2 and 10 weeks of age) 3 biological replicates

first: Cetewayo

middle: S

last: Rashid

first: Lane

middle: J

last: Jaeckle-Santos

first: Yu-Chin

last: Lein

first: Kyoung-Jae

first: Rebecca

middle: A

last: Simmons

first: Amita

last: Bansal


title: Transcriptional coactivator PGC-1α contains a novel CBP80-binding motif that orchestrates efficient target gene expression

city: Rochester

first: Lynne

last: Maquat

state: New York

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

summary: This RNA-seq dataset was generated to identify genes whose transcription relies on the CBP80-binding motif (CBM) of PGC-1α in C2C12 mouse myoblasts.

overall_design: We compared the levels of transcripts expressed in total-cell lysates of WT C2C12 MBs and PGC-1α-KD C2C12 MBs, the latter expressing FLAG alone, FLAG-PGC-1α(WT) or FLAG-PGC-1α(ΔCBM). Each of the four conditions was analyzed in triplicate.

first: Hana

last: Cho

first: Michael

middle: L

last: Gleghorn

first: Xavier

last: Rambout

first: Christopher

middle: R

last: Phipps

first: Keita

last: Miyoshi

first: Phuong

last: Nguyen

first: Rudi

last: Fasan

first: Jason

last: Myers

first: Naoyuki

last: Kataoka

middle: E


title: ZnO-nanoparticles induce changes in the expression of genes associated with stress responses in spinach (Spinacia oleracea) without affecting Zn uptake

status: Public on Sep 10 2018

city: Brookings

first: Jose

middle: L.

last: Gonzalez

state: SD

address: Agricultural Hall

department: Plant Science

institute: South Dakota State University

summary:
Purpose: To examine the gene expression within the spinach root tissues as a response to exposure to nanoparticles.
Methods: Sequenced reads were processed using CLC Genomics Workbench 7.0. The reads were trimmed based on quality, length and ambiguity. Resulting reads were assembled into transcript assemblies. Sequence reads were mapped back to the constructed transcriptome. TAs were BLAST searched against a local blast database of coding sequences of Arabidopsis thaliana. Statistical analysis was performed using Baggerley’s test. Transcript assemblies were tested for gene enrichment using GO annotations and the functional categories were determined. MapMan was used to visualize gene expression data of TAs and study the biological pathways.
Results: De novo assembly of the trimmed reads yielded 147,733 Transcript Assemblies (TA) with an average length of 645 bp. Largest TA was 16,379 bp. Approximately 89% of the quality trimmed reads from the different samples mapped successfully to the assembly reference. Gene expression data for spinach TAs homologous to Arabidopsis genes show upregulation of protein degradation pathways in the nano-ZnO treatment compared to the non-nanoZnO, this upregulation is coupled with a down regulation of the genes in the protein synthesis pathways crucial role in the spinach plant responses to ZnO nanoparticle exposure. Genes associated (REDOX, signaling and transcription factors) with responses to stresses (both abiotic and biotic) were upregulated upon exposure to ZnO nanoparticles. Additionally genes in biosynthesis pathways of jasmonate and gibberellins genes were up-regulated upon exposure to ZnO nanoparticles in spinach.
Conclusions: A de novo transcriptome was developed for spinach. When spinach plants were exposed to ZnO nanoparticles, they seem to sense the nanoparticles similarly to external chemicals or pathogens and induced production of reactive oxygen species. Hormone signaling pathways were activated leading to the induced expression of hormones with different roles in defense.

overall_design: Six spinach root tissue samples, three replicates from each treatment 500 µM-ZnO-nano and 500 µM-ZnO-bulk were then selected for library construction and sequencing on the Illumina HiSeq2000.

first: Padmapriya

last: Swaminathan


title: Circadian Changes in the Pineal and Retina Transcriptomes of the Chicken as  Revealed by RNA Sequencing

status: Public on Sep 08 2018

city: Bethesda

first: Steven

last: Coon

state: MD

address: 10 Center Dr; Room 8S261A

department: NICHD

institute: National Institutes of Health

summary: Here pineal gland and retina transcriptomes of chicken have been characterized  using RNA-seq, with the goals of building a near complete data base of the  thousands of transcripts in these tissues and promoting a better understanding of the genetic basis of their unique and overlapping functions. This effort has extended previous gene profiling efforts by the identification of thousands of transcripts not previously reported to exist in these tissues, hundreds of which exhibit daily rhythms in abundance. Gene expression appears to occur in four waves, peaking at distinct times during the 24 hour period. In this study animals were kept in constant darkness with the intention of identifying changes that occur as a function of the internal clock, not as a function of environmental lighting. Accordingly, the rhythmic changes identified are likely to be truly circadian in nature and to be either part of the biological clock or to be clock controlled genes. Ontological analysis of the tissue enriched transcripts and of the rhythmically expressed transcript revealed that many are linked to visual transduction, circadian clock function and melatonin synthesis.  The findings of this report will be of significant value in future studies of the genetic basis of pineal and retinal function.

overall_design: Three pineal glands or single retinas were collected in triplicate at circadian time 0, 4, 8, 12, 16, 20. Rhythmically expressed transcript were identified through RNA-seq based on these samples.

first: Leming

last: Shi


title: Global gene-expression profiles of WT Arabidopsis (Col-0), npr1-1, and hac1/5 treated with water or INA

status: Public on Sep 07 2018

city: Seoul

first: Hongshi

last: Jin

address: Gwanak_599 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Global gene-expression profiles of WT Arabidopsis (Col-0), npr1-1, and hac1/5 were generated by RNA seq to study functional relationship between NPR1 and HACs in plant defense

overall_design: 4-week-old WT (Col-0), npr1-1, and hac1/5 plants were sprayed with water or INA for 12hr before harvest. Total RNAs were isolated (OD260/280 ratio of 1.8 to 2.2) and cDNA libraries were prepared by Beijing Genomics Institute (BGI) by standard Illumina protocols.

first: Yoo-Sun

last: Noh

first: Bosl

first: Sun-Mee

last: Choi

first: Min-Jeong

last: Kang

first: Se-Hun

last: Yun

first: Dong-Jin

last: Kwon


title: RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

status: Public on Sep 05 2018

city: Palermo

first: Claudia

last: Coronnello

address: via Bandiera 11

country: Italy

institute: Fondazione RiMED

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

overall_design: Refer to individual Series


title: Mitochondrial DNA background significantly alters transcriptional response to a various diets in mice

status: Public on Sep 12 2018

city: New York

first: Rui

last: Xiao

state: NY

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University

overall_design: Purpose: Mutations in the mitochondrial DNA (mtDNA) have been proposed to be essential for metabolic adaptation, and because metabolism is intrinsically associated with multiple disease states, including obesity, we hypothesized that changes in the mtDNA would significantly influence adiposity and gene expression in response to diet. To test these predictions we used Mitochondrial-Nuclear eXchange mice, which have nuclear and mitochondrial genomes that have been exchanged from different M. musculus strains. Methods: Wild type (C57BL6/J – C57n:C57mt and C3H/HeN - C3Hn:C3Hmt) and MNX (C57n:C3Hmt and C3Hn:C57mt) mouse were weaned with Chor diet and continued with Chow or changed to high-fat diet from 6 to 12-13 weeks of age. RNA samples were isolated from white adipose tissues collected from epididymal (eWAT) and inguinal (iWAT) fat, representing visceral and subcutaneous fat depots, respectively with RNeasy kit (Qiagen). Reverse transcribed cDNA libraries were sequenced with an Illumina HiSeq 2000. Read mapping was conducted with a proprietary algorithm by Expression Analysis (www.q2labsolutions.com), and read counts were used as input for differential expression analysis in DESeq2 version 1.10.1, using default settings. Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build mm9). Transcriptional changes were interrogated for 961 genes previously reported to be associated with fat metabolism and 29,209 genes representing the entire mouse transcriptome. These results show that the C57 mtDNA increased the number of DE genes in response to high fat diet in mice harboring the C3H nuclear genome (209% increase; C3Hn:C57mt versus C3Hn:C3Hmt, 165/79) and the C3H mtDNA decreased response in animals carrying the C57 nucleus (46% decrease; C57n:C3Hmt versus C57n:C57mt, 112/206) in eWAT (Figure 2B).  Similarly, the high fat diet resulted in 25 and 231 DE genes in the C3Hn:C3Hmt and C3Hn:C57mt iWAT, respectively, and 344 and 143 DE genes in C57n:C57mt and C57n:C3Hmt iWAT.  This corresponded to a 924% increase in the number of DE genes responding to high fat diet C3Hn:C57mt versus C3Hn:C3Hmt, and a decreased response (58% decrease) in C57n:C3Hmt relative to C57n:C57mt iWAT. Further analysis showed that each MNX and corresponding wild-type shared and had distinct DE genes in eWAT and iWAT. Conclusions: Results also show that the degree of transcriptional response influenced by the mtDNA can vary based upon the type of adipose tissue, suggesting that mtDNA background can have varying effects on the number of nuclear genes differentially responding to stimuli, depending upon tissue and location.

first: Kimberly

last: Dunham-Snary

first: Michael

middle: W

last: Sandel

first: Melissa

last: Sammy

first: David

middle: G

last: Westbrook

first: Zakia

last: Perveen

first: Ryan

last: McMonigle

first: William

middle: F

last: Ratcliffe

first: Arthur

last: Penn

first: Martin

last: Young

first: Scott

last: Ballinger


title: Transcriptome analysis of mouse primitive heart with Dgcr8 deletion

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

country: China

institute: Tsinghua University

type: Non-coding RNA profiling by high throughput sequencing


title: Mononuclear phagocytes locally specify and adapt their phenotype in the inflamed central nervous system, peak of disease expression data

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

summary: We introduce an in vivo imaging approach that allows us to temporally and spatially resolve the evolution of iNOS and Arginase-positive phagocyte phenotypes in a murine MS model. We show that the polarization of individual phagocytes is established after CNS entry, is dependent on the CNS compartment and can be adapted as inflammatory lesions move from expansion to resolution. Our study thus provides a first real-time analysis of phagocyte specification in the intact CNS.

overall_design: Cells were isolated from the CNS of Arginase-YFP X iNOS-Tomato-Cre mice at peak of disease of Experimental Autoimmune Encephalomyelitis. CD11bhigh, CD45high, CD64+ cells were FACS sorted based on their relative expression of the reporter proteins YFP and Tomato, indicative of M2 and M1 macrophage polarization, respectively. Total RNA was extracted from the separated YFP+, Tomato+, YFP+Tomato+ and unpolarized populations.

