title: Aluminum Oxide Nanoparticles and Aluminum Ion Leading to Distinct Physiological and Molecular Responses in Arabidopsis thaliana

city: Hangzhou

first: Yujian

last: Jin

state: Zhejiang

address: Chaowang Road 18

institute: Zhejiang University of Technology

summary: Nano-aluminium oxide (nAl2O3) is one of the most widely used nanomaterials, but the molecular toxic mechanism of nAl2O3 on plants is still not clarified completely. In this study, we compared the toxic effects of nAl2O3 and Al3+ ion at the physiological and molecular levels. The shoot weight and root weight of Arabidopsis thaliana were decrease to 57.01% and 45.15% after the Al3+ ion exposure , while nAl2O3 increased the root weight by 48.07% and length by 38.53% at the selected concentration (98 mmol/L) for 10 d exposure. Physiological research showed that the photosystem (chlorophyll fluorescence parameters down-regulated) and antioxidant system (MDA and H2O2 content up-regulated) in A. thaliana were severely injured by the Al3+ ion. Data from transcriptome analysis clarified how nAl2O3 and Al3+ ion selectively affected root development and growth. nAl2O3 stimulated root growth directly (e.g., up-regulation of the root hair-specific gene family and root development genes, POLARIS protein), or indirectly (e.g., up-regulation of N and P absorption-related genes). Conversely, Al3+ ion disturbed ion homeostasis (up-regulated Al and Cu content) and caused severe oxidative stress, thus activating the salicylic acid (SA) signaling pathway and up-regulating nitric oxide (NO)-related genes, inducing the plant defense response. However, the overproduced SA and NO (up-regulated 2.60-fold) led to the inhibition of CAT activity (down-regulation of CAT1 and CAT2 genes) and increased the H2O2 level (up-regulated 2.84-fold). Subsequently, root development-related genes (e.g., auxin induced in root cultures 1) were down-regulated. This work gives us new insight into understanding the different molecular mechanisms of the plant response to nAl2O3 and Al3+ stresses.

overall_design: Compare the molecular responses of Arabidopsis thaliana after nAl2O3 and ion Al exposure

first: Xiaoji

last: Fan


title: Genome-wide maps of KDM5A/JARID1A/RBP2 and JARID2/JMJ in HL-1 cardiomyocytes.

status: Public on Apr 01 2018

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Illinois at Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the identification of genomic regions bound by RBP2 and JARID2 in mouse cardiomyocytes. RBP2 generates methylated lysine 4 in histone H3. Consistent with previous data, RBP2 binds at the TSS regions. However, we found that overepresentation of gene ontologies (GO) for RBP2 targets in cardiomyocytes is drastically different from those in mouse embryonic stem (ES) cells. In cardiomyocytes, there is overepresentation of genes involved in heart morphogenesis and vasculogenesis. Strikingly, we found that location of JARID2, a factor critical for ES cell function, significantly overlaps with RBP2 location in cardiomyocytes.

overall_design: Examination of two homologous proteins, one of each is a histone demethylase and another is not.

first: Abul

last: Islam


title: Differential gene expression of M. tuberculosis in adipocytes and preadipocytes reveals redundancy of iron storage machinery in a fat rich host

status: Public on Mar 31 2018

city: New Delhi

first: Sheetal

last: Gandotra

address: Sukhdev Vihar, Mathura Road

department: Chemical and System Biology

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

type: Expression profiling by high throughput sequencing

summary: RNA-seq based discovery of physiologic state of M. tuberculosis in fat rich cells

overall_design: We sequenced RNA from M. tuberculosis isolated from infected 3T3L1 adipocytes, preadipocytes and DMEM culture media at 10 days post infection

first: Ananya

last: Nandy

first: Anupam

middle: K

last: Mondal

first: Rajesh

last: Pandey

first: Prabhakar

last: Aramugam

first: Neetika

last: Jaisinghani

first: Vivek

last: Rao

first: Debasis

last: Dash


title: Gfi1b - A key player in genesis and maintenance of AML and MDS

city: Essen

first: Cyrus

last: Khandanpour

state: NRW

address: Hufelandstr. 55

department: Department of Hematology

country: Germany

institute: University Hospital Of Essen

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

overall_design: Refer to individual Series


title: Gfi1b - A key player in genesis and maintenance of AML and MDS [ChIP-seq]

summary: Differentiation of hematopoietic stem cells (HSCs) is regulated by a concert of different transcription factors (TFs). A disturbed function of TFs can be the basis of (pre)malignancies such as myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). Growth Factor Independence 1b (Gfi1b) is a repressing TF with a key role in quiescence of HSCs and emergence and maturation of erythrocytes and platelets. Here, we show that low expression of GFI1B in blast cells is associated with inferior prognosis of MDS and AML patients. Using mouse models with either reduced expression or conditional deletion of Gfi1b, crossed with a mouse model reflecting human MDS or AML, we demonstrate that AML development was accelerated with heterozygous loss of Gfi1b, and latency was further decreased when Gfi1b was conditionally deleted. Loss of Gfi1b significantly enhanced stemness of leukemic cells with upregulation of genes fundamentally involved in leukemia development. On a molecular level, we found that loss of Gfi1b not only increased the levels of reactive oxygen species (ROS) but also induced gene expression changes of key AML pathways such as the p38/AKT pathway. These results demonstrate that Gfi1b functions as an oncosuppressor in MDS/AML development.

overall_design: one sample per genotype has been sequenced

first: Aniththa

last: Thivakaran

first: Lacra

last: Botezatu

first: Judith

last: Hönes

last: Schütte

first: Lothar

last: Vassen

first: Nadine

last: Olberding

first: Yahya

middle: S

last: Al-Matary

first: Renata

last: Köster

first: Klaus

last: Lennartz

first: Andre

last: Görgens

first: Bernd

last: Giebel

first: Bertram

last: Opalka

first: Ulrich

last: Dührsen


title: BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-seq Fat)

city: New York

first: Martin

middle: J.

last: Walsh

state: NY

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

summary: Glucose and fat metabolism are tightly interconnected where endogenous de novo lipogenesis (DNL) serves to convert carbohydrates directly into lipids. Here, we explored the role of the long isoform Brd4 as a key transcriptional co-activator in lipogenesis. As a member of the Bromo-extraterminal (BET) protein family, Brd4 is characterized by two tandem bromodomains that bind acetylated lysine on both histone and non-histone proteins in chromatin. We found that treatment with MS417, a small molecule inhibitor of Brd4 binding to acetylated lysine, suppresses 3T3-L1 adipocyte differentiation. MS417-treated obese (ob/ob) mice displayed resistance to weight gain and loss of fat from steatotic livers. Comprehensive RNA-seq and ChIP-seq analyses delineate a Brd4-driven gene network required for glycolysis-lipogenesis flux that is shared between glycolytic liver and 3T3-L1 adipocytes, but absent in the non-glycolytic white abdominal fat. Our data further reveal that Brd4 functions to provide specific metabolic resources, such as acetyl-CoA and nicotinamide adenine dinucleotide (NAD) cofactors, in cell types utilizing DNL. Collectively, these findings provide a novel view of the critical role Brd4 plays in orchestrating transcription of a network of genes directing metabolic pathways governing carbohydrate fueled lipid metabolism fundamental for controlling glucose homeostasis and body weight.

overall_design: RNA-seq was used to measure gene expression levels in white abdominal fat (WAF) of DMSO (control) and MS417 treated ob/ob (C57BL/6-Lepo) mice.

first: Sabina

last: Benko

first: Fan

last: Zhang

first: Blanca

last: Andino

first: Guangtao

first: SiDe

last: Li

first: Virginia

last: Gillespie

first: Andrew

middle: C

last: Shin

first: Francesca

last: Aguilo

first: Chih-Hung

last: Chen

first: Weijia

first: Christoph

last: Buettner

first: Ming-Ming

last: Zhou

middle: J


title: BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-seq Liver)

overall_design: RNA-seq was used to measure gene expression levels in livers of DMSO (control) and MS417 treated ob/ob (C57BL/6-Lepo) mice.


title: BRD4 directs glycolytic metabolism through a comprehensive epigenomic and transcriptional network


title: BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-Seq 3T3-L1)

overall_design: RNA-seq was used to measure gene expression levels in 3T3-L1 pre-adipocytes, control differentiating and MS417 treated differentiating  (5 days post-induction of differentiation) 3T3-L1 adipocytes.


title: Genome-wide maps of KDM5A/JARID1A/RBP2 and KDM5B/JARID1B/PLU1 in estrogen treated MCF7 cells.

first: Elizaveta

last: Benevolenskaya

summary: We report the identification of genomic regions bound by RBP2 in MCF7 (ER+) cells and the MCF7 cells that were treated with estradiol. RBP2 is recruited to TSS regions and shows preference for GC-rich regions. We find the regions differentially bound by RBP2 after estrogen treatment. These regions will be correlated with binding of ER, H2A.Z and high/low transcriptional activity. We also report genomic regions bound by RBP2 closest homolog, PLU1. PLU1 location does not overlap with RBP2 binding sites. In contrast to RBP2, PLU1 does not show very high enrichment at TSS. This suggests that these two histone demethylases are preferentially located in different regions.

overall_design: Examination of RBP2 location in estrogen-treated and untreated cells; comparison of RBP2 and PLU1 location

first: Abul

last: Islam

first: N

last: Gévry


title: Analysis of differential gene expression in the Streptococcus sanguinis SK36 treated with sub-inhibitory dose of Ampicillin for 3 time periods.

status: Public on Mar 30 2018

city: Richmond

first: Fadi

middle: Elias

last: El-Rami

state: VA

address: 521 N 11th Str, wood bldg, room 424

department: Microbiology & Immunology

institute: Virginia Commonwealth University

summary: Gene expression profile of the Streptococcus sanguinis SK36 exposed to sub-inhibitory dose (0.125 µg/ml) of Ampicillin for three time periods compared to the untreated strain SK36

overall_design: Experiment: SK36 strains were treated with a sub-inhibitory dose (0.125 µg/ml) of Ampicillin for 10,20,30 minutes. Control strain was untreated. Three biological replicates independently grown and prepared for each time point and control.

middle: E

first: Ping

last: Xu


title: Interplay between Nsd1 and PRC2 demarcates regions of H3K27me2 and H3K27me3.

