title: RNA sequencing of small number germ cells including primordial germ cells (PGCs) collected from female embryonic 12.5 day (E12.5), Female germline stem cells (FGSCs), Germinal-stage oocytes (GV oocytes) and Meiosis II oocytes (MII oocytes)

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

summary: Mammalian oogenesis is an intricate and coordinated process involving dramatic changes in the transcriptional architecture. Through the small number of cells RNA sequencing (RNA Seq), we comprehensively uncovered the transcriptome dynamics of the mouse PGCs, FGSCs, GV Oocytes and M II Oocytes using. These results would provide some valuable navigation for the mechanism research of mammalian FGSCs in the future.

overall_design: Examination of RNA level in E12.5 PGCs, FGSCs, GV oocytes and MII oocytes

first: Binbin

last: Ma


title: Expression profiling of etoposide-induced senescent cells

status: Public on Aug 14 2017

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: We report here the RNA-seq data of proliferating IMR90 cells and etoposide-induced senescent cells with control or cGAS knockdown

overall_design: RNA-seq in primary IMR90 cells, two independent biological replicates, sequenced in Illumina NextSeq 500 platform.

first: Zhixun

last: Dou

first: Kanad

last: Ghosh

first: Payel

last: Sen

first: Shelley

middle: L

last: Berger


title: mRNA sequencing  of WT and cyc17∆ cells in conjugation 4, 5, 6 and 7 (C4, C5, C6 anc C7) hours of Tetrahymena thermophila

status: Public on Aug 15 2017

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

summary: The goals of this study is to investigate the function of Cyc17 of Tetrahymena thermophila.

overall_design: Compare the expression of genes amnong WT and CYC17KO cells in C4, C5, C6 anc C7.


title: mRNA sequencing  of WT and e2fl-1∆ cells in conjugation 2, 3, 4, 5, 6 and 7 (C2, C3, C4, C5, C6 and C7) hours of Tetrahymena thermophila

summary: The goals of this study is to investigate the function of E2fl-1 of Tetrahymena thermophila.

overall_design: Compare the expression of genes amnong WT and e2fl-1∆ cells in C2, C3, C4, C5, C6 and C7.


title: rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline [RNA-seq]

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

summary: Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements. It was previously thought that mammals possess four DNA methyltransferase paralogs—Dnmt1, Dnmt3a, Dnmt3b and Dnmt3l—that establish and maintain cytosine-5 methylation. Here we identify a fifth paralog, Dnmt3c, that is essential for retrotransposon methylation and repression in the mouse male germline. From a phenotype-based forward genetics screen, we isolated a mutant mouse called ‘rahu’, which displays severe defects in double-strand-break repair and homologous chromosome synapsis during male meiosis, resulting in sterility. rahu is an allele of a transcription unit (Gm14490, renamed Dnmt3c) that was previously mis-annotated as a Dnmt3-family pseudogene. Dnmt3c encodes a cytosine methyltransferase homolog, and Dnmt3crahu mutants harbor a non-synonymous mutation of a conserved residue within one of its cytosine methyltransferase motifs, similar to a mutation in human DNMT3B observed in patients with immunodeficiency, centromeric instability and facial anomalies syndrome. The rahu mutation lies at a potential dimerization interface and near the potential DNA binding interface, suggesting that it compromises protein-protein and/or protein-DNA interactions required for normal DNMT3C function in vivo. Dnmt3crahu mutant males fail to establish normal methylation within LINE and LTR retrotransposon sequences in the germline and accumulate higher levels of transposon-derived transcripts and proteins, particularly from distinct L1 and ERVK retrotransposon families. Phylogenetic analysis indicates that Dnmt3c arose during rodent evolution by tandem duplication of Dnmt3b, after the divergence of the Dipodoidea and Muroidea superfamilies. These findings provide insight into the evolutionary dynamics and functional specialization of the transposon suppression machinery critical for mammalian sexual reproduction and epigenetic regulation.

overall_design: Six samples total: Dnmt3crahu/+ (three biological replicates) and Dnmt3crahu/rahu (three biological replicates) mice aged 14 days post partum

first: Devanshi

last: Jain

first: Julian

last: Lange

first: Corentin

middle: C

last: Bouuaert

first: Christopher

middle: E

last: Mason

first: Kathryn

middle: V

last: Anderson

first: Scott

last: Keeney


title: RNA-seq transcriptomic profiling for self-renewing (SR) and senescent (SEN) human adult adipose derived mesenchymal stem cells (hADSCs)

city: San Francisco

first: Victoria

last: Lunyak

state: CA

address: 665 Third Street Suite 280

institute: Aelan Cell Technologies

summary: Characterization of gene expression levels with RNA-seq was performed on self-renewing (SR) and senescent (SEN) human adult adipose derived mesenchymal stem cells (hADSCs) using the Roche 454 pyrosequencing platform.