first: Giuseppe

last: Locatelli

first: Delphine

last: Theodorou

first: Marta

last: Jordao

first: Alain

last: Bessis

first: Marco

last: Prinz

last: Kerschensteiner


title: Mononuclear phagocytes locally specify and adapt their phenotype in the inflamed central nervous system


title: RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets (microRNA)

first: Claudia

last: Coronnello

summary: MicroRNAs are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be regulated. To discern further RISC complex functions, we analyzed the activities of two RISC proteins, AGO2 and GW182, in the MCF-7 human breast cancer cell line. We performed three RIP-Chip experiments using either anti-AGO2 or anti-GW182 antibody and compiled a dataset made up of the miRNA and mRNA expression profiles of three samples for each experiment. Specifically, we analyzed the input sample, the immunoprecipitated fraction and the unbound sample resulting from the RIP experiment. We used the expression profile of the input sample to compute several variables, using formulae capable of integrating the information on predicted miRNA binding sites, both in the 3’UTR and coding regions, with miRNA and mRNA expression level profiles. We compared immunoprecipitated vs unbound samples to determine the differentially expressed genes, independently for AGO2 and GW182 related samples. For each of the two proteins, we trained and tested several support vector machine algorithms able to predict the differentially expressed genes that were experimentally detected. The most efficient algorithm for predicting the over-expressed genes in AGO2 immunoprecipitated samples was trained by using variables involving the number of binding sites in both the 3’UTR and coding region, integrated with the miRNA expression profile, as expected for miRNA targets. On the other hand, we found that the best variable for predicting over-expressed genes in the GW182 immunoprecipitated sample was the length of the coding region. Due to the major role of GW182 in GW/P-bodies, our data suggests that the AGO2-GW182 RISC complex recruits genes based on miRNA binding sites in the 3’UTR and coding region, but only the longer mRNAs remain sequestered in GW/P-bodies, functioning as a repository for translationally silenced RNAs.

overall_design: We performed three independent RIP-Chip experiment for each of the two protein AGO2 and GW182 in MCF-7 human breast cancer cell line. In each experiment we analyzed three samples: the Input sample (IN), the immunoprecipitated fraction (IP) and the unbound sample resulting from the RIP experiment (FT). Each sample was analyzed with human whole genome microarray and microRNA microarray, mostly in two replicates.

first: Giovanni

last: Perconti

first: Patrizia

last: Rubino

first: Flavia

last: Contino

first: Serena

last: Bivona

first: Salvatore

last: Feo

first: Agata

last: Giallongo


title: RNA-seq data of lungs from mouse infected with different H5N1 Avian Influenza Viruses

status: Public on Sep 06 2018

city: Yangzhou

first: Jiao

last: Hu

address: 48 Wenhui Road

institute: Yangzhou University

summary:
Long non-coding RNAs (lncRNAs) play multiple key regulatory roles in various biological processes. However, their function in influenza A virus (IAV) pathogenicity remains largely unexplored.
Here, using next generation sequencing, we systemically compared the whole-transcriptome response of the mouse lung infected either with high-pathogenic (A/Chicken/Jiangsu/k0402/2010, CK10) or with nonpathogenic (A/Goose/Jiangsu/k0403/2010, GS10) H5N1 strains.
A total of 370 significantly differentially expressed (DE) lncRNAs from three replicates were identified associated with the high virulence of CK10, whereas the corresponding number for GS10 was 229.

overall_design: Total three biological samples are analyzied, each of them had triplication.The three samples are CK10-infected mouse lung,the GS10-infected mouse lung and Mock PBS-infected mouse lung.

first: Zenglei


title: RNAseq of Islets Isolated from Near Term Fetal Sheep after 7-day Infusion of Norepinephrine or Vehicle Control

city: Tucson

first: Sean

last: Limesand

state: AZ

address: 4101 N Campbell Ave

department: Animal & Comparative Biomedical Sciences

institute: University of Ariziona

summary: The study objective was to determine differentially expressed mRNA transcripts in pancreatic islets from fetal sheep exposed to persistent elevations in stress hormone norepinephrine to isolate effects of chronic adrenergic signaling on fetal islets. Ultimately, these data can be compared to islets from fetuses with placental insufficiency-induced intrauterine growth restriction, where there is known increases in norepinephrine.

overall_design: Islets were isolated for high-throughput sequencing from near term sheep fetuses from a group receiving 7-day norepinephrine infusion and a group receiving saline-vehicle control.

first: S

first: A

middle: C

last: Kelly


title: The expression profile of CD4lowHLA-G+ T cells

city: ShangHai

first: Chao

last: Wang

address: 1954HuaShan road

institute: Shanghai Jiao Tong University

summary: The aim of the dataset was to demonstrate that CD4lowHLA-G+ T cells were not TH2 cells by comparing the expression profiles of CD4lowHLA-G+ T cells to those of TH2 cells induced from CD4+ T cells under TH2-polarzing conditions.

overall_design: mRNA profiles of CD4lowHLA-G+ T cells isolated from prostate cancer patients with androgen deprivation therapy were generated by deep sequencing, in duplicate, using Illumina HiSeq X Tten. The sequencing data of TH2 cells were acquired from GEO database, accession number GSE71645. Sample 'GSE71645_2' is GSM1842243 and 'GSE71645_3' is GSM1842244.

first: Yan

last: Zhang

first: Wei

middle: Q

last: Gao


title: Gene expression in mouse mammary cells: whole mammary gland, EpCAM-Int and CD29-High subset and lung-colonizing cells

city: Montreal

first: Katrina

last: Podsypanina

state: QC

address: 110 Avenue des Pins Ouest

country: Canada

institute: IRCM

summary: The experiment was carried out to identify gene expression changes between mammary cells that colonize lungs following intravenous delivery, a subset of the dissociated mammary cells that contains lung colonizing subset, and the intact mammary gland.

overall_design: The experiment was designed to determine LCC gene expression profile, and to identify differentially expessed genes between LCC, E-Int29-Hi, and MG samples. For each experiment, mammary glands from 8 FVB.GFP females were dissociated and injected i.v. in two 2.5x10^6 doses into 4 FVB recipients. One day after injection, the lungs of recipient mice were dissociated and GFP or DDAO-stained cells isolated by a MoFlo (Beckman Coulter) flow sorter. The RNA from pooled LCC sample and the controls was extracted using MagMAXtm-96 Total RNA Isolation kit (AM1830, Ambion) according to manufacturer’s instructions. Best quality RNA as determined by 18S/28S fluorescence (Agilent 2100) was used for the sequencing experiment, and other preparations were used for RT-PCR applications.

first: Cedric

last: Darini


title: Mutant p53R270H drives altered metabolism and increased invasion in pancreatic ductal adenocarcinoma

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Pancreatic cancer is characterized by nearly universal activating mutations in KRAS. Among other somatic mutations, TP53 is mutated in more than 75% of human pancreatic tumors. Genetically engineered mice have proven instrumental in studies of the contribution of individual genes to carcinogenesis. Oncogenic Kras mutations occur early during pancreatic carcinogenesis and are considered an initiating event. In contrast, mutations in p53 occur later during tumor progression. In our model, we recapitulated the order of mutations of the human disease, with p53 mutation following expression of oncogenic Kras. Further, using an inducible and reversible expression allele for mutant p53, we inactivated its expression at different stages of carcinogenesis. Notably, the function of mutant p53 changes at different stages of carcinogenesis. Our work establishes a requirement for mutant p53 for the formation and maintenance of pancreatic cancer precursor lesions. In tumors, mutant p53 becomes dispensable for growth. However, it maintains the altered metabolism that characterizes pancreatic cancer and mediates its malignant potential. Further, mutant p53 promotes epithelial-mesenchymal transition (EMT) and cancer cell invasion. This work generates new mouse models that mimic human pancreatic cancer and expands our understanding of the role of p53 mutation, common in the majority of human malignancies.

overall_design: This study consists of 12 RNA-seq samples. These samples were isolated from subcutaneous tumors of KCip53-1 cells grown in NSG mice. Tumor treatment consisted of three groups: animals treated with dox for the entire course of the experiment (Dox), animals never treated with dox (No Dox), and animals who began the experiment on dox and then had it removed (Off Dox). In the KCip53-1 mouse pancreatic cancer cell line, dox induces the expression of mutant p53R270H.

first: Heather

middle: K

last: Schofield

first: Joerg

last: Zeller

first: Carlos

last: Espinoza

first: Annachiara

last: del Vecchio

first: Brian

last: Magnuson

first: Christopher

last: Halbrook

first: Tania

last: Fabo

first: Ayse

last: Daylan

first: Ilya

last: Kovalenko

first: Ho-Joon

last: Lee

last: Yan

first: Ying

last: Feng

first: Saadia

last: Karim

first: Daniel

middle: M

last: Kremer

first: Chandan

last: Kumar-Sinha

first: Costas

last: Lyssiotis

first: Jennifer

middle: P

last: Morton

first: Stefanie

last: Galban

first: Eric

last: Fearon

first: Marina

last: di Magliano


title: Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm [RNA-Seq]

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

summary: In this study, we compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of splicing events. Three different cell lines were treated with CX-4945, a drug that severely affects splicing. To make a fair comparison, we developed EventPointer, an algorithm that detects and labels alternative splicing events in both junction arrays and RNA-seq. Common results and discrepancies between both technologies were validated or resolved by more than 200 PCRs.

overall_design: Three different triple negative breast cancer cell lines (MDA-MB-231, MDA-MB-468, SUM 149) treated with CX4945 and DMSO with 5 replicates. A total of 30 samples

first: María

last: Ortiz-Estévez

first: Ander

last: Muniategui

first: Soraya

last: Carrancio

first: Fernando

last: de Miguel

last: Carazo

first: Luis

last: Montuenga

first: Matthew

last: Trotter

first: Remco

last: Loos

first: Rubén

last: Pío

first: Angel

last: Rubio


title: Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system

status: Public on Sep 09 2018

city: Stockholm

first: Francois

last: Lallemend

state: Stockholm

address: Tomtebodavägen 16

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Spiral ganglion (SG) neurons of the cochlea convey all auditory inputs to the brain, yet the cellular and molecular complexity necessary to decode the various acoustic features in the SG has remained unresolved. Using unbiased single-cell RNA sequencing, we identified four types of SG neurons, including three novel subclasses of type I neurons and the type II neurons, and provide a comprehensive genetic framework that define their potential synaptic communication patterns. The connectivity patterns of the three subclasses of type I neurons with inner hair cells and their electrophysiological profiles suggest that they represent the intensity-coding properties of auditory afferents. Moreover, neuron type specification is already established at birth, indicating a neuronal diversification process independent of neuronal activity. Thus, this work provides a transcriptional catalog of neuron types in the cochlea, which serves as a valuable resource for dissecting cell-type-specific functions of dedicated afferents in auditory perception and in hearing disorders.

overall_design:
Exploring heterogeneity of spiral ganglion neurons in both P3 and adult mice

Please note that  the single cells were sorted into 384-well plates, and cells from each well were barcoded afterwards using Nextera index adapters during library preparation. Therefore the number of the well (A1-P24) represents each cell (A1-P24).