status: Public on Mar 29 2018

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: The core Polycomb Repressor Complex 2 (PRC2) is composed of Ezh1/2, Suz12, Eed and is responsible for mediating both H3K27me2 and H3K27me3. However, the mechanisms by which PRC2 demarcates these two repressive modifications in the genome are unknown. In a functional screen, we identified the H3K36 dimethyltransferase Nsd1 as a modulator of PRC2-mediated di- and trimethylation of H3K27. ChIP-Seq analysis following the depletion of Nsd1 revealed a global reduction in H3K36me2 and an increase in H3K27me3 at sites previously marked by H3K27me2. We show that the H3K36me2 at H3K27me2 marks co-occupy regions and provide evidence that the presence of H3K36me2 functions to restrict the spatial distribution of Polycomb mediated H3K27me3 domains.

overall_design: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from mouse embryonic stem cells transduced with shRNA targeting Nsd1 (pLKO.TRC1shNsd1.1 and pLKO.TRC1shNsd1.2) and non-targeting control shRNA (pLKO.TRC1shLuciferase). For two of the three experiments presented, ChIP with spike-in using Drosophila melanogaster chromatin was performed.

first: Gundula

last: Streubel

first: Andrea

last: Scelfo

first: Sri

last: Ganesh Jammula

first: Adrian

last: Bracken

first: Diego

last: Pasini


title: C. elegans FBF iCLIP from spermatogenic and oogenic germlines

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: PUF RNA-binding proteins control stem cells in diverse species, including mammalian, arthropod, and nematode, in addition to other biological functions.  The C. elegans PUF protein FBF serves as a paradigm for  metazoan PUFs. FBF is essential for the maintenance of germline stem cells but also regulates the hermpahrodite sperm/oocyte cell fate switch and is critical for the process of spermatogenesis. We have attempted to “disentangle” the different roles of FBF by comparing its targets in spermatogenic and oogenic germlines.  To this end, we used FBF iCLIP to learn its binding profile in an adult hermaphrodite germline that is sexually transformed and makes only sperm due to a temperature-sensitive sex-determination mutant.  As a control, we analyzed FBF iCLIP data from oogenic germlines at the same temperature.  Using a modified peak calling algorithm, we identified FBF binding sites in oogenic animals at 20°C, oogenic animals at 25°C, and spermatogenic animals at 25°C.  Oogenic FBF targets were similar at 20°C and 25°C. By contrast,  FBF mRNA targets in spermatogenetic animals had a distinct profile, revealing sperm-specific targets that are likely critical for the FBF role in spermatogenesis. Most importantly, we found FBF bound to mRNAs regardless of germline gender.   In particular,  a group of 22 mRNAs clustered as bound with high frequency in a gender- and temperature-independent manner.  These 22 mRNAsencode RNA-binding proteins and stem cell regulators and may be crucial for the FBF role in in stem cell maintenance.

overall_design: We generated FBF-1 and FBF-2 iCLIP datasets from animals with somatic tissues of the same gender but germline tissues of opposite gender. For each FBF, we used an N-terminally FLAG-tagged single copy fbf transgene in a strain lacking the endogenous gene (e.g. tagged FLAG::FBF-1 in an fbf-1 null mutant ).  Adult hermaphrodites with a sexually transformed germline that are strictly spermatogenic were obtained using a temperature sensitive gain of function mutation in the fem-3 gene (Barton and Kimble 1987).  These fem-3 (ts, gf) mutants are spermatogenic at restrictive temperature (25°C). We therefore introduced FLAG-tagged FBF-1 or FBF-2 into the fem-3(ts,gf) mutant, again removing the corresponding endogenous fbf gene in each strain. We then performed FBF iCLIP from adults that were either oogenic or spermatogenic, both raised at 25 °C.   For each strain (each FBF, each germline gender), we processed three biological replicates. Three negative control datasets were produced for each germline gender in parallel by omitting the FLAG antibody.

middle: F

first: Aman

last: Prasad

first: Brian

last: Carrick

first: Peggy

last: Kroll-Connor

first: Marv

last: Wickens

first: Judith

last: Kimble


title: RNA-seq analysis of differential gene expression in jejunal epithelial from Holstein Friesian bulls undergoing diet restriction and compensatory growth

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

institute: Teagasc Grange

summary: The objective of this study was to examine the effect of dietary restriction and subsequent re-alimentation induced compensatory growth on the global gene expression profile of jejunum epithelial  Holstein Friesian bulls (n=40) were assigned to one of two groups: restricted feed allowance (RES; n=20) for 125 days (Period 1) followed by ad libitum access to feed for 55 days (Period 2) or (ii) ad libitum access to feed throughout (ADLIB; n=20).  All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependent on each treatment group. At the end ofeach period, 10 animals from each treatment group (RES, ADLIB) were slaughtered, and jejunum epithelial collected from all animals. RNA was extracted and jejununal epithelium gene expression was examined using RNAseq technology on all samles collected (end of Period 1: 10 samples each from ADLIB and RES groups; end of Period 2: 10 samples each from ADLIB and RES groups). Dietary restriction and subsequent re-alimentation were associated with altered expression of genes involved in digestion and metabolism, aswell as cellular protection and detoxification in jejunal epithelia. This information may be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction.

overall_design: 40 jejunumal epithelium RNA samples were analysed in total. 10 samples were from jejunum epithelium collected at the end of a period of dietary restriction (d 125; Period 1) and 10 samples were from jejunum epithelium collected after 55 days of compensatory growth (d 55 of re-alimentation, Period 2). In addition,  RNA was also anlaysed from 10 samples collected from animals fed ad libitum at the end of both Period 1 and Period 2.

first: Sinead

last: Waters

first: Paul

last: Cormican

first: Alan

last: Kelly

first: David

last: Kenny


title: A single cell hematopoietic landscape resolves 8 lineage trajectories and defects in Kit mutant mice

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

summary: Haematopoietic stem and progenitor cells (HSPCs) maintain the adult blood system and their dysregulation causes a multitude of diseases. However, the differentiation journeys towards specific haematopoietic lineages remain ill defined, and system-wide disease interpretation remains challenging. Here, we have profiled 44,802 mouse bone marrow HSPCs using single cell RNA-Sequencing to provide a comprehensive transcriptional landscape with entry points to eight different blood lineages. We identified a common basophil/mast cell bone marrow progenitor, and characterised its molecular profile at the single cell level. Transcriptome sequencing of 13,815 HSPCs from the c-kit mutant W41 mouse model revealed the lack of a distinct mast cell lineage entry point, together with global shifts in cell type abundance. Proliferative defects were accompanied by reduced Myc expression. Compensatory processes included upreglation of the integrated stress response pathway and downregulation of pro-apoptotic gene expression in erythroid progenitors, thus providing a template of how single cell transcriptomics can reveal qualitative, quantitative and molecular aspects of mutant phenotypes.

overall_design: To determine the transcriptional landscape of mouse HSPCs in normal and perturbed haematopoiesis.

first: Rebecca

last: Hannah


title: Modulation of synaptic phosphodiesterase PDE2A activity is a new therapeutic approach for Fragile X Syndrome in newborns and adolescents.

status: Public on Mar 28 2018

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: FMR1 HITS-CLIP experiments of mice cerebellum, cortex and Hypocamppi

overall_design: 2 replicate for cerebellum, 4 for cortex and 5 for hippocamppus region of mice brain.

first: T

last: MAURIN

first: K

last: LEBRIGAND

first: B

last: BARDONI


title: BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (ChIP-Seq 3T3-L1)

first: Martin

last: Walsh

overall_design: Examination of Brd4 binding in 3T3-L1 differentiating adipocytes.

first: Sabina

last: Benko

first: Fan

last: Zhang

first: Blanca

last: Andino

first: Guangtao

first: SiDe

last: Li

first: Virginia

last: Gillespie

first: Andrew

last: Shin

first: Francesca

last: Aguilo

first: Chih-Hung

last: Chen

first: Weijia

first: Christoph

last: Buettner

first: Ming-Ming

last: Zhou


title: The synergestic effects of western diet and carbon tetrachloride (CCl4) to develop non-alcoholic steatohepatitis (NASH) and liver tumor in mice

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: NASH is a combination of hepatic steatosis and severe inflammation, which can lead to fatal liver disease such as cirrhosis and hepatocellular carcinoma. While a variety of models have been descirbed, they have several limitations. Therefore, it is of urgent importance to create animal model that recapitulate the physiology, histology and outcome seen in human with NASH. We created western diet-fed and CCl4-treated mouse model. they showed characteristic histological features of NASH such as fibrosis, ballooning and steatosis at 12 weeks and liver cancers developed at 24 weeks. Their transcritomic changes were also similar to those seen in human NASH.

overall_design: We examined transcriptomic changes of liver in normal diet-fed mice, CCl4-treated mice, western diet (WD)-fed mice and WD-fed and CCl4-treated mice at 12 weeks and 24 weeks. Also, we examined  transcriptome of liver cancer which developed at 24 weeks in WD-fed and CCl4-treated mice. Liver samples were pooled from 4 indepedent mice.

first: Takuma

last: Tsuchida

first: Naoto

last: Fujiwara

first: Youngmin

middle: A

last: Lee

first: Scott

middle: L

last: Friedman


title: RNA-seq of naked mole-rat liver from young and old animals

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: Comparison of gene expression level by Illumina sequencing of naked mole-rat liver from young and old animals. We identified differentially expressed genes and provide functional profiles, which give insights into the aging process of long-lived rodents.

overall_design: 9 liver samples; 2 groups: 1) 6 young animals, 2) 3 old animals

first: Martin

last: Bens

first: Karol

last: Szafranski

first: Susanne

last: Holtze

first: Arne

last: Sahm

first: Thomas

middle: B

last: Hildebrandt

first: Matthias

last: Platzer


title: Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

city: Newcastle Upon Tybe

first: Michael

last: Jackson

address: International Centre for Life

institute: Institute of Genetic Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) are numerically abundant in human, predominantly derived from protein coding genes, and some can act as microRNA sponges or cis-acting transcriptional regulators. Changes in circRNA abundance have been identified during human development which may be functionally important, but lineage-specific analyses are currently lacking. To address this, we performed RNAseq analysis of human embryonic stem (ES) cells differentiated for 90 days towards 3D laminated retina. A transcriptome-wide increase in circRNA abundance, size, and exon count was observed which reached a plateau by day 45. Parallel analyses, controlling for sample and locus specific effects, identified 239 circRNAs with expression patterns distinct from the transcriptome-wide pattern, but these also increased in abundance over time. Surprisingly, circRNAs derived from long non-coding RNAs (lncRNAs) were found to account for a significantly larger proportion of transcripts from their loci of origin than circRNAs from coding genes. The most abundant, circRMST:E12-E6, showed a >100X increase during differentiation which was associated with altered promoter usage, and accounts for >99% of RMST transcripts in many adult tissues. The second most abundant, circFIRRE:E10-E5, accounts for >98% of FIRRE transcripts in differentiating human ES cells, and is one of 39 FIRRE circRNAs many of which include multiple unannotated exons. Our results suggest that during human ES cell differentiation, changes in circRNA abundance are primarily globally controlled. They also suggest that RMST and FIRRE, genes with established roles in neurogenesis and topological organisation of chromosomal domains respectively, encode circular lncRNAs with only minor linear species.

overall_design:
Human H9 embyonic stem cells (ESC) were differentiated towards retinal pigment epithelium cells (with and without Igf1), and rRNA depleted total RNA samples from 3 biological replicates at days 0, 45 and 90 were sequenced. All samples were analysed using PTESFinder v 1 (http://sourceforge.net/projects/ptesfinder-v1/ [Izuogu et al., 2016]) to identify back-splice junctions. Differential expression analyses of circRNAs identified from H9 ESC were performed separately for circRNAs originating from protein-coding and non-coding loci, after controlling for locus-specific expression changes and global changes in expression upon differentiation. Cluster anlyses of total canonical junctions and circRNA expression were performed to identify relative expression changes upon differentiation.