first: Charles

last: Petitpré

first: Haohao

last: Wu

first: Anil

last: Sharma

first: Anna

last: Tokarska

first: Paula

last: Fontanet

first: Yiqiao

last: Wang

first: Françoise

last: Helmbacher

first: Kevin

last: Yackle

first: Gilad

last: Silberberg

first: Saida

last: Hadjab

first: François


title: RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets (mRNA)

first: Claudia

last: Coronnello

first: Giovanni

last: Perconti

first: Patrizia

last: Rubino

first: Flavia

last: Contino

first: Serena

last: Bivona

first: Salvatore

last: Feo

first: Agata

last: Giallongo


title: Mononuclear phagocytes locally specify and adapt their phenotype in the inflamed central nervous system, postimmunization expression data.

first: Ori

last: Staszewski

overall_design: Cells were isolated from the CNS of Arginase-YFP X iNOS-Tomato-Cre mice at clinical onset of Experimental Autoimmune Encephalomyelitis. Cd11bhigh, CD45high, CD64+ cells were FACS sorted based on their relative expression of the reporter proteins YFP and Tomato, indicative of M2 and M1 macrophage polarization, respectively. Total RNA was extracted from the separated YFP+, Tomato+, YFP+Tomato+ and unpolarized populations.

first: Giuseppe

last: Locatelli

first: Delphine

last: Theodorou

first: Marta

last: Jordao

first: Alain

last: Bessis

first: Marco

last: Prinz

first: Martin

last: Kerschensteiner


title: Targeted DamID reveals differential binding of mammalian pluripotency factors

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

country: United Kingdom

institute: The Gurdon Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The precise control of gene expression by transcription factor networks is critical to organismal development. The predominant approach for mapping transcription factor-chromatin interactions has been chromatin immunoprecipitation (ChIP). However, ChIP requires a large number of homogeneous cells and antisera with high specificity. A second approach, DamID, has the drawback that high levels of Dam methylase are toxic. Here we modify our Targeted DamID approach (TaDa) to enable cell type-specific expression in mammalian systems, generating an inducible system (mammalian TaDa or MaTaDa) to identify protein/DNA interactions in 100 to 1000 times fewer cells than ChIP. We mapped the binding sites of key pluripotency factors, OCT4 and PRDM14, in mouse embryonic stem cells, epiblast-like cells and primordial germ cell-like cells (PGCLCs). PGCLCs are an important system to elucidate primordial germ cell development in mice. We monitored PRDM14 binding during the specification of PGCLCs, identifying direct targets of PRDM14 that are key to understanding its critical role in PGCLC development. We show that MaTaDa is a sensitive and accurate method to assess cell type specific transcription factor binding in limited numbers of cells.

overall_design: MaTaDa of OCT4 and PRDM14 in ESCs, EpiLCs and PGCLCs

first: Seth

last: Cheetham

first: Wolfram

middle: H

last: Gruhn

first: Jelle

last: van den Ameele

first: Robert

last: Krautz

first: Tony

middle: D

last: Southall

first: Toshihiro

last: Kobayashi

first: M

last: Surani


title: CARM1 Methylates MED12 to Regulate its RNA Binding Ability

city: Smithville

first: Yue

last: Lu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

summary: The coactivator-associated arginine methyltransferase (CARM1) functions as a regulator for transcription, splicing and chromatin regulation by methylating a diverse array of substrates. In this study, we used CARM1 substrate antibodies to perform immunoprecipitation coupled with mass spectrometry (IP-MS) in MEFs and identified Mediator Subunit 12 (MED12) as a novel substrate for CARM1. ChIP-seq analysis using CARM1, MED12 and H3R17me2a (represents ‘CARM1 activity’) antibodies revealed that MED12 targeted by CARM1 is recruited to the EREs (estrogen-responsive elements). Additionally, RT-PCR studies showed that the MED12R1899K mutation disrupting the methylation site reduced the expression of ER-target genes. Thus, MED12 methylation targets it to ER-specific enhancers and positively modulates transcription of Estrogen-driven genes.

overall_design: ChIP-seq of CARM1, MED12 and H3R17me2a in MCF7 cells

first: Donghang

last: Cheng

first: Vidyasiri

last: Vemulapalli

first: Mark

last: Bedford


title: Chromatin protein profiling during the mammalian cell cycle reveals the extent of mitotic preservation of the regulatory landscape

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: We report a novel method to quantify bulk changes of chromatin associated proteins in different cellular states and apply it to the mammalian cell cycle

overall_design:
Sequencing of DNA from Cesium Chloride fractionated chromatin. This purification has been traditionally done to clean-up chromatin before ChIP, but hasn't been sequenced before. The proteins in this chromatin fraction were used for mass spec analysis, with the goal of quantifying bulk chromatin-protein changes in different cell states. We performed high throughput sequencing to determine whether purification of chromatin in this manner led to biases in which genomic regions we were analyzing.

This series also contains ATAC-seq data for T98G cells synchronized in G1 and Mphase of the mammalian cell cycle.

first: Paul

last: Ginno

first: Lukas

last: Burger

last: Schübeler


title: Single Cell and Open Chromatin Analysis Reveals Molecular Origin of Epidermal Cells of the Skin

city: Aurora

first: Xiying

last: Fan

state: CO

department: Dermatology

institute: University of Colorado Anschutz Medical Campus

summary: Skin and its appendages such as hair follicle and sweat gland are formed by Keratin-5 expressing (Krt5+) epidermal cells that are specified from primitive, Keratin-8 expressing (Krt8+) ectodermal progenitors shortly after gastrulation. Here we show that transcription factor ∆Np63 is required for converting Krt8+ ectodermal progenitors to Krt5+ epidermal progenitors and priming the underlying dermal cells to form dermal condensate by activating the Wnt/ß-Catenin pathway. These findings unearth the molecular cascades during the fate specification of epidermal cells, illuminate the essential role of ∆Np63 in initiating the Wnt signaling in the epidermis and programming the underlying dermal cells and provide new possibilities to harness the intrinsic developmental program for generating the skin and its appendages.

overall_design: RNA-seq and ATAC-seq on early epidermis  isolated from  Ctrl and P63KO mice.

first: Dongmei

last: Wang

first: Jeremy

last: Burgmaier

first: Yudong

last: Teng

first: Rose-Anne

last: Romano

first: Satrajit

last: Sinha

first: Rui

last: Yi


title: RNA expression changes in HOXA9/MEIS1 leukemia cells

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

summary: Aberrant expression of homeobox transcription factor HOXA9 is a central component of the leukemogenic program driven by diverse oncogenes. Here we show that HOXA9 overexpression in myeloid progenitor cells and pro-B cells leads to significant rearrangement of the epigenetic landscape with prominent emergence of cancer specific de novo enhancers. HOXA9 acts as a pioneer factor at the de novo enhancers and is required for recruitment of transcription factor CEBP/a and the histone H3K4 methyltransferase MLL3/MLL4 complex. HOXA9 function at the de novo enhancer is distinct from its physiological role at distal enhancers during normal hematopoietic development. Genetic deletion of MLL3/4 specifically affects the active enhancer signatures at de novo enhancers and inhibits HOXA9/MEIS1-mediated leukemogenesis. Our study reveals a previously uncharacterized role of HOXA9 and the MLL3/4 complex in leukemogenesis and provide mechanistic insights in epigenetic deregulation during malignant transformation.

overall_design: RNA-seq for untransformed myeloid progenitors (MP)

first: Yuqing

last: Sun

first: Jay

last: Hess


title: RNA-seq and ChIRP-seq analysis performed on Charme muscle specific lnc-RNA

status: Public on Sep 04 2018

city: Rome

first: Andrea

last: Cipriano

state: Italy

address: Piazzale Aldo Moro 5

department: Biologia e Biotecnologue C. Darwin

institute: La Sapienza

summary: The main function of chromatin-associated long non coding RNAs (lncRNA) is to tether specific combinations of regulatory factors to target genomic sites. Here we show the characterization of a conserved lncRNA, Charme, that acts as an architectural scaffold to bring together distantly located genomic loci. The functional knock-down of Charme revealed a direct link between the formation of chromosomal loops and the down-regulation of genes therein contained, which are crucial for the correct control of muscle homeostasis. Notably, several Charme-target genes were previously linked to human cardiomyopathies and Charme deficiency in mice indeed resulted in a very strong cardiac phenotype. Altogether, these data disclose that the chromosomal architecture controlled by Charme is relevant for fine tuning the myogenic programme and for proper tissue homeostasis in vivo.

overall_design: Gene expression profile upon Charme Knock-down obtained through an RNA-Seq experiment with two biological replicates in each condition. We silenced Charme expression using separately two different sets of gapmers (GAP-2 GAP-2/3) and both conditions were compared with control cells treated with GAP-scr. ChIRP-Seq analysis was performed to identify genomic binding sites of Charme. The long non coding RNA was pulled down using two different sets of probes (even and odd) and co-purified genomic DNA  was sequenced and compared with input genomic DNA. LacZ DNA probes were used as negative controls.

first: Monica

last: Ballarino

first: R

last: Tita

first: T

last: Santini

first: F

last: Desideri

first: M

last: Morlando

first: A

last: Colantoni

first: C

last: Carrieri

last: Nicoletti

last: Musarò

first: D

last: O' Carrol

first: I

last: Bozzoni


title: Genome wide expression profiling of hosA deletion strains

status: Public on Sep 03 2018

city: Innsbruck

first: Ingo

last: Bauer

state: Tirol

address: Innrain 80-82

department: Institute of Molecular Biology

country: Austria

institute: Medical University of Innsbruck

summary: An outstanding feature of filamentous fungi is their ability to produce a wide variety of small bioactive molecules that contribute to their survival, fitness and pathogenicity. The vast collection of these so-called secondary metabolites (SMs) includes molecules that play a role in virulence, protect fungi from environmental damage, act as toxins or antibiotics that harm host tissues or hinder microbial competitors for food sources. Many of these compounds are used in medical treatment, however, biosynthetic genes for the production of these natural products are arranged in compact clusters that are commonly silent under growth conditions routinely used in laboratories. Consequently, a wide arsenal of yet unknown fungal metabolites is waiting to be discovered. Here we describe the effects of deletion of hosA, one of four classical histone deacetylase (HDACs) genes in Aspergillus nidulans; we show that HosA acts as global regulator of SMs in Aspergillus with converse regulatory effects depending on the metabolite gene cluster examined. Co-inhibition of all classical enzymes by the pan HDAC inhibitor trichostatin A and the analysis of HDAC double mutants indicate that HosA is able to override known regulatory effects of other HDACs such as the class 2 type enzyme HdaA. Chromatin immunoprecipitation analysis revealed a direct correlation between hosA deletion, the acetylation status of H4 and the regulation of SM cluster genes, whereas H3 hyperacetylation could not be detected in all the upregulated SM clusters examined. Our data suggest that HosA has inductive effects on SM production in addition to its classical role as a repressor via deacetylation of histones. Moreover, a genome wide transcriptome analysis revealed that in addition to SMs, expression of several other important protein categories, such as enzymes of the carbohydrate metabolism or proteins involved in disease, virulence and defense are significantly affected by the deletion of HosA.