This series includes amplicon sequencing to verify FIRRE splice junctions.

first: Osagie

middle: G

last: Izuogu

first: Abd

last: Alhasan

first: Jonathan

last: Hyslop

first: Francesco

last: Mastrosa

first: Carla

last: Mellough

first: Joseph

last: Collin

first: Richard

last: Gallon

first: Majlinda

last: Lako

first: David

last: Elliott

first: Mauro

last: Santibanez-Koref

first: Ingrid

last: Ehrmann


title: Genome-wide changes in DNA methylation upon Dnmt3b loss in melanoma

city: New Haven

first: Goran

last: Micevic

state: CT

address: 200 S Frontage Road NSB287

institute: Yale University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: We report the genome wide DNA methylation changes in melanoma associated with inactivation of Dnmt3b.

overall_design: Examination of DNA methylation in melanomas from Dnmt3bwt and Dnmt3bKO mice by RRBS.

first: Viswanathan

last: Muthusamy


title: Total differential RNA-seq in the marine proteobacterium Vibrio harveyi

status: Public on Mar 27 2018

city: Leioa

first: Ander

middle: Hernández

last: Plágaro

state: Bizkaia

address: Barrio Sarriena S/N

department: Immunology, Microbiology and Parasitology

country: Spain

institute: University of the Basque Country

summary:
Objectives: determination of transcription start sites in Vibrio harveyi genome and discovery of new transcripts
Methods: we performed differential seqencing of total RNA isolated from o.n. control Vibrio harveyi cultures. Sample treatment with Terminator EXonuclease (TEX) allowed differenciation of primary and secondary transcripts, helping in the definition of transcription start sites (TSS)
Results: by data-mining RNA-seq data and performing some Northern Blot experiments we were able to detect new putative small-RNAs, along with these results, a more deep analisys of our RNA-seq data will give futher insight into genetic organization of Vibrio harveyi genome to help in its investigation

sample_organism: Vibrio harveyi NBRC 15634 = ATCC 14126 = KCTC 12724

overall_design:
Total RNA was isolated from control o.n. cultures of Vibrio harveyi cells, strain ATCC 14126, by triplicate. RNA samples were differentialy treated with TEX and sequenced. Reads were aligned to Vibrio harveyi strain ATCC 43516 to detect TSS
contributor: Vertis Biotechnologie AG

first: A

middle: H

first: V

middle: R

last: Kaberdin

first: P

last: Peerman


title: Single cell RNA sequencing of murine basophil/mast cell progenitors and granulocyte/monocyte progenitors

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

summary: We have performed single cell RNA sequencing of murine bone marrow progenitors to study the early differentiation into the mast cell and basophil lineages.

overall_design: Single cell RNA-sequencing of 94 basophil/mast cell progenitors (BMCPs) and 47 granulocyte/monocyte progenitors (GMPs) isolated from bone marrow of three female C57BL/6 mice.

first: Joakim

last: Dahlin

first: W

middle: Y

last: Lau

first: Sonia

last: Nestorowa

first: Bertie

last: Göttgens


title: Genome-wide association study and transcriptome analysis of the white/red earlobe color in Qingyuan Partridge chicken

city: Guangzhou

first: Wei

last: Luo

state: Guangdong

address: Wushan Road

department: The College of Animal Science

country: China

institute: South China Agricultural University

summary: Gene expression comparison between red group and white group (Red_vs_White) showed that there were 81 differentially expressed genes (DEGs) (fold changes ≥ 1.5; adjusted P-value < 0.05) between the two samples, in which 27 were up-regulated and 54 were down-regulated. Further functional analysis on DEGs showed that, no significant KEGG pathways or GO terms could be clustered, but a number of genes including TP63 etc, could be clustered into HPO terms of Thickened skin, Epidermal thickening, Hyperkeratosis, Dry skin and Alopecia

overall_design: Earlobes from 3 male 114-day QYPs exhibiting white earlobe color and 3 male 114-day QYPs exhibiting red earlobe are separately collected for RNA-seq

first: Jiguo

last: Xu


title: Epigenetic regulation of in vivo B cell Differentiation

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

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

overall_design: Refer to individual Series and includes ATAC-seq and RNA-seq


title: Division-Specific Accessibility Program of B cell Differentiation

summary: B cell differentiation occurs over multiple cellular divisions and involves a switch in transcriptional programs that allows for antibody secretion.  The transcription factors that drive this process have been studied but the epigenetic mechanisms and sites these factors function at are not well understood. Here we investigated the distinct changes in chromatin accessibility that occured at distinct cellular divisions during in vivo B cell differentiation.

overall_design: Congenically marked B cells were CFSE labelled and adoptively transferred into uMT mice that lack B cells.  One day post-transfer, mice were innoculated with LPS and transferred cells isolated three days later.  Using CFSE and the plasma cell marker CD138, cells representing undivided (Div0) or had progressed through 1, 3, or 5 divisions (Div 1, 3, 5) and not aquired CD138, and cells that had gone through at least 8 divisions (Div8+) and acquired CD138 were isolated by FACS.  ATAC-seq was performed on the isolated cells.

first: C

middle: D

first: J

middle: M

last: Boss


title: Collateral sensitivity of antibiotic resistant bacteria to antimicrobial peptides

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

summary: Cationic antimicrobial peptides (CAPs) are promising novel alternatives to conventional antibacterial agents, but the overlap in resistance mechanisms between small-molecule antibiotics and CAPs is unknown. Does evolution of antibiotic resistance decrease (cross-resistance) or increase (collateral sensitivity) susceptibility to CAPs? We systematically addressed this issue by studying the susceptibilities of a comprehensive set of antibiotic resistant Escherichia coli strains towards 24 antimicrobial peptides. Strikingly, antibiotic resistant bacteria frequently showed collateral sensitivity to CAPs, while cross-resistance was relatively rare. We identified clinically relevant multidrug resistance mutations that simultaneously elevate susceptibility to certain CAPs. Transcriptome and chemogenomic analysis revealed that such mutations frequently alter the lipopolysaccharide composition of the outer cell membrane and thereby increase the killing efficiency of membrane-interacting antimicrobial peptides. Furthermore, we identified CAP-antibiotic combinations that rescue the activity of existing antibiotics and slow down the evolution of resistance to antibiotics. Our work provides a proof of principle for the development of peptide based antibiotic adjuvants that enhance antibiotic action and block evolution of resistance.

overall_design: 84 samples were collected from Escherichia coli lines adapted to one of 12 antibiotics as well as from non-adapted controls. Two parallel lines for each antibiotic were included in the assay. Sample groups contain 3 biological replicates.

first: Viktoria

last: Lazar

first: Ana

last: Martins

first: Reka

last: Spohn

first: Lejla

last: Daruka

first: Gergo

last: Fekete

first: Gabor

last: Grezal

first: Monika

last: Szamel

first: Pramod

middle: K

last: Jangir

first: Balint

last: Kintses

last: Csorgo

first: Adam

last: Gyorkei

first: Andras

last: Kincses

last: Der

first: Fruzsina

last: Walter

first: Maria

last: Deli

first: Zsofia

last: Hegedus

last: Olajos

first: Orsolya

last: Mehi

first: Istvan

last: Nagy

first: Tamas

last: Martinek

last: Papp

first: Csaba

last: Pal


title: Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [ATAC-Seq]

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

summary: To identify regions of genome accessibility influenced by LSD1 inhibition, THP1 AML cells were subjected to ATAC sequencing.

overall_design: To identify regions of genome accessibility influenced by LSD1 inhibition, THP1 AML cells were subjected to ATAC sequencing in the presence or absence of an LSD1 inhibitor OG86.


title: Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [anti-LSD1, MYB, and GFI1 ChIP-Seq]

summary: To identify genomic binding regions, THP1 AML cells were subjected to ChIP sequencing (ChIPseq) using anti-LSD1, MYB or GFI1 antibodies.

overall_design: To identify genomic binding regions, THP1 AML cells were subjected to ChIP sequencing (ChIPseq) using anti-LSD1, MYB or GFI1 antibodies in the presence or absence of an LSD1 inhibitor OG86.


title: Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia

overall_design: Refer to individual Series


title: Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [RNA-Seq experiments]

summary: To determine whether changes in histone modifications directly correlate with changes in transcription, THP1 AML cells were treated with a potent and selective LSD1 inhibitor (OG86) and then subjected to concomitant RNA sequencing (RNAseq) and ChIP sequencing (ChIPseq) for monomethyl-, dimethyl- and trimethyl histone H3 modifications.

overall_design: THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in semi-solid culture. Two technical replicates were analysed for each sample.


title: Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [ChIP-Seq: histone modifications]

overall_design: THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in semi-solid culture.


title: Human MAIT cells exit peripheral tissues and re-circulate via lymph in steady state conditions

status: Public on Mar 26 2018

city: Cape Town

first: Valentin

last: Voillet

state: Western Cape

address: First Floor Wembley Square, 3 McKenzie St, Gardens

country: South Africa

institute: cape town hvtn immunology laboratory

summary: Mucosal-associated invariant T (MAIT) cells recognize bacterial metabolites as antigen and are found in blood and tissues, where they are poised to contribute to barrier immunity. Recent data demonstrate that MAIT cells located in mucosal barrier tissues are functionally distinct from their blood counterparts, but the relationship and circulation of MAIT cells between blood and different tissue compartments remains poorly understood. Previous studies raised the possibility that MAIT cells do not leave tissue and may either be retained or undergo apoptosis. To directly address if human MAIT cells exit tissues, we collected human donor-matched thoracic duct lymph and blood and analyzed MAIT cell phenotype, transcriptome and TCR diversity by RNAseq.