overall_design: Two strains, wild type and hosA deletion, grown for 24 h and 60 h, were analyzed in triplicates.

first: Angelo

last: Pidroni

first: Birgit

last: Faber

first: Gerald

last: Brosch

first: Stefan

last: Graessle


title: Transcript profiling of the roots and leaves of opt3-2 mutant and wild type Arabidopsis

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

state: Missouri

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

summary: Illumina 100bp single end sequencing was used to profile the transcriptomes of wild type (Columbia) and opt3-2 mutant Arabdiopsis leaves and roots under hydroponic conditions ( 4 weeks old, bolting stage).  Sequencing resulted in 381 million uniquely mapping reads accross 36 libraries.  Each sample was barcoded and divided into three sequencing lanes, while each genotype/tissue combination is represented by 3 biological replicates consisting of 3-4 individual plants (2 genotypes x 2 tissues x 3 biological replicates x 3 technical replicates = 36 libraries).  Our results show the leaves and roots of the opt3-2 mutant have different iron sensing transcriptional programs in place which is independent of the iron status of the plant.

first: David

last: Mendoza-Cózatl

first: Mather

last: Khan


title: Characterize the regulon of 6C sRNA in Mycobacteria smegmatis

status: Public on Sep 02 2018

city: Toronto

first: Juntao

last: Mai

address: 661 univerisity ave

institute: Univerisity of Toronto

summary: Purpose: The goals of this study are to identify the putative mRNA targets that are regulated by the 6C sRNA. We constuct an inducible vector to transiently overexpressed the 6C sRNA in M. smegmatis, and then we perform RNA-Seq to look for genes that are differicently expressed upon the over-expression of 6C sRNA, which we think these genes are the potential targets of the 6C sRNA.

overall_design: Methods: Purified RNA was used to construct cDNA library according to the TruSeq Stranded RNA LT Guide from Illumina. High-throughput sequencing was carried out on an Illumina HiSeq 2000 system according to the manufacturer's instructions (Illumina HiSeq 2000 User Guide) and 150-bp paired-end reads were obtained. The raw reads were filtered by Seqtk and then mapped to the M. smegmatis MC2 155 strain reference sequence (GenBank NC_008596) using Bowtie2 (version: 2-2.0.5). Counting of reads per gene was performed using HTSeq followed by TMM (trimmed mean of M-values) normalization.  Differentially expressed genes were defined as those with a false discovery rate < 0.05 and fold-change >2 using the edgeR software.

first: Jun

last: Liu


title: PRMT5 regulates the homologous recombination DNA repair pathway by controlling the alternative splicing of key epigenetic factors

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary:
We found that PRMT5 deletion or inhibition impairs homologous recombination (HR) DNA repair, leading to DNA damage accumulation, p53 activation, cell cycle arrest and cell death through missplicing of KAT5.
We show that PRMT5 inhibitors and PARP inhibitors have synergistic effects on human acute leukemia cell lines, demonstrating the advantages of combining targeted epigenetic and non-epigenetic inhibitors.

overall_design: RNA from sorted E14.5 Ter119-/+ mouse fetal liver cells from Vav-cre;PRMT5fl/fl (KO) and PRMT5fl/fl (WT) were subjected to high-throughput RNA sequencing. RNA from sorted LK cells from Mx1-cre;PRMT5fl/fl (KO) and PRMT5fl/fl (WT) collected 7 days after poly(I:C) injections were subjected to high-throughput RNA sequencing.

first: Pierre-Jacques

last: Hamard

first: Karl

last: Daniel


title: Gene expression changes in human iPSC-derived cardiomyocytes after X-ray irradiation

city: Munich

first: Benjamin

last: Becker

address: Neuherbergstr. 11

department: Genomics II

institute: Bundeswehr Institute for Radiobiology

summary: Within the present study we evaluated hiPSC-CMs as a possible methodological extension for the assessment of organ specific responses to ionizing radiation regarding gene expression changes. We aimed to review the feasibility of hiPSC-CMs as a valid testing model for gene expression changes and to determine alterations within the gene expression pattern of hiPSC-CMs after exposure to X-ray radiation, subsequently.

overall_design: 2 samples with 3 biological replicates, one sham irradiated, one irradiated with 5 Gy x-ray radiation

middle: V

first: Reinhard

last: Ullmann


title: Mononuclear phagocytes locally specify and adapt their phenotype in the inflamed central nervous system, blood monocyte and brain microglia expression data

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

institute: University Medical Center Freiburg

summary: We introduce an in vivo imaging approach that allows us to temporally and spatially resolve the evolution of iNOS and Arginase-positive phagocyte phenotypes in a murine MS model. We show that the polarization of individual phagocytes is established after CNS entry, is dependent on the CNS compartment and can be adapted as inflammatory lesions move from expansion to resolution. Our study thus provides a first real-time analysis of phagocyte specification in the intact CNS.

overall_design: Cells were isolated from the Blood and CNS of Arginase-YFP X iNOS-Tomato-Cre mice at clinical onset of Experimental Autoimmune Encephalomyelitis. CD11b_high, CD45_low microglia cells and CD45_positive, CD115_positive, Ly6c_high monocytes were FACS sorted respectively. Total RNA was extracted from the separated populations.

first: Giuseppe

last: Locatelli

first: Delphine

last: Theodorou

first: Marta

middle: J

last: Jordao

first: Alain

last: Bessis

first: Marco

last: Prinz

first: Martin

last: Kerschensteiner


title: Discovery of canonical and non-canonical miRNAs in brain frontal cortex in control and maternal nutrient restricted fetal baboon

city: San Antonio

first: Laura

middle: L

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

summary: We have developed a baboon nonhuman primate (NHP) model of maternal nutrient reduction during fetal development (30% global maternal nutrient reduction, MNR) to evaluate the impact of reduced nutrient availability on primate fetal development. We reported (Antonow-Schlorke et al. PNAS, 2011) that MNR induced major cerebral developmental disturbances at mid gestation (0.5G); however, the impact of MNR at late gestation (0.9G) and the mechanisms mediating these effects have not been determined. We hypothesized that MNR alters developmental trajectories of the fetal prefrontal cortex in the late gestation via miRNA regulation of key transcriptional and translational signaling pathways. Pregnant baboons were fed either ad libitum (control; CON; females n=3; males n=3) or a globally reduced diet (70% of controls; females n=3; males n=3) from 0.16G through 0.9G that produces IUGR (14% reduction in fetal weight). Fetuses were removed by Cesarean section at 0.9G, and prefrontal cortex (PFC) sections collected for analysis. Transcriptome (gene arrays) and small transcriptome (small RNA-Seq) analyses of fetal PFC were performed and gene and miRNA profiles were compared between MNR and CON. We present for the first time transcriptome (GSE42756) and small RNA transcriptome expression profiles of the fetal baboon PFC at 0.9G. Pathway analysis showed that MNR had sex-specific effects on key cellular signaling pathways. We conclude that moderate maternal global nutrient reduction during pregnancy can alter signaling pathways related to nutrient sensing and cell proliferation in the late gestation PFC. In addition, inverse expression of miRNAs known to target genes in these pathways suggests that miRNA mechanisms play a role in these changes.

overall_design: Detection of miRNA profiles of 6 control and 6 maternal nutrient restricted (MNR) fetal frontal cortex

first: Jeremy

last: Glenn

first: Cox

last: Laura


title: RNAseq of FACS Drd1 and Drd2 receptor expressing medium spiny neurons (direct and indirect medium spiny neurons) from 5-6 month Q175 Huntington's disease model mice, compared to WT littermates.

status: Public on Sep 01 2018

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: mRNAseq for baseline transcriptional profiling of D1 and D2 receptor-expressing medium spiny neurons from 5-6 month  Q175 mice compared to WT littermates.

overall_design:
Heterozygous zQ175 (C57/BL6) × Drd2-EGFP BAC (C57/BL6) and  zQ175 (C57/BL6) × Drd1-EGFP BAC (C57/BL6) mice were generated. Drd2-EGFP BAC (C57/BL6) and Drd1-EGFP BAC (C57/BL6) mice were obtained by backcrossing the Drd2-EGFP BAC (FVB) and Drd1-EGFP BAC (FVB) MMRRC lines onto C57/BL6J background.  zQ175 heterozygous knock-in HD model mice (C57/Bl6J) were obtained from CHDI Foundation (CHDI-81003003).
Fluorescence activated cell sorting (FACS) for GFP was used to isolate  Q175 het or WT  - indirect pathway medium spiny neurons (iMSNs) and direct pathway medium spiny neurons (dMSNs) from the D2BAC-EGFP or D1BAC-EGFP x HD model crosses, respectively. Cells were pooled from four animals (150,000 cells/animal) to create iSPN and dSPN pools for sequencing. RNA was extracted, and sequencing was performed by Expression Analysis on an Illumina Hi-seq 2000. Paired-end sequencing was performed, 4-plexed across lanes for a total of around 38 million 50mer paired reads per sample.

first: Jim

last: Rosinski


title: Temporal profile of germ-free and conventionally raised male mice (epididymal white adipose tissue (WAT))

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

summary: Gut microbiota and the circadian clock both regulate metabolism. The circadian clock and associated feeding rhythms were shown to impact on the microbial community. However, to what extent gut microbiota reciprocally affect daily rhythms of gene expression and physiology in the host remains elusive. Here, we analyzed the transcriptomes of male and female germ-free mice. While this revealed subtle changes in circadian clock gene expression in liver, intestine, and white adipose tissue, germ-free mice showed considerably altered expression of genes associated to rhythmic physiology. Strikingly, absence of microbiome severely compromised liver sex-dimorphism at the transcriptome and metabolome level. Their sex-specific rhythmicity was strongly attenuated. The resulting feminization of male and masculinization of female hepatic gene expression in germ-free animals is likely caused by altered sex-dimorphism in sex and growth hormone secretion, linked to differential activation of xenobiotic receptors. This defines a novel mechanism by which the gut microbiome regulates host metabolism.

overall_design: Total RNA-Seq of conventional raised (convR) and Germ-free (GF) male under ad libitum feeding regime. Temporal mRNA profiles of WAT were assessed every 4 hours during the diurnal cycle (Zeitgerber time (ZT) 2-22).

last: Weger

first: Cedric

last: Gobet

first: Jake

last: Yeung

first: Eva

last: Martin

first: Sonia

last: Jimenez

first: Aurélie

last: Balvay

first: Anne

last: Foussier

first: Aline

last: Charpagne

first: Chieh-Jason

last: Chou

first: Felix

last: Naef

first: Frederic


title: Temporal profile of germ-free and conventionally raised male mice (DUODENUM and ILEUM)

overall_design: Total RNA-Seq of conventional raised (convR) and Germ-free (GF) male under ad libitum feeding regime. Temporal mRNA profiles of duodenum and ileum were assessed every 4 hours during the diurnal cycle (Zeitgerber time (ZT) 2-22).