overall_design: mRNA profiles of CD8+MAIT from blood and lymph were generated by RNA-seq from four patients, in duplicate

first: Martin

last: Prlic


title: Retinoic Acid Related Receptor Orphan Receptor a (RORa) expressing T regulatory cells thwart type-2 cutaneous allergic inflammation

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: We used RNA-sequencing to profile gene expression differences between Tregs from skin and LNs of Foxp3 cre-efyp WT mice. We further compared skin Tregs from control and Foxp3 cre Rora fl/fl (Rora cKO) mice in the steady state and after allergic inflammation was induced using MC903.

overall_design: RNA seq analysis of mouse Tregs sorted from skin and skin draining LNs as CD45+CD3+CD4+YFP+ T cells

first: Nidhi

last: Malhotra

first: Unmesh

last: Jadhav

first: Olga

last: Barreiro

first: Manuel

last: Leyva-Castillo

first: Francoise

last: Meylan

first: Nicholas

last: O’Neill

first: Dennis

last: O’Leary

first: Pierre

last: Chambon

first: Ulrich

last: Von Andrian

first: Richard

last: Siegel

first: Eddy

last: Wang

first: Raif

middle: S

last: Geha


title: Gene expression in protoapothecia from Pyronema confluens

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

summary: The aim of this analysis was to analyze gene expression in young fruiting bodies of the filamentous ascomycete Pyronema confluens. Young fruiting bodies were isolated by laser microdissection, RNA was extracted, amplified and used for RNA-sequencing. The resulting data were compared to data from total vegetative and sexual mycelium from a previous analysis.

overall_design:
Three independent biological replicates were performed and sequenced for protoapothecia.
RNA-seq reads from a previous analysis (Traeger et al. 2013, PLoS Genet 9: e1003820, GEO accession number GSE41631) were also included in the analysis.

first: Stefanie

last: Traeger


title: Profiling of N6-Adenosine (m6A) Methylation in HepG2 cells

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: N6-methyladenosine (m6A) modification is the most abundant internal RNA modification in eukaryotes. Recent studies have shown that the dynamic and reversible regulation of m6A modifications in mRNAs or non-coding RNAs plays critical roles in tissue development, stem cell self-renewal and differentiation, control of heat shock response, and circadian clock controlling, as well as in RNA metabolism and processing. METTL14 is a major m6A writer which together with METTL3 forms the core of the methyltransferase complex that catalyzes the conversion of adenosine (A) to m6A. To investigate the effect of METTL14 on m6A modfication, we performed m6A-seq in HepG2 cells with stably expressed shRNAs against METTL14 (shMETTL14) or non-specific control shRNA (shNS).

overall_design: m6A-seq in HepG2 cells with stably expressed shMETTL14 or shNS.

first: Huilin

last: Huang

first: Hengyou

last: Weng

first: Wenju

last: Sun

first: Boxuan

last: Zhao

first: Chuan

last: He

first: Jianhua

last: Yang


title: Gcn4 binding in coding regions can activate internal and canonical 5’ promoters in yeast [ChIP-seq]

status: Public on Mar 23 2018

city: Bethesda

first: Yashpal

last: Rawal

state: Maryland

address: 6 Center Dr., Bldg 6, Room 233

department: 1Laboratory of Gene Regulation and Development

institute: NICHD-NIH

summary: Gcn4 is a yeast transcriptional activator induced by amino acid starvation. ChIP-seq analysis revealed 546 genomic sites occupied by Gcn4 in starved cells, representing ~30% of all Gcn4 binding-motifs. Deviation from the consensus motif and nucleosome occupancy are key negative determinants of Gcn4 binding.  Surprisingly, only ~40% of the bound sites are in promoter regions, and only ~50-67% of these activate transcription, indicating extensive negative control over Gcn4 function. Most of the remaining ~300 Gcn4-bound sites are within coding sequences (CDS), with ~75 representing the only bound sites near Gcn4-induced genes. Many such unconventional sites map between divergent antisense and sub-genic sense transcripts induced within CDS, adjacent to induced TBP peaks—consistent with Gcn4 activation of cryptic, bidirectional internal promoters. Mutational analysis confirms that Gcn4 sites within CDS can activate sub-genic and full-length transcripts from the same or adjacent genes, showing that functional Gcn4 binding is not confined to promoters.

overall_design:
Immunopurified sonicated DNA fragments were subjected to paired-end sequencing.
Paired-end sequencing study of (1) ChIP samples for Gcn4 (Affinity purified Gcn4 antibody was described in Zhang et al., Mol Cell Biol. 2008 Nov;28(20), (2) ChIP samples for the Rpb3 subunit of Pol II, (3) ChIP samples for the TBP(SPT15)-myc13.

first: Razvan

last: Chereji

first: Vishalini

last: Valabhoju

first: Hongfang

last: Qiu

first: Josefina

last: Ocampo

first: David

middle: J

last: Clark

first: Alan

last: Hinnebusch


title: Clock-dependent chromatin topology modulates circadian transcription and behavior

city: Lausanne

first: Felix

last: Naef

address: AAB 040 Station 15

department: Bioengineering

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

summary: The circadian clock dynamically rewires promoter-enhancer loops in tissues to drive robust daily rhythms in gene transcription and locomoter activity.

overall_design: Total RNA and crosslinked genomic DNA extracted from mouse tissues during the dirunal cycle. Mouse genotype conditions include WT, Bmal1 KO, and Cry1Intron KO.

first: Jerome

last: Mermet

first: Jake

last: Yeung

first: Clemence

last: Hurni

first: Daniel

last: Mauvoisin

first: Kyle

last: Gustafson

first: Celine

last: Jouffe

first: Damien

last: Nicolas

first: Yann

last: Emmenegger

first: Cedric

last: Gobet

first: Paul

last: Franken

first: Frederic

last: Gachon


title: c-kitCre Knock-ins Fail to Identify, Effectively Recombine and Fate-Map Cardiac Stem Cells

city: Catanzaro

first: Daniele

last: Torella

address: Viale Europa

department: Medical and Surgical Sciences

country: Italy

institute: Magna Graecia University

summary: A recent cell-fate mapping study by Van Berlo et al. using a Cre knock-in (KI) into the c-kit locus, and  two other studies using a similar genetic approach to track the fate of Cardiac Stem/progenitor Cells (CSCs) concluded that c-kitpos cells only negligibly generate cardiomyocytes. These papers questioned our findings that tissue-specific c-kitposCSCs are endogenous regenerative agents necessary and sufficient for cardiomyocyte regeneration/replenishment after injury. We consider answering whether the c-kitCre-KI approach properly identifies and fate-maps c-kitposCSCs and/or whether c-kitCre-KI-insertion affects CSC biology and cardiomyogenic potential. To test this hypothesis, we crossed the the c-kitCre-KI mouse to different reporter mouse models. We concluded that the c-kitCre-KI approach neither identifies nor fate-tracks the c-kitposCSCs, because c-kit expression level in these cells is too low to produce enough Cre to effectively recombine the floxed marker and permanently tag the CSC and their progeny.

overall_design: RNA-seq data from CSCs, isolated from wt and c-kitCre mice (triplicated) have been analysed and compared.

first: Carla

last: Vicinanza

first: Iolanda

last: Aquila

first: Eleonora

last: Cianflone

first: Mariangela

last: Scalise

first: Fabiola

last: Marino

first: Teresa

last: Mancuso

first: Francesca

last: Fumagalli

first: Emilia

last: Dora Giovannone

last: Cristiano

first: Enrico

last: Iaccino

first: Pina

last: Marotta

first: Annalaura

first: Roberto

last: Latini

first: Valter

last: Agosti

first: Pierangelo

last: Veltri

first: Konrad

last: Urbanek

first: Andrea

last: Isidori

first: Dieter

last: Saur

first: Ciro

last: Indolfi

first: Bernardo

last: Nadal-Ginard


title: Human iPSC-derived cells and microengineered Organ-Chip enhance neural development.

status: Public on Mar 22 2018

city: Los Angeles

first: Samuel

last: Sances

address: 8500 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars Sinai

summary: We show neural enhancement and induction of vascular interaction genes in iPSC-derived spinal motor neurons that have been incubated in a microengineered chip.

overall_design: Spinal motor neuron progenitors were plated in a 96 well plate either in neural media or in the presence of iPSC-derived endothelial cell conditioned media, and in a microphysiological chip cultured alone or in direct contact with iPSC-derived endothelial cells.


title: Modulation of ESRP2 and MBNL2 in normal kidney and clear cell renal cell carcinoma cell lines for analysis of stability programs

city: Montreal

first: Hamed

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

summary: While analyzing mRNA expression profiles of clear cell renal cell carcinoma (ccRCC) tumors, we found that the mRNAs that are bound at their 3' UTRs by muscleblind-like splicing regulator 2 (Mbnl2) and epithelial splicing regulatory protein 2 (ESRP2) are up-regulated in tumor compared to patient-matched normal tissues. Given that MBNL2 increases the stability of its targets and ESRP2 destabilizes its targets, we predicted that, in ccRCC tumors, MBNL2 activity increases, while ESRP2 activity decreases. To investigate the effect of each of these two RNA-binding proteins (RBPs) on the transcriptome of the cell, we used shRNA to knockdown MBNL2 in two different cell line models of ccRCC (786-O and A-498), and also to knockdown ESRP2 in normal primary renal proximal tubule epithelial cells (PRPTEC). RNA-seq revealed that MBNL2 knockdown partially reverses the ccRCC-associated transcriptome in ccRCC cell lines, whereas ESRP2 knockdown shifts the transcriptome of PRPTEC toward that of ccRCC.

overall_design: Two independent shRNAs were used for each protein in each cell line. Each cell line was also infected by a control shRNA in two replicates. The transcriptome after infection with MBNL2- or ESRP2-specific shRNA was compared to the transcriptome after infection with control shRNA.

first: H

first: P

last: Jandaghi

first: M

last: Safisamghabadi

first: Y

last: Riazalhosseini


title: Firefly genomes illuminate parallel origins of bioluminescence in beetles

city: Athens

first: Robert

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Fireflies and their fascinating luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of their bioluminescence remains unclear. To shed light on this long-standing question, we sequenced the genomes of two firefly species that diverged over 100 million-years-ago: the North American Photinus pyralis and Japanese Aquatica lateralis. To compare bioluminescent origins, we also sequenced the genome of a related click-beetle, the Caribbean Ignelater luminosus, with bioluminescent biochemistry near-identical to fireflies, but anatomically unique light organs, suggesting the intriguing but contentious hypothesis of parallel gains of bioluminescence. Our analyses support two independent gains of bioluminescence between fireflies and click-beetles, and provide new insights into the genes, chemical defenses, and symbionts that evolved alongside their luminous lifestyle.