first: Benjamin


title: Temporal profiles of germ-free and conventionally raised female and male mice (LIVER)

overall_design: Total RNA-Seq of conventional raised (convR) and Germ-free (GF) female and male under ad libitum feeding regime. Temporal mRNA profiles of liver were assessed every 4 hours during the diurnal cycle (Zeitgerber time (ZT) 2-22).


title: Quantitative Analysis of Cardiomyocyte-specific Tbx20 Overexpression and Control Mouse Heart Transcriptomes Using Next Generation Sequencing

city: Cincinnati

first: Katherine

last: Yutzey

state: OH

address: 3333 Burnet Ave

department: Heart Institute

institute: Cincinnati Children's Hospital

summary: Purpose: The goals of this study is to determine the differential expression of transcriptome in cardiomyocyte-specific Tbx20 overexpressing adult heart (DTG) compared to controls (STG).

overall_design: Tbx20 overexpression in cardiomyocytes was induced in 8-week old mice. The differential expression of transcriptome in cardiomyocyte-specific Tbx20 overexpressing adult heart compared to controls was analyzed 4 weeks after.

first: Fuli

last: Xiang

first: Minzhe

last: Guo


title: Trancriptome analysis of Agrobacterium tumefaciens C58 cells in the presence of abundant opines

city: Gif-sur-Yvette

first: Almudena

last: González Mula

state: Ile-de France

address: 1 Avenue de la Terrasse

country: France

institute: CNRS

summary: Purpose:  The goals of this study is to compare the reponse of Agrobacterium tumefaciens C58 in the presence and absence of the two opines nopaline and agrocinopine (more precisely agrocinopine A) to delineated the key-genes associated to opines-response in A. tumefaciens C58.

overall_design: Agrobacterium tumefaciens C58 RNA profiles in the presence and absence of nopaline and agrocinopine A were generated by deep sequencing, in triplicate, using HiSeq technology.

last: Gonzalez Mula

first: Julien

last: LANG


title: RNA-seq reveals quorum sensing-dependent activation of genes involved in ecological fitness during Pcb1692 potato-host infection

city: Pretoria

first: Stanford

last: Kwenda

state: Gauteng

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

summary: Pectobacterium carotovorum subsp. brasiliense 1692 (Pcb1692) is an emerging pathogen of significance affecting potato production globally. In the current study, we reveal the complete transcriptome of Pcb in planta at the early and later stages of infection (24 and 72 hour post inoculation (hpi), respectively) using RNA-seq. We identified713 differentially expressed genes at 24hpi and an additional 157 differentially expressed genes at 72 hpi. Genes encoding PCWDEs and iron acquisition were up-regulated. The type VI secretion system (T6SS) and the bacteriocin (carotovoricin) gene clusters were both highly up-regulated, suggesting they might play a role in antibacterial activity in eliminating competition for nutrients with other microbes within the niche. Additionally, our results suggest the importance of genes involved in amino acid, carbohydrates, citrate metabolism, adhesion, chemotaxis, motility, metabolism as these were differentially expressed at 24 hpi. To establish the Pcb1692 quorum sensing regulon, the transcriptome of Pcb1692 wild-type compared to that of Pcb1692∆expI during in vitro growth and in planta at 24 hpi in potato tubers was analyzed. Important virulence factors such as T2SS, T6SS, and citrate metabolism were found to be under quorum sensing regulation while, carotovoricin did not appear to be quorum sensing dependent.

overall_design: Examination of Pcb 1692  gene expression in potato tuber at 24 and 72 hpi. Additionally, the transcriptome of Pcb1692 wild-type was compared to that of Pcb1692∆expI during in vitro growth and in planta at 24 hpi in potato tubers

first: Lucy

middle: N

last: Moleleki

first: Collins

last: Tanui

first: Divine

middle: Y

last: Shyntum


title: Temporal profile of Liver of Cry1/2 double knockout (DKO) mice

first: Frédéric

last: Gachon

overall_design: Total RNA-Seq of night fed Cry1/2 DKO male mice. Temporal mRNA profiles of liver were assessed every 4 hours during a diurnal cycle (Zeitgerber time (ZT) 2-22). Night fed wild-type animals corresponding to the Cry1/2 DKO series are available under the accession numbers: GSM1897844-GSM1897855.

last: Weger

first: Cedric

last: Gobet

first: Jake

last: Yeung

first: Eva

last: Martin

first: Sonia


title: Comparing gene expression in livers of 1-month vs 6-month old mice following DEN treatment

city: Jerusalem

first: Jacob

last: Rachmilewitz

address: Ein -Kerem

country: Israel

institute: Hadassah Hebrew University medical center

summary: To look for age-related changes in the liver that take place during DNA damage resolution, we used RNAseq gene expression analysis to characterize mRNA expression profile in livers from 1-month vs. 6-month-old mice either before or 2 days (representing the peak of DNA damage response) and 6 days (representing the resolution phase of DNA damage) after DEN treatment.

overall_design: Liver mRNA profile of 1-month and 6-month old C57BL/6 male mice were generated by deep sequencing in triplicate (each sample is a pool of three mice) using Illumina NextSeq. The sequence reads passed quality filters. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Avital

last: Guedj


title: Genome-wide expression ChIP analysis of mouse PHF13 in testis

city: Erlangen

first: Soeren

last: Lukassen

address: Schwabachanlage 10

department: Institute of Human Genetics

institute: Friedrich-Alexander Universitaet Erlangen Nuernberg

summary: We report binding profiles for SPOC1 (PHF13) in mouse testes. The X- and Y-chromosomes are preferential targets.

overall_design: ChIP-Seq and input: 3 samples each

first: Andreas

last: Winterpacht


title: Investigation of the role of SPOC1/PHF13 in mouse spermatogenesis

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

overall_design: Refer to individual Series


title: Neuregulin 1 type III reduces severity in a mouse model of Congenital Hypomyelination Neuropathy

city: Buffalo

first: Jie

last: Wang

state: NY

address: Elm and Carlton Streets

department: Department of Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

summary:
Purpose: We hypothesised that neuregulin 1 type III would reverse CHN. Using a faithful mouse model of CHN, we rescued the myelination defects by activation of Nrg1 type III. Unexpectedly, rescue did not depend on upregulation of Egr2 or major myelin genes. Therefore we asked whether we could identify any transcriptomic signature of the canonical pathways downstream of Nrg1 type III that could explain the increase in myelination in the sciatic nerve.
Methods: Sciatic nerve mRNA profiles of 30-day-old wild-type (WT), P0 mutant (Q215X/+), trangenic HA-NRG1 type III, and HA-NRG1 type III:Q215X mice were generated by deep sequencing, in duplicate, using Illumina HiSeq2500 . The sequence reads that passed quality filters were aligned to the mouse reference genome (mm10) with the transcript annotation (UCSC mm10 annotation download from TopHat website) using TopHat (v2.0.9). Quantification for the gene expression and differential expression analysis were done by the software Cufflinks (v2.2.0).
Results:  A comprehensive transcriptomic analysis of signals downstream of neuregulin 1 type III in rescued CHN nerves revealed imbalanced activation of MAPK/ERK signals and minor myelin genes, such as Pmp2 and Omg.
Conclusions: Our findings demonstrate that although augmented Nrg1 type III activity modifies the composition of myelin, it still promotes thicker myelin and ameliorates nerve conduction velocity in a mouse model of CHN. Controlled increase of Nrg1 type III activity may be a therapeutic strategy in some hypomyelinating neuropathies.

first: Sophie

last: Belin

first: Francesca

last: Ornaghi

first: Ghjuvan’Ghjacumu

last: Shackleford

first: Camilla

last: Lopez-Anido

first: Nicholas

last: Silvestri

first: Neil

last: Robertson

first: Courtney

last: Williamson

first: Akihiro

last: Ishii

first: Carla

last: Taveggia

first: John

last: Svaren

first: Rashmi

last: Bansal

first: Markus

last: Schwab

first: Klaus

last: Nave

first: Maurizio

last: D’Antonio

first: Laura

last: Feltri

first: Lawrence

last: Wrabetz


title: Replicated transcriptome profiling of Normal and Cancerous Prostate Cells [RNA-Seq]

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

institute: Garvan Institute of Medical Research

summary: To identify differentially expressed transcripts  in Cancer and Normal Prostate cells global transcript abundance was assayed by replicated (n=3) stranded RNA-Sequencing

overall_design: PolyA+ RNA profiles of LNCaP (n=3) and PrEC (n=3) cell lines were generated by deep sequencing. Libraries were generated by Illumina TruSeq kits (maintaining strand information). The resultant cDNA libraries were sequenced at the Kinghorn Center for Clinical Genomics (The Garvan Institute of Medical Research, Darlinghurst, NSW, Australia) using the Illumina HiSeq 2500 platform.

first: Hugh

last: French

first: Kate

last: Gould

first: Sue

last: Clark

first: Fatima

last: Valdes Mora

first: Jenny

middle: Z

last: Song

last: Skulte


title: Whole transcriptome analysis of human macrophages infected with H5N1 and H1N1 influenza viruses reveals the significant up-regulation of RIG-I-like receptor signaling pathway [miRNA-seq]

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

summary: For the small RNA portion in the whole transcriptome, a total of 105,842,096 filtered high-quality sequencing reads, representing 2,854,995 unique miRNA species, were generated for miRNAs for H1N1- or H5N1- infected macrophage cell populations at 1-, 3-, and 6-hr post-infection. A total of 361 mature miRNAs and 113 mature star miRNAs were identified from the samples. We calculated the miRNA expression fold change in influenza A viruses infected cells compared to mock-infected control cells andassessed the significance of the differential expression for each miRNA using Z-statistics. A total of 241 mature miRNAs were identified with a minimum fold-change of 1.2 and 102 of them have a Z-score ≥ 3.

overall_design: We studied the whole transcriptome of a highly pathogenic influenza virus H5N1 and a low virulent H1N1 in human monocyte-derived macrophages at 1-, 3-, and 6-hr post-infection to identify the molecular events leading to virus pathogenesis at early infection stages by comparing with the mock infected cells. This data set is corresponding to the small RNA portion of the whole transcriptome.

last: Zhang

first: Yun-Juan

first: Amy

last: Tong

first: Lok

last: Si

first: Suki

last: Lee


title: The mouse microbiome is required for sex-specific diurnal rhythms of gene expression and metabolism

first: Frédéric

last: Gachon

summary: The circadian clock and associated feeding rhythms have a profound impact on metabolism and the gut microbiome. To what extent microbiota reciprocally affect daily rhythms of physiology in the host remains elusive. Here, we analyzed transcriptome and metabolome profiles of male and female germ-free mice. While mRNA expression of circadian clock genes revealed subtle changes in liver, intestine, and white adipose tissue, germ-free mice showed considerably altered expression of genes associated to rhythmic physiology. Strikingly, absence of microbiome severely compromised liver sexual dimorphism, showing strongly attenuated sex-specific rhythmicity. The resulting feminization of male and masculinization of female germ-free animals is likely caused by altered sexual development and growth hormone secretion, associated to differential activation of xenobiotic receptors. This defines a novel mechanism by which the microbiome regulates host metabolism.

overall_design: Total RNA-Seq of conventional raised (convR) and Germ-free (GF) male and female mice under ad libitum feeding regime. Cry1/2 KO mice were night fed. Temporal mRNA profiles of liver were assessed every 4 hours during the diurnal cycle.

first: Benjamin

last: Weger

first: Cedric

last: Gobet

first: Jake

last: Yeung

first: Eva

last: Martin

first: Sonia

last: Jimenez

first: Aurélie

last: Balvay

first: Anne

last: Foussier

first: Aline

last: Charpagne

first: Chieh-Jason

last: Chou

first: Felix

last: Naef

first: Frederic


title: Genome-wide expression profiles from mouse Phf13 wildtype and knockout testes

first: Soeren

last: Lukassen

summary: We report expression profiles for mouse testes carrying a Phf13 knockout in comparison to wildtype testes. Upregulation of X- and Y-linked genes is evident after loss of PHF13.

overall_design: RNA-Seq of 3 samples each from wildtype and Phf13 knockout mice.

first: Andreas

last: Winterpacht


title: Transcriptome profiling of Normal and Cancerous Prostate Cells [RNA-Seq]

first: Timothy

last: Peters

summary: To identify differentially expressed transcripts (both annotated and unannotated) in Cancer and Normal Prostate cells global transcript abundance was assayed by RNA-Sequencing.

overall_design: RNA profiles of LNCaP and PrEC cell lines were generated by deep sequencing. Libraries were generated by Illumina TruSeq kits with PolyA+ selection (without maintaining strand information). The resultant cDNA libraries were sequenced at the Next Generation Genome Sequencing Facility (University of Western Sydney, Hawkesbury, NSW, Australia) using the Illumina HiSeq 1500 platform.

first: Hugh

last: French

first: Jenny

last: Song

first: Fabian

middle: A

last: Buske

first: Clare

last: Stirzaker

first: Susan

last: Clark


title: Spatially Constrained Tandem Bromodomain Inhibition Bolsters Sustained Repression of BRD4 Transcriptional Activity for TNBC Cell Growth

status: Public on Aug 31 2018

city: new york

first: MING-MING

last: ZHOU

address: 1425 madison ave

institute: Icahn School of Medicine at Mount Sinai

summary: We performed RNA-seq of MDA-MB-231 cells that were treated with MS645 or JQ1 at 50 nM and 500 nM in an effort to understand how MS645 exerts such a profound cell growth inhibition on cancer cells.

overall_design: MDA-MB-231 cells were treated with DMSO and different concentrations of JQ1 and MS645 for 18 hrs to compare the compounds' effect in transcriptional regulation.

first: Chunyan

last: Ren

first: Ming-ming

last: Zhou


title: Transcriptome wide analysis of Cnot3 target mRNA in mouse hearts

city: Akita

first: Keiji

last: Kuba

address: 1-1-1 Hondo

department: Biochemistry and metabolic science

country: Japan

institute: Akita University

summary: Through RNA immunoprecipitation with anti-Cnot3 antiboy from mouse heart lysates and RNA-seq (Cnot3 RIP-seq) and gene ontology analyses, we show the comprehensive picute of cardiac Cnot3 target genes.

overall_design: mRNA expression profiles in anti-Cnot3 IgG RIP, control IgG RIP and Input  (heart lysates of 4 week old mice) (N=2 experiments) were generated by RNA sequencing. RNA was extracted using TRIZOL reagent (Invitrogen). RNA sequencing was conducted in the laboratory of Yutaka Suzuki, The University of Tokyo (Tokyo, Japan).

first: Shinji

last: Nakaoka

first: Yutaka

last: Suzuki

first: Tomokazu

last: Yamaguchi


title: Whole transcriptome analysis in 661W photoreceptor cells

status: Public on Aug 30 2018

city: Southampton

first: Gabrielle

last: Wheway

address: Tremona Road

department: Faculty of Medicine

institute: University of Southampton

summary: This experiment aimed to characterise the complete transcriptional profile of 661W cells to identify their origin as cone photoreceptor cells. Cells were either grown in complete media or subjected to 72 hours of serum starvation to encourage differentiation.

overall_design: 661W cells were either grown in normal complete medium containing serum, or exposed to 72 hours of serum starvation. This was repeated across 3 independent experiments, with cells of passage number 24, 26 and 27. Total RNA was extracted using TRI reagent,  samples treated with Dnase, and cleaned on an RNA clean and concentrate column.RNA-seq was performed on an Illumina NextSeq 500 instrument with six libraries multiplexed and run across 4 lanes per flow-cell using 75 bp single end reads in high output mode.


title: Rice interploidy crosses disrupt epigenetic regulation, gene expression, and seed development

city: Nanjing

first: Limei

last: Wang

address: 1 Weigang Road

department: State Key Laboratory of Crop Genetics and Germplasm Enhancement

institute: Nanjing Agricultural University

summary: Seed development in angiosperms requires a 2:1 maternal-to-paternal genome ratio (2m:1p) in the endosperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures. Here we report that the defective endosperm was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt siRNAs were enriched in the 5’ and 3’ flanking sequences of nonadditively expressed genes in the interploidy crosses and negatively associated with the expression of imprinted genes. Furthermore, some PRC2 gene family members and the genes for DNA methylation including OsMET1b and OsCMT3a were upregulated in the 2X4 cross but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes including starch metabolic and storage protein genes during grain filling were associated with DNA methylation or H3K27me3 and repressed in both 2X4 and 4X2 crosses. WUSCHEL homeobox2 (WOX2)-like (WOX2L), an endosperm-preferred gene, was expressed specifically in the rice endosperm, on contrary to WOX2 expression in the Arabidopsis embryo. CRISPR/Cas9 editing of WOX2L in transgenic rice blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m:1p genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.

overall_design: mRNA-seq and small RNA-seq

first: Jingya

last: Yuan

first: Yujie

last: Ma

first: Wu

last: Jiao

first: Wenxue

last: Ye

first: Dong-Lei

last: Yang

first: Chuandeng

last: Yi

first: Z

last: Chen


title: RNA profiling of 6xAOM induced colon tumors from wt, miR-34a IEC deficient, p53 IEC deficient and miR-34a/p53 IEC deficient mice

city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

summary: P53 induced Mir34a is a tumor suppressor microRNA that plays important roles in cancer related processes such as proliferation, invasion and metastasis. Simultaneous loss of Mir34a and p53 is often observed in CRC. Here we show that, combined deletion of Mir34a and p53 has synergistic effects in suppressing tumor initiation, progression, invasion and metastasis in CRC by using mice lacking Mir34a and p53 in their intestinal epithelium. By in vivo inhibition of IL6R and SERPINE1, which we identified as up-regulated Mir34a targets in tumors of Mir34a/p53 deficient mice, we obtained preclinical evidence for their therapeutic value for treatment of sporadic CRC.

overall_design: 12 samples were analyzed. We compared 3 wt colon tumor samples, 3  miR-34a IEC deficient tumors, 3 p53 IEC deficient tumors, and 3 miR-34a/p53 IEC deficient tumors

first: Meryem

last: Gülfem Oner

first: Heiko

last: Hermeking


title: High-throughput RNA seq data of mouse embryonic stem cells and intermediate states throughout their differentiation into motor neurons

city: New York City

first: Josefina

middle: Inés

last: del Mármol

address: 1230 York Avenue

institute: The Rockefeller University

summary: Piezo1 is a mechanosensitive (MS) ion channel with characteristic fast-inactivation kinetics expressed in multiple mammalian cells. We found a slowly-inactivating MS current in mouse embryonic stem (mES) cells and characterized it throughout a model differentiation into motor neurons in order to investigate its components. MS currents were large and slowly-inactivating in the stem cell stage, and became gradually smaller and faster-inactivating throughout the differentiation. We found that Piezo1 is expressed in mES cells, and its knockout abolishes MS currents, indicating that the slowly-inactivating current in mES cells is carried by Piezo1. To investigate the reason for its uncharacteristic slow inactivation kinetics in these cells, we cloned Piezo1 cDNA from mES cells and studied whether the expressed variant displays intrinsic slow kinetics. The variant of Piezo1 found in mES cells displays fast-inactivation kinetics in heterologous expression, indicating that sources of modulation other than the amino acid sequence determine its slow kinetics in mES cells.

overall_design: 6 stages were analyzed: days 0 (mES cells), 2, 3, 4, 5 and 7 (motor neurons). 3 biological replicates were analyzed for days 0, 2 and 3. 4 biological replicates were analyzed for day 4. 2 biological replicates were analyzed for days 5 and 7.

middle: I

first: Kouki

last: Touhara

first: Roderick

last: MacKinnon


title: Differentially expressed genes in the fly brain under condtions of sugar and complete starvation

city: Oxford

first: Naveen

last: Prasad

state: Oxfordshire

address: Mansfield Road

department: Dept of Physiology, Anatomy & Genetics

institute: Centre for Neural Circuits & Behaviour

summary: In order to study the transcriptional response of the fly brain to sugar and complete starvation, we first confirmed that 24 hours of sugar and complete starvation in flies is sufficient to elicit a homeostatic response. Subsequently, we used holidic medium to study effects of deficiency of a specfic macronutrient- cabohydrate in the food. To do so , we generated RNA- seq libraries from brains of 5 day old mated adult male  flies maintained on different feeding regimes and used the sequencing data to identify diffrentially expressed genes in the brain under different feeding regimes.

overall_design: For each condition, we used RNA prepared from 120-130 manually dissected adult fly brains maintained under complete starvation or sugar starvation regime for 24 hours.