overall_design: MethylC-seq libraries were prepared from high molecular weight (HMW) DNA extracted from four Photinus pyralis Mercer Meadows New Jersey (MMNJ) males according to a previously published protocol (Urich et al. 2015; doi:10.1038/nprot.2014.114) and sequenced on an Illumina NextSeq 500 to an expected depth of ~36x. Sequencing data was aligned to Ppyr1.3 assembly using the latest version of methylpy (Schultz et al. 2015; doi:10.1038/nature14465; https://bitbucket.org/schultzmattd/methylpy/wiki/Home). In total, 49.4M reads were mapped corresponding to an actual sequencing depth of ~16x. A sodium bisulfite non-conversion rate of 0.17% was estimated from Lambda phage genomic DNA.

first: Adam

last: Bewick


title: SRA of transcriptome of Hevea brasiliensis

status: Public on Mar 25 2018

city: Danzhou

first: Wei-Min

last: Tian

state: Hainan

address: Baodao Village

department: Chinese Academy of Tropical Agricultural Sciences

institute: Rubber Research Institute

summary: We report here the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of two Hevea brasiliensis clones (93-114 and Reken501). Illumina sequencing generated a total of about 7-8G raw reads from each of the six batches (two batches for control and four batches for cold-treatment) of rubber tree clone 'Reken501' and '93-114', respectively. By using these reads, 167,911 unigenes with an average length of 847 bp were obtained by de novo assembly with a series of optimized parameters. Base on limit rule with FDR≤0.001 and |log2 Ratio|≥1, 2052 unigenes were up-regulated and 3440 unigenes were down-regulated under 1 h cold treatment in 'Reken501', whereas 2403 unigenes were up-regulated and 18376 unigenes were down-regulated under 1 h cold treatment in'93-114', and the amounts of up-regulated and down-regulated unigenes were respectively 6923 and 6282 in 'Reken501', whereas it was respectively 5295 unigenes and 21229 unigenes in'93-114' . Functional analysis showed mass of categories were reprogrammed between two clones. In detail,anthocyanin, flavonoid, isoflavonoid biosynthesis and starch and sucrose metabolism were shown more active in the cold-sensitive clone 'Reken 501', while the nitrogen metabolism, vitamin B6 metabolism, biosynthesis of unsaturated fatty acids and other processes of circadian rhythm-plant, spliceosome and RNA polymerase were more robust in the relatively cold-tolerant clone '93-114'. Moreover, the 'heat' module and 'Thinredoxin' module in the cellular stress response were highly induced in clone '93-114'.

overall_design: The transcriptome of leaf (control and cold treatment of Reken501 and 93-114) in Hevea brasiliensis

first: Xiao-Min

last: Deng

first: Jian-Xiao

last: Wang

first: Weimin


title: Studying iPSCs from a hibernating mammal reveals molecular mechanisms of cold resistance in neural tissues

first: Yizhao

last: Luan

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen university

summary: To explore the cold resistant feature of ground squirrel neuron cells, we compared transcriptomes of human and ground squirrel iPSC derived neurons in the response to cold treatment. We identified several key pathways that are critical for the maintenance of neuronal microtubule cytoskeleton integrity at low temperature.

sample_organism:
Homo sapiens
Ictidomys tridecemlineatus

platform_organism:
Homo sapiens
Ictidomys tridecemlineatus

overall_design: Neuron cultures of human and ground squirrel iPSC derivate incubated at 4 °C or the normal 37 °C for 1 hour or 4 hours, respectively. Totally, we obtained 18 transcriptomes, including 3 replicates of squirrel_4c_1h, 3 of squirrel_37c_1h, 2 of human_37c_1h, 2 of human_4c_1h, 2 of squirrel_37c_4h, 2 of squirrel_4c_4h, 2 of human_37c_4h and 2 of human_4c_4h.

first: Wei

last: Li

first: Jingxing

last: Ou

first: Zhi

last: Xie

first: Tantai

last: Zhao


title: Transcriptomic profiling of ex vivo isolated  CD3+CD4+ T cells from spleens of colitic Rag-/- mice received naïve ERαfl/fl and CD4CreERαfl/fl CD4+ T cells

city: Turku

first: Imran

middle: Ahammad

last: Mohammad

state: Finland

address: Tykistokatu 6

department: Lymphocytes and Inflammation

country: Finland

institute: Turku center for Biotechnology

summary: To study the role of estrogen receptor alpha (ERα) in T cell mediated inflammation, colitis was induced in Rag-/- mice by injecting FACS sorted CD4 T cells from control (ERαfl/fl) and ERα deficient (CD4CreERαfl/fl). After 8 weeks of injection, the CD4+ T cells were FACS sorted from Rag-/- spleens. RNA extraction was carried out and libraries were prepared using Illumina TruSeq RNA sample Preparation kit according to the manufacturer’s instructions.

first: Wendy

last: Watford

first: Inna

last: Starskaia

first: Tamas

last: Nagy

first: Jitao

last: Guo

first: Emrah

last: Yatkin

first: Kalervo

last: Väänänen

first: Zhi Jane

last: Chen


title: Small RNAs in undifferentiated and differentiating mouse embryonic stem cells

city: Pasadena

first: Diane

middle: E

last: Trout

address: 1200 E California Blvd M/C 156-29

department: Biology

institute: California Institute of Technology

summary: We report the identification of small RNAs in undifferentiated (d0) and differentiating (d4) mouse embryonic stem (ES) cells using high-throughput sequencing.  The goal of this study was to identify small RNAs involved in X-chromosome inactivation (XCI).  We have identified a subset of small RNAs that are generated from transposon sequences and map to the X-chromosome, suggesting their involvement in transposon control on the inactivating X-chromosome.

overall_design: Examination of 5 small RNA and 4 RNA-seq libraries in 3 ES cell states.

first: Daniel

last: Kim

first: Georgi

last: Marinov


title: Transcriptomic analysis genes involved in the establishment and maintenance of FMDV persistent infection

city: Wuhan

first: han

middle: ling

last: ling

state: Hubei

address: Bayi road

department: College of life science

institute: Wuhan University

summary: In FMDV persistent infection cell lines, we found that many FMDV-free cells (BHK_VEC) occupied. The BHK_VEC cells exhibited resisted to the parental FMDV, and could re-establish a persistent infection when infected with FMDV-OP, revealing a fact that host cells evolved during the persistent infection. To further explore the underlying molecular mechanism, transcriptomic analyses of BHK_VEC, BHK21 and BHK-Op cells were performed by using RNA-seq

overall_design: mRNA profiles of wild-type BHK21 , FMDV persistent infection cells (BHKOp) and FMDV-free cells of persistent infection (VEC) were generated by in-depth sequencing, in triplicate, using Illumina GAIIx.

first: Lingling

last: Han


title: Heat stress induced alternative splicing in a species-dependent manner

status: Public on Mar 21 2018

city: Sn diego

first: sumetha

last: kannan

state: California

address: 5500 Campanile Dr

institute: San DIego State University

summary: Patterns of alternative splicing during heat stress in Arabidopsis thaliana and Boechera depauperata indicate complex and species-specific interactions between differential expression and alternative splicing.

sample_organism:
Arabidopsis thaliana
Boechera depauperata

overall_design: RNA-Seq analysis of root during heat stress in Arabidopsis thaliana and Boechera depauperata.

first: Sumetha

last: Kannan

first: Elizabeth

last: Waters

first: Tanya

last: Renner

first: Gillian

last: Halter


title: Spatiotemporal regulation of liquid-like condensates in epigenetic inheritance

first: Scott

last: Kennedy

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Non-membrane bound organelles such as nucleoli, processing bodies, cajal bodies, and germ granules form via spontaneous self-assembly of specific proteins and RNAs. How these biomolecular condensates form and interact are poorly understood. Here we identify two proteins (ZNFX-1 and WAGO-4) that localize to C. elegans germ granules (P granules) in early germline blastomeres. Later in germline development, ZNFX-1/WAGO-4 separate from P granules to define an independent liquid-like condensate that we term the Z granule. In adult germ cells, Z granules assemble into ordered tri-droplet assemblages with P granules and Mutator foci that we term the PZM granule. Finally, we show that one biological function of ZNFX-1 and WAGO-4 is to interact with RNAs in the C. elegans germline to promote transgenerational epigenetic inheritance (TEI). We speculate that the temporal and spatial ordering of liquid droplet organelles may help cells organize and coordinate the complex RNA processing pathways underlying gene regulatory systems, such as RNA-directed TEI.

overall_design: Small RNA sequencing of WT, znfx-1 and wago-4 animals in P0 and F1 generations after feeding oma-1 RNAi. Total RNA seq was done in order to capture small RNA population around the gene targeted with or without dsRNA (oma-1). We use two mutants (znfx-1 and wago-4) to ask whether the dsRNA directed small RNAs are dependent on these two genes.

first: Gang

last: Wan


title: Comparison of the expression profiles of kdrl:mCherry-positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin-positive cells upon injury   compared to the rest of cardiac cells.

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: Contrary to mammals, zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart, and activated endocardial kdrl:mCherry cells, postnb:citrine fibroblasts and the rest of the cells at 7 days post injury.

overall_design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.

first: N

last: Mercader

first: R

last: Costa

first: H

last: Sánchez-Iranzo


title: Overexpression of OsNAC14 improves drought tolerance in rice

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

summary: Plants have evolved to possess adaptation mechanism to cope with drought stress by reprograming transcriptional networks through drought responsive transcription factors, which in turn mediate morphological and physiological changes. NAM, ATAF1-2, and CUC2 (NAC) transcription factors are known to be associated with various developmental processes and stress tolerance. In this study, we functionally characterized the rice drought responsive NAC transcription factor OsNAC14. OsNAC14 was predominantly induced at meiosis stage, and induced by drought, high salinity, ABA and low temperature in leaves than roots. Overexpression of OsNAC14 resulted in drought tolerance at the vegetative growth stage and enhanced filling rate at vegetative growth. OsNAC14 overexpression elevated expression of genes related to DNA damage repair, defense response, strigolactone biosynthesis, which correlated with resistance to drought tolerance. Furthermore, OsNAC14 directly bound to the promoter of drought inducible OsRAD51A1, a key component in homologous recombination in DNA repair system. These results indicate that OsNAC14 mediate drought tolerance by recruiting factors involved in DNA damage repair and defense response to enable plant to protect from cellular damage caused by drought stress, thereby provide mechanism for drought tolerance.

overall_design: RNA-seq using leaves of NT (nontransgenic plants), PGD1:OsNAC14 transgenic plants that were generated by deep sequencing using Illumina Hiseq 2500.

first: Jae-Sung

last: Shim

first: Nuri

last: Oh

first: Pil-Joong

first: Ju-Kon


title: Comparison of the expression profile of GFP-positive cells from Tg(-6.8wt1a:EGFP) with the rest of the cells in adult zebrafish cardiac ventricles

summary: wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP-positive cells to the rest of the cells of the ventricle.

overall_design: Four paired biological replicates of wt1a:GFP-positive and wt1a:GFP-negative cells obtained from pools of 3-5 zebrafish heart ventricles.


title: Next-generation sequencing of matched ectopic and eutopic endometrium identifies novel endometriosis-related genes and highlights the role of general metabolism

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

institute: Wellcome Sanger Institute

summary:
AmpliSeq IonTorrent sequencing of mRNA derived from ectopic lesions and matched eutopic endometrium. There were 4 matched pairs overall; all donors were in mid-secretory phase.