first: Korneel

last: Hens


title: Quantitative RNA-seq analysis unveils osmotic and thermal adaptation mechanisms relevant for ectoine production in Chromohalobacter salexigens

city: Seville

first: Carmen

last: Vargas

state: Seville

address: C/profesor García Gonzalez n2

country: Spain

institute: University of Seville

summary: Quantitative RNA sequencing (RNA-seq) and the complementary phenotypic assays were implemented to investigate the transcriptional responses of Chromohalobacter salexigens to osmotic and heat stress. These conditions trigger the synthesis of ectoine and hydroxyectoine, two compatible solutes of biotechnological interest. Our findings revealed that both stresses make a significant impact on C. salexigens global physiology. Apart from compatible solute metabolism, the most relevant adaptation mechanisms were related to “oxidative- and protein-folding- stress responses”, “modulation of respiratory chain and related components”, and “ion homeostasis”. A general salt-dependent induction of genes related to the metabolism of ectoines, as well as repression of ectoine degradation genes by temperature, was observed. Different oxidative stress response mechanisms, secondary or primary, were induced at low and high salinity respectively, and repressed by temperature. A higher sensitivity to H2O2 was observed at high salinity, regardless of temperature. Low salinity induced genes involved in “protein-folding-stress response”, suggesting disturbance of protein homeostasis. Transcriptional shift of genes encoding three types of respiratory NADH dehydrogenases, ATP synthase, quinone pool, Na+/H+ antiporters, and sodium-solute symporters, was observed depending on salinity and temperature, suggesting modulation of the components of the respiratory chain and additional systems involved in the generation of H+ and/or Na+ gradients. Remarkably, the Na+ intracellular content remained constant regardless of salinity and temperature. Disturbance of Na+- and H+-gradients with specific ionophores suggested that both gradients influence ectoine production, but with differences depending on the solute, salinity, and temperature conditions. Flagellum genes were strongly induced by salinity, and further induced by temperature. However, salt-induced cell motility was reduced at high temperature, possibly caused by an alteration of Na+ permeability by temperature, as dependence of motility on Na+-gradient was observed. The transcriptional induction of genes related to the synthesis and transport of siderophores correlated with a higher siderophore production and intracellular iron content only at low salinity. In addition, compared to low salinity external iron increased hydroxyectoine accumulation by 20% at high salinity, but reduced the intracellular content of ectoines by 50% at high salinity plus high temperature. These findings support the relevance of iron homeostasis for osmoadaptation, thermoadaptation and accumulation of ectoines, in C. salexigens

overall_design: For transcriptomic analysis, three different growth conditions were used: low salinity (0.6 M NaCl, 37 ºC), high salinity (2.5 M NaCl, 37 ºC) and high salinity plus high temperature (2.5 M NaCl, 45 ºC). Three replicated cultures were grown for each condition.

first: Manuel

last: Salvador

first: Montserrat

last: Argandoña

first: Emilia

last: Naranjo

first: Francine

last: Piubeli

first: Joaquín

last: Nieto

first: Laszlo

middle: C

last: Csonka


title: Transcriptome profiling of DCP5 using strand-specific RNA-sequencing in Arabidopsis

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: Arabidopsis DCP5, a homolog of human RNA-associated protein 55, is a nessary component of eukaryotic processing bodies (P-bodies). knockdown mutant of dcp5-1 showed compromised RNA decapping activity and reduced P-body size. Here we profiled Arabidopsis transcriptome of roots, shoots, and inflorensences in Col-0 and DCP5-1 mutant using strand-specific RNA-sequencing. Our analysis identified a large number of DCP5-regulatd transcripts in Arabidopsis.

overall_design: Transcriptom profiling in roots, shoots, inflorensences of WT and DCP5-1 plants with 3 biological replicates.

first: Choonkyun

last: Jung

last: Xu

first: Shulin

last: Deng

first: Huan

last: Wang

first: Nam-Hai

last: Chua


title: Transcriptome profiling of Normal and Cancerous Prostate Cells

first: Timothy

last: Peters


title: Dissection of heterogeneity during cardiac maturation process by single-cell RNA sequencing

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: To improve the maturity and reduce the heterogeneity of iPSC-cardiomyocytes, we addressed the diversity of iPSC-cardiomyocytes by single-cell RNA sequencing and analyzed in detail about heterogeneity during cardiac maturation process.

overall_design: mRNA profiles of differentiated iPSC-cardiomyocytes at several differentiation stages; day0, day21, day30.

first: A

first: M

last: Nakamura

first: S

last: Funakoshi

first: Y

last: Yoshida

last: Yamanaka


title: RNA-seq analysis in dermis and epidermis of WT (control), LSL-Shh (Shh overexpression in epidermis), and E14.5d skin

city: New York

first: Chae Ho

last: Lim

state: New York

address: 550 First Ave.

department: Dermatology

institute: New York University School of Medicine

summary: We found Shh overexpression in epidermis can induce hair follicle neogenesis in wounded skin. We analyzed gene expression profile in dermis and epidermis of WT (control), LSL-Shh (Shh overexpression in epidermis) and E14.5d skin

overall_design: Cells were isolated from dermis and epidermis of WT and LSL-Shh (2 days after scab detachment) and E14.5d skin for RNA-seq analysis

first: Mayumi

last: Ito


title: Gene expression changes in fibroblasts with constitutively active Nrf2 reflect a senescence-associated secretory phenotype (SASP)

city: Zurich

first: Paul

last: Hiebert

address: Otto-Stern-Weg 7

institute: ETH Zurich

summary: Nrf2 is a key regulator of the cellular antioxidant defense system, and pharmacological Nrf2 activation is a promising strategy for cancer prevention. Here we discovered a novel role of Nrf2 as a regulator of the matrisome. Activation of Nrf2 in fibroblasts induced early onset of cellular senescence. Mechanistically, this resulted from Nrf2-mediated transcription of matrix and matrix-remodeling genes. Fibroblasts with activated Nrf2 deposited a senescence-promoting matrix, with plasminogen-activator inhibitor being the key inducer of the senescence program. In vivo, this promoted keratinocyte proliferation and re-epithelialization during wound healing, but also skin tumorigenesis. Analysis of the gene expression profile of fibroblasts with activated Nrf2 and published data sets revealed that Nrf2 activates genes characteristic for cancer-associated fibroblasts. These data identify Nrf2 as a key player in the control of the cancer-associated fibroblast phenotype and highlight the need for careful use of Nrf2-activating pharmaceuticals.

overall_design: Primary fibroblasts were isolated and cultured from the skin of newborn transgenic mice with Cre-recombinase expressed in fibroblasts (Col1a2Cre). Fibroblasts from 3 mice with Cre plus a constitutively active Nrf2 (caNrf2) mutant and 3 mice with Cre only (ctrl) were used. Fibroblasts were allowed to proliferate in culture for 6 days to allow for sufficient numbers for RNA sequencing. Total RNA was isolated from cells followed by RNA-seq analysis.

first: Sabine

last: Werner


title: Identification of genes regulated by long noncoding RNA H19 in skeletal muscle

city: Farmington

last: Zhang

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

summary: Soleus muscle has the most abundant H19 expression compared to other skeletal muscle tissues. In order to identify genes regulated by long noncoding RNA H19 in skeletal muscle, we performed RNA-Seq with dissected WT and H19KO soleus muscles from 21 week old mice. Among the differentially expressed genes, we found skeletal muscle - overexpressed gene DUSP27, which potentially plays an important role in regulating skeletal muscle glucose metabolisim by regulating the activitiy of AMPK, might be a target of H19 mediated regulation.

overall_design: Soleus muscle was harvested from 21-week old mice, followed by total RNA extraction, library preparation and RNA-seq analysis to compare trancript profiles between WT and H19KO conditions.

first: Gordon

middle: G

last: Carmichael

first: Yingqun

last: Huang


title: Identification of genes regulated by Long noncoding RNA H19 in hepatic cells

summary: We used high throughput sequencing to compare the differential gene expression of HepG2 cells with and without H19 knockdown. We found critical genes involved in glucose production changed significantly after H19 konckdown compared to control.

overall_design: HepG2 cells were transfected with either control siRNA or siH19. 48h after transfection, total RNA was extracted for library preparation and RNA-seq analysis to compare trancript profiles between siCon and siH19 cells.


title: RNA-Seq analysis to identify novel genes associated with Neuropilin-1 expression in the BT-474 breast cancer cell model

city: Muscat

first: Adviti

last: Naik

address: Al Khoud

department: Biology

country: Oman

institute: Sultan Qaboos University

summary:
Background: Neuropilin-1 (NRP-1) is a non-tyrosine kinase glycoprotein receptor that elicits multiple functions depending on the ligand bound. It is known to promote cancer progression however; transcriptome-wide changes triggered by NRP-1 are not defined. In this study we aimed to identify novel molecules associated with NRP-1 expression using a global transcriptomic approach in a recombinant breast cancer cell model.

Methods: NRP-1 was stably overexpressed in the BT-474 breast cancer cell line (BT-474 NRP-1) and subjected to next generation RNA sequencing using the Illumina HiSeq 4000 sequencing system. Two replicates each of the control BT-474 and BT474-NRP1 were utilized for sequencing. The count per million (CPM) method was utilized for filtering low counts/noise by NOISeq. The clean reads were mapped to reference genome using HISAT/ Bowtie2 tool. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) method was utilized to calculate the expression levels. False Detection Rate (FDR) ≤ 0.001, absolute value of Log2 ratio ≥ 2 and consistency between the two replicates were used as the default threshold to identify significant DEGs.

Results: A total of 22,655,647 clean reads from 22,914,684 raw sequencing reads were generated upon sequencing. 22 upregulated and 61 downregulated genes were identified. Among the DEGs, 11 upregulated and 11 downregulated genes were shortlisted based on their known roles in cancer and/or EMT for confirmation with real-time qPCR. 2 upregulated genes TNC and TARP and 5 downregulated genes ACE, APOD, DDIT3, P2RX6 and ATF3 indicated consistently differential expression with qPCR.

Conclusion: We report for the first time the global transcriptome-wide changes elicited by NRP-1 overexpression in a breast cancer cell model. Our study identified the novel association between several candidate molecules such as TNC, a known oncogene, and NRP-1 expression that may controbute to the tumourigenic role of NRP-1 in breast cancer.

overall_design: Transcriptome-wide profile changes were determined on Neuropilin-1 overexpression in the BT-474 breast cancer cell line using Illumina HiSeq4000-based RNA sequencing

first: Sirin

last: Adham


title: Hepatic transcriptome by Next Generation Sequencing of WT and clock mutant mice fed a HFD ad libitum or time-restricted feeding.