[SUBMITTER_CITATION]:
A. V. Predeus, E. S. Vashukova, A. S. Glotov, M. M. Danilova, N. S. Osinovskaya, O. V. Malysheva, N. Yu. Shved, N. Ganbarli, M. I. Yarmolinskaya, T. E. Ivashchenko, V. S. Baranov - Next-Generation Sequencing of Matched Ectopic and Eutopic Endometrium Identifies Novel Endometriosis-Related Genes.

overall_design: Each diluted library was amplified through emulsion PCR on Ion Sphere Particles (ISPs) using the Ion One Touch 200 Template kit with the Ion One Touch 2 system (Thermo Fisher Scientific, Inc.). Next, ISPs were recovered from the emulsion. Template-positive ISPs were enriched using Dynabeads MyOne Strepavidin C1 beads (Thermo Fisher Scientific, Inc.) by the OneTouch™ ES Instrument (Thermo Fisher Scientific, Inc.). ISP enrichment was confirmed by the Qubit 2.0 fluorimeter (Invitrogen, Carlsbad, CA, USA) using fluorescently labeled oligonucleotides complementary to adapter sequences. The enriched template-positive ISPs were loaded into Ion 318 Chip and sequenced on the Ion Torrent Personal Genome machine (Thermo Fisher Scientific, Inc.) using the Ion PGM Sequencing 200 Kit (Thermo Fisher Scientific, Inc.) according to the manufacturer's instructions.

middle: V

first: Elena

last: Vashukova

first: Andrey

last: Glotov

first: Maria

last: Danilova

first: Natalia

last: Osinovskaya

first: Olga

last: Malysheva

last: Shved

middle: I

last: Yarmolinskaya

first: Tatyana

last: Ivaschenko

first: Vladislav

last: Baranov


title: microRNAs in early pregnant porcine endometrium revealed by Illumina sequencing

city: Freising

first: Veronika

middle: L

last: Flöter

address: Weihenstephaner Berg 3

department: Life Science Center Weihenstephan

institute: Technische Universität München

summary:
Preimplantational estrogen exposure to pregnant gilts has been associated with implantation failure, embryonic losses and changes in endometrial mRNA expression. Small non-coding RNAs (ncRNA), especially miRNAs, play a key role in regulation of gene expression. Effects of estrogens on endometrial microRNAs (miRNA), however, have not been investigated in this context so far. Thus, we studied the influence of estradiol-17β (E2) on the endometrial expression profile of miRNAs in the pig at gestational day 10.
E2 administered early during pregnancy resulted in significantly higher endometrial estrogen concentrations even at a low dose, but did not disrupt the expression profile of endometrial miRNAs.

overall_design: Starting at insemination, sows were fed E2 at either 0.05, 10 and 1000 μg E2/kg body weight/day, respectively, or ethanol carrier only until examination at day 10 of pregnancy. 4 samples per treatment group were analyzed by high throughput sequencing (in the lowest dose group, tissue from one sow was extracted twice represeting a biological replicate).

first: Anne-Kathrin

last: Lorenz

first: Benedikt

last: Kirchner

first: Stefan

last: Bauersachs

first: Michael

middle: W

last: Pfaffl

first: Susanne

last: Ulbrich


title: Thyroid Dysfunction, Neurological Disorder and Immunosuppression as the Consequences of Long-term Combined Stress

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Stress is a powerful modulator of neuroendocrine, behavioral, and immunological functions. So far, the molecular mechanisms of response to stressors still remain elusive. In the current study, after 10 days of repeated chronic stress (hot-dry environment and electric foot-shock), a murine model of combinedstress (CS) was created in the SPF Wistar rats. Meanwhile, we established an ulcerative-colitis (UC) rat model induced by 2,4,6-trinitrobenzene sulfonic acid (TNBS)/ethanol enema according to previous studies. The blood, hypothalamus, and colon tissues of these rats from CS, normal control (NC), UC and sham (SH) groups, were collected for further investigations. Comparing to the NC group, the serum levels of T3, T4, fT3 and fT4 were obviously decreased in the CS group after chronic stress, indicating that thyroid dysfunction was induced by long-term combined stress. Moreover, the application of RNAseq and subsequent analyses revealed that neurological disorder and immunosuppression were also caused in the hypothalamus and colon tissues, respectively. Comparing with SH group, besides the induced colon infammation, thyroid dysfuntion and neurological disorder were also produced in the UC group, suggesting that hypothalamic-pituitary-thyroid (HPT) axis and gastrointestinal system might not function in isolation, but rather, have intricate crosstalks.

overall_design: Thyroid dysfuntion was induced by combined stress

first: Jingping

last: Zhang

first: Yi


title: A model that cancer cells’ metastatic competence is determined by their states

status: Public on Mar 20 2018

city: Hangzhou

first: Xia

last: Lin

address: Jiefang Road 88

institute: Zhejiang University

summary: A polyclonal mouse model of breast tumor heterogeneity using model cell line 4T1 was developed previously. It was shown that 4T1 cells were composed of mixed subpopulations with specializations, including dominating the primary tumor, contributing to metastatic populations, etc. Here in a different angle, we reveal that each 4T1 cells can switch between 2 distinct states, which could be easily misclassified into 2 subpopulations, as the 2 states can be distinguished by distinct patterns of gene expression, dramatic difference of metastatic competence, stem-cell like feature or not, etc. The event for each 4T1 cell to exhibit one state or another is stochastic and the metastatic competence of clones generated from a single 4T1 cell is variable rather than stable.  Further, given that metastatic competence of 4T1 cells is not stable, classification of clones based on metastatic competence is highly biased. Similarly, the classification of 4T1 clones based on gene expression profiles is also highly biased. Taken together, our data support that the exhibition of metastatic competence depends on the state of 4T1 cells and do not support the existence of subpopulations with specialization. To the best of our knowledge, no similar work has ever been reported.

overall_design: 4T1 cells were cultivated in 96-well plate at the concentration of one cell per well with 200 μL complete RPMI-1640. After 14 days of culture, 10 SC clones and 10 NSC clones were randomly collected. We collect three batches of SC and NSC from 3 independent experiments. Total RNA was extracted using the RNeasy kit (Qiagen, Germany). The quality of the total RNA was verified with the BioAnalyzer (Agilent, Santa Clara, CA, USA).

first: Xun

last: Hu

first: Chunpeng

last: Zhu

first: Hao

last: Wu


title: Arabidopsis ZED1-related kinases mediate temperature-sensitive intersection of immune response and growth homeostasis

city: Beijing

first: Wang

last: Zhicai

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, Chinese Academy of Sciences

summary:
The rationale: Activation of the immune response antagonizes plant growth and development in absence of pathogen, and such autoimmune phenotype is often suppressed by the elevation of ambient temperature. However, the molecular regulation of ambient temperature-sensitive intersection of immune response and growth is largely elusive.
Methods: A genetic screen identified an Arabidopsis mutant, zed1-D, by its high temperature-dependent growth retardation. A combination of molecular, cytological and genetic approaches was used to investigate the molecular basis behind the temperature-sensitive growth and immune response in zed1-D.
Key results: A dominant mutation in HOPZ-ETI-DEFICIENT 1 (ZED1) is responsible for a high temperature-dependent autoimmunity and growth retardation in the zed1-D. The autoimmune phenotype in the zed1-D is dependent on the HOPZ-ACTIVATED RESISTANCE 1 (ZAR1). ZED1 and some ZED1-related kinases (ZRKs) are induced by elevated temperature and function cooperatively to suppress the immune response by modulating the transcription of SUPPRESSOR OF NPR1-1 CONSTITUTIVE 1 (SNC1) in absence of pathogen.
Main conclusion: Our data reveal a previously unidentified role of ZRKs in ambient temperature-sensitive immune response in absence of pathogen, and thus disclose a possible molecular mechanism underlying temperature-mediated intersection of immune response and growth in plants.

overall_design: Compared the transcriptome of zed1-D with WT plants after being transferred from 18 into 28oC at different time points, 0h, 3h, 12h, and 48h.

first: Zhicai

last: Wang

first: Dayong

last: Cui

first: Yuxin


title: HPV

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

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

overall_design: Refer to individual Series


title: A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers (MBD-Seq)

summary: The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from The Cancer Genome Atlas.

overall_design:
MBD-sequencing data for 50 HPV+ HNSCC tumors, 25 normal UPPP, 2 HPV+ HNSCC patient derived xenografts, and 2 HPV+ HNSCC cell lines (SCC-090, SCC-047)
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Submitter declares that the raw data from patients will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

first: Daria

middle: A

last: Gaykalova

first: Joseph

last: Califano

first: Alexander

last: Favorov


title: Total RNA-Seq in WT and rrp6-delta strains of S. pombe

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

institute: Institut Curie

summary: Recent studies have revealed that eukaryotic genomes are pervasively transcribed by RNA polymerase II, producing a plethora of non-coding RNAs which frequently overlap protein-coding genes. Despite the fact that overlapping transcription is well known to repress transcription initiation from downstream promoters, the mechanism behind this phenomenon has remained elusive. It was proposed that transcriptional interference relies on the act of transcription rather than the RNA itself to block access of the transcription machinery to downstream promoters. Here, we use the fission yeast Schizosaccharomyces pombe to demonstrate that an RNA and chromatin-dependent mechanism is responsible for transcriptional interference. This relies on co-transcriptional recruitment of the histone deacetylase Clr3 to nascent non-coding RNA, leading to formation of hypoacetylated chromatin and repression of the downstream protein-coding gene. Our findings highlight the unexpected requirement for RNA as well as trans-acting protein factors in mediating the repressive effects imposed on gene expression through overlapping non-coding transcription.

overall_design: Strand-specific total RNA-Seq was prepared for WT and rrp6Δ cells. Both samples were sequenced in duplicates.

first: Beth

middle: R

last: Watts

first: Sina

last: Wittman

first: Camille

last: Gautier

first: Sofia

last: Battaglia

first: Patrick

last: Cramer

first: Antonin

last: Morillon

first: Lidia

last: Vasiljeva


title: A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers (RNA-Seq)

overall_design:
RNA-sequencing data for 47 HPV+ HNSCC tumors, 25 normal UPPP, 2 HPV+ HNSCC patient derived xenografts, and 2 HPV+ HNSCC cell lines (SCC-090, SCC-047)
----------------------------------------------
Submitter declares that the raw data from patients will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.


title: White Leaf and Panicle 2 encoding a PEP-associated protein, is required for chloroplast biogenesis under heat stress in rice (Oryza sativa L.)

first: lv

middle: yu

last: song

address: CNRRI

institute: CNRRI

summary: We performed a transcriptomics analysis in the wild type and the mutant, and the expression levels of PEP-encoded genes, chloroplast development and heat-strss-related genes genes were  affected inwlp2s mutant.

overall_design: RNA-sequencing analysis was performed on an Illumina Hiseq2500 (LC Sciences, USA) following the vendor's recommended protocol

first: Yusong

last: Lv

first: Xiangjin

last: Wei


title: JIP1 knockout in PE and TSA treated NRVMS

city: Aurora

first: Philip

middle: David

last: Tatman

state: Colorado

department: Department of Pharmacology

institute: University of Colorado

summary: Jip1 was knocked out in neonatal rat ventricular myocytes in the presence of phenylephrine and trichostatin a

overall_design: rnaseq of cardiomyocytes

first: Phil

first: Tim

last: McKinsey


title: An epigenetically-deregulated tumor state reveals a new role for embryonic transcription factors as cancer drivers

city: Basel

first: Renato

last: Paro

address: Mattenstrasse 26

department: D-BSSE

institute: ETH Zurich

summary: Tumor initiation is often linked to a loss of cellular identity. Transcriptional programs determining cellular identity are preserved by epigenetically-acting chromatin factors. Although such regulators are among the most frequently mutated genes in cancer, it is not well understood how an aberration of the epigenetic status contributes to tumor onset. In this work, we investigated the transcriptional signature of tumors caused by disruption of the Drosophila epigenetic regulator, polyhomeotic (ph). In larval tissue, ph mutant cells show a shift towards an embryonic-like signature. Using loss- and gain-of-function experiments, we uncovered the embryonic transcription factor knirps (kni) as a new cancer driver. The oncogenic potential of kni lies in its ability to activate JAK/STAT signaling and block differentiation. Conversely, tumor growth in ph mutant cells can be substantially reduced by overexpressing a differentiation factor. This demonstrates that epigenetically derailed tumor conditions can be reversed by induction of differentiation.

overall_design: Transcriptome analysis of ph505-tumors in Drosophila. Mutant clones FRT19A, ph505 generated in eye-antennal imaginal discs.

first: Joana

last: Torres

first: Remo

last: Monti

first: Jorge

last: Beira

first: Ariane

last: Hofmann

first: Makiko

last: Seimiya

first: Yanrui

last: Jiang

first: Niko

last: Beerenwinkel

first: Christian

last: Beisel


title: Oncogenes hijack the stress response machinery in T cell acute lymphoblastic leukemia [GRO-Seq]

city: New York

first: Nikos

last: Kourtis

address: 550 First Avenue

institute: NYU School of Medicine

summary: Oncogenes NOTCH1 and MYC directly regulate HSF1 and other critical proteins of the stress-response pathway in T-ALL. This GRO-Seq experiment demonstrates that release from NOTCH1 inhibition results in upregulation of HSF1 and other key HSPs.

overall_design: Nascent RNA was extracted from 10 million CUTLL1 cells using Trizol extraction (Invitrogen) according to the manufacturer’s protocol following the global run-on (GRO) reaction and BrUTP labeling. Nascent BrUTP-containing RNA was purified using BrdU beads (Santa Cruz) which was then used for library preparation. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. The experiment was performed at stready state (DMSO) and various time points post release from NOTCH1 signaling inhibition (γ-secretase inhibitor)

first: Charalampos

last: Lazaris


title: Effect of HDAC inhibition on nascent transcription by RNAPII in fission yeast

first: Maxime

last: Wery

overall_design: NET-seq was performed in WT cells either untreated (-TSA) or treated (+TSA) for 2.5 hours with 20 µg/ml of the HDAC inhibitor Trichostatin A (TSA). Both samples were sequenced in duplicates.

first: Beth

last: Watts

first: Sina

last: Wittman

first: Camille

last: Gautier

first: Sofia

last: Battaglia

first: Patrick

last: Cramer

first: Antonin

last: Morillon

first: Lidia

last: Vasiljeva


title: Micro RNAs involved in crosstalk betweeen Wnt signaling and TGF-beta signaling

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary:
The miRNAs play important roles in regulating gene expression at post-transcriptional level through fine-tuning of protein-encoding gene expression, and are involved in regulating important biological processes in different cells and tissue types, including osteoblast differentiation. Canonical Wnt signaling is also known to play pleiotropic roles in regulating cell differentiation during mammalian osteogenesis, although the role of miRNAs is not established for Wnt signaling in osteoblast differentiation. Here we examined the role of candidate miRNAs expressed differentially after Wnt3a expression during osteoblast differentiation.
Overexpression of the Wnt3a gene resulted in increased transcription of the ALP gene, but in decreased transcription of the Runx2, Col1a and OCN genes in osteoblastic MC3T3-E1 cells. Analysis of miRNA expression profile showed that 14 miRNAs were up-regulated and 21 miRNAs were down-regulated after Wnt3a overexpression in MC3T3-E1 cells. TGF-beta3 is presumed to be a candidate target gene of one of the down-regulated miRNAs with database search. Transfection of the miRNA mimic into MC3T3-E1 cells significantly inhibited the TGF-beta3 mRNA level and resultant protein expression, although overexpression of the Wnt3a gene could reverse the effect of the miRNA, resulting in the increased TGF-beta3 mRNA and protein levels. These results suggest that the miRNA is involved in osteoblast differentiation as a critical regulatory factor, mediating crosstalk between Wnt3a signaling pathway and TGF-beta3 signaling pathway.

overall_design: 4 samples

first: Hironobu

last: Katsuyama

first: Shigeko

last: Fushimi

first: Tsutomu

last: Nohno


title: postnb lineage traced cells at 7 and 60 days post cryoinjury (dpi) during adult zebrafish cardiac ventricle regeneration

first: Manuel

last: Gomez

summary: Contrary to mammals, zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast-like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP-GFP-loxP-mCherrycz1701 double transgenic line, we permanently label cells that expressed postnb at 3 and 4 days post injury (dpi) with mCherry by administration of 4-OHT. We sequenced mCherry-labelled cells obtained from the ventricular apex at 7 and 60 dpi.

overall_design: postnb-derived cells were FAC sorted from a pool of three to five  biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.

first: N

last: Mercader

first: H

last: Sánchez-Iranzo


title: Hijacking of stress response machinery by oncogenes in acute leukaemia [ChIP-seq]

first: Nikos

last: Kourtis

summary: HSF1 orchestrates the heat shock response pathway. This pathway is co-opted in cancer and provides critical stress relief from oncogenic stress. HSF1 has a diverse occupancy signature depending on the cell type. In this study, we performed HSF1 ChIP-seq analysis using the human T-ALL cell line CUTLL1 and P12. These results revealed the HSF1 chromatin binding signature in CUTLL1 and P12 cells. MYC is a driving oncogene in T-ALL. The non-oncogene addiction pathways that act downstream of this transcription factor to support anabolic pathways are not well-understood. For this reason, we performed MYC ChIP-seq analysis using the human T-ALL cell line CUTLL1. These results revealed that HSF1 and HSF1 targets are included in the MYC binding signature.

overall_design: Twenty million cells were used for the ChIP and precipitated using 5 micrograms of antibody (cell signaling, 4356) against human HSF1. Twenty million cells were used for the ChIP and precipitated using 5 micrograms of antibody (santa cruz biotechnology, N-262) against human MYC


title: Hijacking of stress response machinery by oncogenes in acute leukaemia


title: Single-cell RNAseq analysis of the empty and i8TF cell lines after 3 days of BL-CFC culture

city: Monterotondo

first: Christophe

last: Lancrin

state: RM

address: Via Ramarini 32

department: EMBL Rome

institute: EMBL

summary: The aim of the experiment was to assess the cell heterogeneity after the doxycycline treatment and the subsequent induction of the 8 transcription factors in the BL-CFC culture.

sample_organism:
Homo sapiens
Mus musculus
other sequences

overall_design: A2lox.empty and A2lox.i8TFs cell lines were used for this experiment. A2lox.empty is used a negative control while the doxycycline is inducing the expression of Erg, Fli1, Tal1, Lyl1, Lmo2, Runx1, Cbfb and Gata2 in the A2lox.i8TFs  cell line. Cells were cultured in BL-CFC culture for 1 day before doxycycline treatment and were cultured for an additional 48hours with (i8TFs_plus and E_plus) or without doxycycline (i8TFs_minus and E_minus). As additional controls of the single cell RNA seq experiment, bulk A2lox.i8TFs cells were collected at the same time point from the condition without doxycycline (Pos_Ctrl), also buffer only was used as negative control (Neg_Ctrl) and a human cell line as other control (K562).

first: Isabelle

last: Bergiers


title: Transcriptional study of ARN8 cells treated with novel DHODH inhibitors

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

summary: We have previously observed protein level changes after treating human cells with two novel inhibitors of the enzyme DHODH. This study was designed to study up to what degree these protein differences can be also observed at level of mRNA. As part of the de novo pyrimidine synthesis pathway, DHODH inhibition is expected to decrease the levels of total RNA in cells. However, some effector proteins associated with the p53 pathway are increased after treatment with these inhibitors. This study aims to answer if the observed protein differences are based on an increased transcription or due to protein stabilization.

overall_design: The data represent three independent experiments. In each experiment ARN8 cells were treated with two DHODH inhibitors (DrugA and DrugM) and a vehicle control.

first: Gergana

last: Popova

first: Sonia

last: Lain


title: Hijacking of stress response machinery by oncogenes in acute leukaemia [RNA-seq]

country: USA

summary: Our data demonstrate binding of NOTCH1 on the promoters of HSF1 and HSF1 targets. We performed RNA-seq upon control conditions, inhibition of the NOTCH1 pathway by gSI, HSF1 knockdown and combination of HSF1 knockdown and gSI treatment. Our results show that NOTCH1 regulates the expression of heat shock response genes. Moreover, combination of HSF1 downregulation and gSI treatment further decreased the expression of heat shock response genes compared to single treatments.