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

summary: Increased susceptibility of circadian clock mutant mice to metabolic diseases has led to the understanding that a molecular circadian clock is necessary for metabolic homeostasis. Circadian clock produces a daily rhythm in activity-rest and an associated rhythm in feeding-fasting. Feeding-fasting driven programs and cell autonomous circadian oscillator act synergistically in the liver to orchestrate daily rhythm in metabolism. However, an imposed feeding-fasting rhythm, as in time-restricted feeding, can drive some rhythm in liver gene expression in clock mutant mice. We tested if TRF alone, in the absence of a circadian clock in the liver or in the whole animal can prevent obesity and metabolic syndrome. Mice lacking the clock component Bmal1 in the liver, Rev-erb alpha/beta in the liver or cry1-/-;cry2-/- (CDKO) mice rapidly gain weight and show genotype specific increased susceptibility to dyslipidemia, hypercholesterolemia and glucose intolerance under ad lib fed condition. However, when the mice were fed the same diet under time-restricted feeding regimen that imposed 10 h feeding during the night, they were protected from weight gain and other metabolic diseases. Transcriptome and metabolome analyses of the liver from there mutant mice showed TRF reduces de novo lipogenesis, increased beta-oxidation independent of a circadian clock. TRF also enhanced cellular defense to metabolic stress. These results suggest a major function of the circadian clock in metabolic homeostasis is to sustain a daily rhythm in feeding and fasting. The feeding-fasting cycle orchestrates a balance between nutrient stress and cellular response to maintain homeostasis.

overall_design: Circadian time course of liver mRNA profile of WT, Bmal1-liverKO, Rev-erbα/β-liverdoubleKO, Cry1Cry2 double KO after 12 weeks of high fat diet feeding ad libitum or time-restricted feeding.

first: Amandine

last: Chaix

first: Satchidananda

last: Panda


title: Effects of Maternal Energy Intake on Genomic Imprinting in Fetal Sheep

status: Public on Aug 29 2018

city: Storrs

first: Xiuchun

last: Tian

address: 1390 Storrs Road, ABL220D

department: Animal Science

institute: University of connecticut

summary:
Background: Genomic imprinting is an epigenetic phenomenon of differential allelic expression based on parental origin. To date a total of 255 imprinted genes have been identified or predicted among all investigated mammal species. However, only 21 have been described in sheep and 11 are annotated in current ovine genome.
Results: Here we aim to use DNA/RNA throughput sequencing to identify monoallelically expressed and imprinted genes in organs of day 135 fetal sheep, and 2) to determine whether different levels of maternal energy intake (100% of NRC energy requirement or control, 140% or over-, and 60% or under-fed) influence genomic imprinting. We report strategies to solve technical challenges in the next-generation sequencing data analysis pipeline, including alignment bias of RNA sequencing reads and filtering potential false positives. We identified 80 monoallelically expressed and 18 putatively imprinted genes using the list of 255 stated above as a guide. Five (45.6% of 11) were already known imprinted genes in sheep, the other 13 were known imprinted in other mammals. Sanger sequencing confirmed four putative sheep imprinted genes INPP5F, PLAGL1, CASD1 and PPP1R9A. Among the 13 putative imprinted genes, five localized in the known sheep imprinting clusters of MEST domain on chromosome 4, DLK1/GTL2 domain on chromosome 18 and IGF2/H19 domain on chromosome 21, three were in a novel sheep imprinted cluster on chromosome 4 known in other species as PEG10/SGCE. Additionally, we found that the imprinted genes PHLDA2, SLC22A18, DIRAS3, and IGF2 were differentially expressed, albeit without allelic expression reversal, among the three maternal nutritional groups.
Conclusions: Together, our results expanded the sheep imprinted gene list to 34 and demonstrated the influence of maternal diet on fetal imprinting under the conditions studied.

overall_design:
DNA sequencing of ram and RNA sequencing of fetal tissus was used to discover novel genomic imprinting genes in sheep day 135 fetal tissues. Then the maternal nutruition effects was determined.
Please note that [1] re-sequenced Ram DNA (for the purpose of genotype individual father for each fetus) is an essential part of the study and therefore included in the records.
[2] Since reads were mapped to both reference/alternative genome, there are 2 processed files for Ram genotypes, but for fetuses, the reads coverage from two genomes were averaged, therefore one 1 file for each.

first: Jingyue

middle: E

last: Duan

first: Mingyuan

first: Kaleigh

last: Flock

first: Sahar

last: Seesi

first: Ion

last: Mandoiu

first: Amanda

middle: K

last: Jones

first: Sambhu

middle: M

last: Pillai

first: Maria

last: Hoffman

first: Hesheng

last: Jiang

first: Sarah

last: Reed

first: Kristen

last: Govoni

first: Steve

last: Zinn

first: Zongliang


title: Next Generation Sequencing Facilitates identification of genes differentially expressed during feather elongation

city: Arlington

first: Ang

last: Li

state: TX

address: 655 W Mitchell St, SEIR 244

department: Kinesiology

institute: University of Texas at Arlington

summary: Purpose: The goals of this study is to identify genes differentially expressed at different stages of feather elongation

overall_design: Hamburger & Hamilton (H&H) stage 31 (Embryonic day 7) and H&H 35 (Embryonic day 9) chicken dorsal skins were dissected out. Epithelium and mesenchyme were separated in 2X CMF. Total RNA was extracted using Trizol reagent. For library construction we used TruSeq RNA Sample Prep Kit Version2 (Illumina). Two biological replicates were sent for sequencing (50bp, single end) with Illumina HiSeq 2000 in the USC Epigenome Center.

first: Ping

last: Wu


title: Comparing oestrogen-responsive genes in endometrial and breast cancer cell lines

city: Brisbane

first: Eva

last: Baxter

address: 300 Herston Road

department: Cell and Molecular Biology

institute: QIMR Berghofer Medical Research Institute

summary: Up to 80% of endometrial and breast cancers express the oestrogen receptor ERa. Unlike breast cancer, anti-oestrogen therapy has had limited success in endometrial cancer, raising the possibility that oestrogen has different effects in the two cancer types. We investigated the role of oestrogen in endometrial and breast cancers using cell lines and found that oestrogen-responsive genes were predominantly unique between the two cancer types.

overall_design: Endometrial and breast cancer cell lines were treated with oestradiol or vehicle for three hours and RNA sequenced in duplicate.

first: Karolina

last: Windloch

first: Greg

last: Kelly

first: Jason

middle: S

last: Lee

first: Frank

last: Gannon

first: Donal

last: Brennan


title: Polycomb complexes associate with enhancers to promote oncogenic transcriptional programs in cancer

city: Miami

first: Ho Lam

last: Chan

state: FL

address: 1501 NW 10th Ave. BRB 742A

department: Human Genetics

institute: University of Miami

summary: The Polycomb repressive complexes PRC1 and PRC2 play an essential role in cell fate decisions, embryonic development and gene regulation. While the functions of PRC2 in cancer are under intense study, the function of PRC1 in cancer remains largely unexplored. Here, we show that RNF2, the gene encoding RING1B, and canonical PRC1 (cPRC1) genes are amplified and overexpressed in breast cancer. Specifically, in estrogen receptor positive (ER+) breast cancer cells, cPRC1 is functionally associated with enhancers and genes regulated by ERa, while in triple negative breast cancer (TNBC) cells, a different cPRC1 variant is recruited to enhancers and promoters occupied by the bromodomain protein BRD4. Mechanistically, cPRC1 complexes are recruited to active enhancers independently of PRC2 and RING1B enzymatic activity. Moreover, RING1B has a dual role in regulating enhancer activity and gene transcription as it is recruited to enhancers to maintain and promote gene expression of breast cancer oncogenes. We also show that RING1B regulates chromatin accessibility of oncogenic transcription factors. Finally, we provide evidence that association of PRC1 to active enhancers is not restricted to breast cancer, demonstrating that RING1B recruitment to transcriptionally active sites occurs in multiple cancer types. Our work highlights a non-classical function of cPRC1 complexes in regulating specific oncogenic programs in cancer through its association with enhancer regions.

overall_design:
ChIP-seq of RING1B, H3K27me3, H2AK119ub1, H3K4me3, and H3K27ac in iPSCs, MCF10A, MDA-MB-231 and T47D; PCGF2 and H3K36me3 in MCF10A, MDA-MB-231, and T47D; H3K4me1 in MDA-MB-231 and T47D; ERa in T47D; and BRD4 in MDA-MB-231.
RNA-seq of RING1B-depleted MDA-MB-231, T47D, and SKBR3 in duplicates.
ATAC-seq of RING1B-depleted MDA-MB-231 and T47D in duplicates.

first: Ho

first: Felipe

last: Beckedorff

first: Jenaro

last: Garcia-Huidobro

first: Yusheng

last: Zhang

first: Antonio

last: Colaprico

first: Hua

last: Figueroa

first: John

last: LaCava

first: Ramin

last: Shiekhattar

first: Lluis

last: Morey


title: RNA maps of the non-canonical RNA-binding site of Gemin5

city: Madrid

first: Begona

last: Aguado

state: Madrid

address: Nicolas Cabrera 1

department: Genomics and NGS Service

institute: CBMSO

summary: We report the CLIP-seq data of the non-canonical RNA-binding site of Gemin5. This region consists of two domains, RBS1 and RBS2, differing in their RNA-interaction features. Interestingly, the most abundant RNA target of the RBS1 polypeptide was the Gemin5 mRNA. Biochemical and functional characterization of this target demonstrated that RBS1 domain physically interacts with a stem-loop upregulating mRNA translation by counteracting the negative effect of Gemin5 protein on global protein synthesis. We propose that the RBS1 domain of Gemin5 performs a dual role on translation control, which depends on the target RNA, allowing fine-tune the availability of Gemin5 to play its multiple roles in gene expression control

overall_design: Identification of the cellular RNA targets of the RBS1 and RBS2 domains of Gemin5 by CLIP

first: R

last: Francisco-Velilla

first: J

last: Fernandez-Chamorro

first: I

last: Dotu

first: E

last: Martinez-Salas


title: Global Transcriptional analysis of human spinal cord and neocortical neuroepithelial stem (NES) cells

city: New Haven

first: Stephen

last: Strittmatter

address: 295 Congress avenue

department: Neurology

institute: Yale University

summary: We report the transcriptional profile of human spinal cord and neocortical neuroepithelial stem cells (SC-NES and NCX-NES cells) to identify potential engraftment markers in the lesioned spinal cord. We report that cells with a homologous neuroanatomical origin robustly integrate in the host tissue compared to cells with a different regional identity. Specifically, we describe that SC-NES cells display elective integration properties in the lesioned spinal cord compared to NCX-NES cells and that these properties are due to a combination of intrinsic and extrinsic factors. Upon transplantation, SC-NES cells differentiate into neurons and glial cells and extend lond-distance axons, whereas NCX-NES cells remain undifferentiated and display poor integration properties. SC-NES cell upregulate genes related to neurogenesis. In particular. we emphasize the upregulation of MTURN (maturin), ATCAY, PTN (pleiotropin), KAL1 (anosmin), SYT4 and SYT13.

overall_design: We handled 6 samples, 3 for SC-NES cells and 3 for NCX-NES cells. Each sample was handled in triplicate for a total of 18 samples. For SC-NES cells we had:  undifferentiated cells in vitro (SC-NES), differentiated for 2 months in vitro (SC-Neurons) and differentiated for two months in vivo upon tranplantation (SC-Graft). Similarly, we had three samples for NCX-NES cells: undifferentiated NCX-NES cells, differentiated in vitro for two months (NCX-Neurons) and differentiated for two months in vivo after transplantation (NCX-Graft)

first: Maria

middle: T

last: Dell'Anno

first: Mingfeng

last: Li