overall_design: Whole RNA was extracted from 1 million CUTLL1 cells treated as described below using the RNAeasy kit (Qiagen) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Differential gene expression analysis was performed between shRenilla_DMSO vs shRenilla_gSI, shRenilla vs shHSF1 and shHSF1_DMSO vs shHSF1_GSI.

first: Charalampos

last: Lazaris


title: Crown transcriptome analysis of Norstar (NO), Manitou (MA), and the near-isogenic lines (NIL) spring Norstar (SN) and winter Manitou (WM) under field conditions

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

summary: To explore transcriptional regulations in common wheat cultivars Norstar (NO), Manitou (MA), and the near-isogenic lines (NIL) spring Norstar (SN) and winter Manitou (WM) during seasonal cold acclimation.

overall_design: Total RNA were extracted from crowns of wheat NIL lines, up to five time points, for each line, in each year.

first: Brian

last: Fowler


title: Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks (ChIP-Seq)

first: Elana

last: Fertig

summary: Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV+) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis.

overall_design:
ChIP-sequencing data for 2 normal UPPP, 2 HPV+ HNSCC patient derived xenografts, and 2 HPV+ HNSCC cell lines (SCC-090, SCC-047) for H3K4me3, H3K9ac, H3K9me3, and H3K27ac histone marks
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Submitter declares that the raw data from patients will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

first: Daria

last: Gaykalova

first: Joseph

last: Califano

first: Alexander

last: Favorov


title: RNA-seq analysis comparing WT, TAp63-null, and DNp63-null primary murine keratinocytes

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

summary: We performed an RNA-seq analysis characterizing expression profiles in primary keratinocytes obtained from E18.5 mice of 3 different genotypes (WT, TAp63-/-, and ΔNp63-/-). We aimed to identify the specific transcriptional target genes regulated by TAp63 and ΔNp63 in physiological conditions.

overall_design: Examination of primary murine keratinocytes in 3 different genotypes (WT, TAp63-/-, and ΔNp63-/-).

first: Marco

last: Napoli


title: Analysis of p63-isoform specific direct target genes in primary murine keratinocytes

overall_design: Refer to individual Series


title: p63 ChIP-seq analysis comparing WT, TAp63-null, and DNp63-null primary murine keratinocytes

summary: We performed a ChIP-seq analysis characterizing the p63 binding sites in primary keratinocytes obtained from E18.5 mice of 3 different genotypes (WT, TAp63-/-, and ΔNp63-/-). We aimed to identify the specific genomic regions bound by TAp63 and ΔNp63 in physiological conditions.


title: Rheumatoid arthritis: aortic biopsies

status: Public on Mar 19 2018

city: Lillehammer

first: Ingvild

last: Oma

address: Anders Sandviks gate 17

country: Norway

institute: Innlandet Hospital Trust

summary: Analysis of biopsies of the ascending aorta from coronary artery disease patients with and without rheumatoid arthritis

overall_design: We examined aortic specimens from 8 contol patients with coronary artery disease (CAD) and 8 patients with CAD and rheumatoid arthritis. The speciments were routinely removed from their ascending aorta during constrution of the proximal aortacoronary veingraft anastomosis during coronary artery bypass grafting surgery. For patient's safety, the anastomoses were preferably made at sites with less pronounced signs of atherosclerosis.

first: Ivana

last: Hollan

first: Ole

middle: K

last: Olstad


title: ICE1 promotes the link between splicing and nonsense-mediated mRNA decay

city: Bethesda

first: Thomas

last: Baird

address: 50 South Drive, Room 2339

department: Biochemistry and Biophysics

institute: NIH/NHLBI

summary: Identification of RNAs differentially expressed during depletion of ICE1, UPF1 or a non-targeting control (NS) in HEK-293TO cells.

overall_design: Paired-end high throughput RNA sequencing on 293 cells treated with siRNA against ICE1, UPF1 or a non-targeting control (NS).

middle: D

first: J

last: Hogg


title: Intrahepatic Aggregates of CD8+ T cell and B Cells are Associated with the Antiviral Response to Toll-Like Receptor 7 Agonist GS-9620

city: Foster City

first: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

summary: RNA-Seq analysis of GS-9620 treated chronic hepatitis B chimpanzees

overall_design: HBV-infected chimpanzees were dosed orally 3 times per week for 4 weeks with 1 mg/kg GS-9620 (days 1-25) and then for 4 weeks with 2 mg/kg GS-9620 (days 31-57) with a 1 week rest between dosing cycles. GS-9620 was not administered to one animal (4x0139) on study days 43, 45 and 47 due to liver enzymes elevations after the first week of treatment at 2 mg/kg. Dosing of this animal resumed on day 50 and continued through end-of-study (day 57).

first: Vivian

last: Barry

first: Stephane

last: Daffis

first: Congrong

last: Niu

first: Erik

last: Huntzicker

first: Dorothy

middle: M

last: French

first: Robert

last: Landord

first: William

last: Delaney IV

first: Simon

middle: P

last: Fletcher


title: Transcriptomic analysis of human tonsillar TFH subsets

status: Public on Apr 03 2018

city: Cambridge

first: Vinay

middle: S

last: Mahajan

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

summary: We used an IL4-capture assay followed by FACS sorting, to isolate IL4-secreting TFH cells from a human tonsil and compared their transcriptomic profiles with CXCR5hi PD1hi IL4-negative tonsillar TFH cells and IL4-producing CXCR5neg non-TFH cells (TH2 cells). Our studies validate the notion of functionally distinct TFH subsets and identify genes that are specifically expressed in and define the human IL-4 secreting TFH cell  subset.

overall_design:
T follicular helper cell subset mRNA profiles from human tonsils were generated by deep sequencing. Naive CD4 T cells, IL4-producing nonTFH CD4 T cells (i.e. TH2), and IL4-producing TFH cells and PD1hi TFH cells were analyzed.

DOI: 10.26508/lsa.201800050

first: Hamid

last: Mattoo

first: Shiv

last: Pillai


title: miR-126-5p by direct targeting of JNK-interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence

city: Thuwal, Jeddah

first: Arnab

last: Pain

address: Building 2, Level 4

department: Biological and Environmental Sciences and Engineering

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Theileria annulata is an apicomplexan parasite that infects and transforms bovine macrophages that disseminate throughout the animal causing a leukaemia-like disease called tropical theileriosis. Using deep RNAseq of T. annulata-infected B cells and macrophages we identify a set of microRNAs induced by infection, whose expression diminishes upon loss of the hyper-disseminating phenotype of virulent transformed macrophages. We describe how infection-induced upregulation of miR-126-5p ablates JIP-2 expression to release cytosolic JNK to translocate to the nucleus and trans-activate AP-1-driven transcription of mmp9 to promote tumour dissemination. In non-disseminating attenuated macrophages miR-126-5p levels drop, JIP-2 levels increase, JNK1 is retained in the cytosol leading to decreased c-Jun phosphorylation and dampened AP-1-driven mmp9 transcription. We show that variation in miR-126-5p levels depends on the tyrosine phosphorylation status of AGO2 that is regulated by Grb2-recruitment of PTP1B. In attenuated macrophages Grb2 levels drop resulting in less PTP1B recruitment, greater AGO2 phosphorylation, less miR-126-5p associated with AGO2 and a consequent rise in JIP-2 levels. Changes in miR-126-5p levels therefore, underpin both the virulent hyper-dissemination and the attenuated dissemination of T. annulata-infected macrophages.

overall_design: miRNA profiles of Theileria infected and uninfected cells were generated in triplicate using Illumina HiSeq4000

first: Malak

last: Haidar

first: Zineb

last: Rchiad

first: Hifzur

last: Ansari

first: Fathia

last: Ben-Rached

first: Shahin

last: Tajeri

first: Perle

last: Latre De Late

first: Gordon

last: Langsley


title: Single-cell RNAseq analysis of the i8TF cell lines with/without exposure to dox

first: Christophe

last: Lancrin

summary: The aim of the experiment was to assess the cell heterogeneity after the doxycycline treatment and the subsequent induction of the 8 transcription factors.

overall_design: Cells were cultured in BL-CFC culture for 1 day before sorting for eVSM cells. Then, sorted eVSM were cultured in hemogenic endothelium medium for 24h with or without doxycycline. Cells from the two conditions were then mixed at a 1:1 ratio.

first: Tallulah

last: Andrews


title: RNA sequencing of WT and ERRαγAd-/- brown adipose tissue treated with CL316,243

first: Anastasia

last: Kralli

address: 725 N Wolfe Str

department: Physiology

institute: Johns Hopkins University

summary: Adrenergic stimulation of brown adipose tissue (BAT) activates thermogenesis, by uncoupling oxidative phosphorylation and enabling high rates of substrate oxidation. Moreover, adrenergic stimulation signals to the nucleus, inducing gene expression changes that increase BAT thermogenic and oxidative capacity. The purpose of this study was to determine the role of two orphan nuclear receptors, ERRα and ERRγ, in adipose tissue function in response to adrenergic stimulation. Here we identify ERRα and ERRγ as collectively critical effectors of the adrenergic induced transcriptional program in BAT. Mice lacking adipose ERRs (ERRαγAd-/-) have diminished oxidative and thermogenic capacity, and become rapidly hypothermic when exposed to cold. Notably, the ability of the β3-adrenergic agonist CL316,243 to expand BAT oxidative and thermogenic capacity, increase energy expenditure, promote weight loss, and improve glucose tolerance is lost in ERRαγAd-/-. At the transcriptional level, RNA sequencing experiments show that the bulk of the response of BAT to CL316,243 (>80% of CL316,243-induced genes) relies on ERRs. These findings establish ERRα and ERRγ as essential BAT regulators that act coordinately to relay adrenergic signals and expand the capacity for thermogenesis and energy expenditure.

overall_design: WT and ERRαγAd-/- male mice were treated witht the β3-adrenergic agonist CL316,243 (1 mg/kg) or equivalent volume of PBS for 10 days. Mice were euthanized 24 hours after the last CL316,243 dose for BAT tissue collection. Total RNA was isolated from BAT and 3 samples from each condition were submitted for RNA sequencing (WT PBS, WT CL316,243, ERRαγAd-/- PBS, and ERRαγAd-/- CL316,243).

first: Erin

last: Brown

first: Bethany

middle: C

last: Hazen

first: Elodie

last: Eury

first: Jean-Sébastien

last: Wattez

first: Marin

last: Gantner

first: Verena

last: Albert

first: Sarah

last: Chau

first: Manuel

last: Sanchez-Alavez

first: Bruno

last: Conti