overall_design: RNA-seq library from single replicates of self-renewing (SR) and senescent (SEN) human adult adipose derived mesenchymal stem cells (hADSCs) were sequeced using the Roche 454 pyrosequencing platform.

first: Lu

last: Wang


title: Gene expression profiling of CD45+CD3-CD11b+MHCII+ subsets in P5 (day 5 after birth) and 1.5M (1.5 months after birth) mouse epidermal cells

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dymanics Research

country: Japan

institute: RIKEN

summary: The primary Langerhans cells (LCs) network in the mouse skin epidermis is established within a week after birth by differentiation of skin-seeded embryonic LC precursors into mature LCs. Through binding to distinct receptors, two members of the TGFβ superfamily, BMP7 and TGFβ1, initiate cellular signaling essential for inducing LCs differentiation and for preserving LCs in a quiescent state, respectively. However, how these two processes are regulated remains elusive. Here we show that loss of Cbfβ2, one of two RNA splice variants of the Cbfb gene, results in long-term persistence of embryonic-derived immature LCs after their developmental arrest at the transition into the EpCAM+ stage. This phenotype is caused by selective loss of TGFβ receptor signaling, essential for LCs differentiation with intact signaling, which maintains the quiescent state. Interestingly, skin residential Cbfβ2-defcient LC precursors could differentiate further upon transgenic Cbfβ2 expression, but only around postnatal period and not when it was expressed in one month old mice. Loss of developmental potency in the precursor cells was accompanied by diminished BMP7-BMPR1A signaling. Collectively, our results reveal an essential and selective requirement for the Cbfβ2 variant in LC differentiation, and provide a novel insight into how establishment and homeostasis of the LCs network is regulated.

overall_design: Examination of wild type and Cbfβ2 knock out at P5 (day 5 after birth) and 1.5M (1.5 months after birth).

first: Mari

last: Tenno

first: Ichiro

last: Taniuchi


title: mRNA sequencing  of WT and cdk3∆ cells in conjugation 1, 2 and 3 (C1, C2 and C3) hours of Tetrahymena thermophila.

summary: The goals of this study is to investigate the function of Cdk3 of Tetrahymena thermophila.

overall_design: Compare the expression of genes amnong WT and cdk3∆ cells in C1, C2 and C3.


title: RNAseq data for Arabidopsis TF mutants during germination

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary: RNAseq profiling of eight transcription factor mutants during germination in Arabidopsis, at 24 h in the light (after 48h of stratification).

overall_design: Total RNA was extracted from 50-100 mg Arabidopsis seeds in duplicates.

first: Reena

last: Narsai


title: VapCs of Mycobacterium tuberculosis Cleave RNAs Essential for Translation

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

summary: The major human pathogen Mycobacterium tuberculosis can survive in the host organism for decades without causing symptoms. A large cohort of Toxin-Antitoxin (TA) modules contribute to this persistence. Of these, 48 TA modules belong to the vapBC (virulence associated protein) gene family. VapC toxins are PIN domain endonucleases that, in Enterobacteria, inhibit translation by site-specific cleavage of initiator tRNA. In contrast, VapC20 of M. tuberculosis inhibits translation by site-specific cleavage of the universally conserved Sarcin-Ricin loop (SRL) in 23S rRNA. Here we identify cleavage targets for 12 VapCs from M. tuberculosis by applying UV-crosslinking and deep sequencing. Remarkably, these VapCs are all endoribo-nucleases that cleave RNA targets that are essential for decoding at the ribosomal A-site. Eleven VapCs cleave specific tRNAs while one exhibits SRL cleavage activity. These findings suggest that multiple vapBC modules contribute to the survival of M. tuberculosis in its human host by reducing the level of translation.

overall_design: Six VapC toxins were tagged with the dual affinity tag His-TEV-FLAG tag and expresed in Mycobacterium smegmatis. VapC-HTF expression was induced at OD600 0.3-0.4 for 20min and irradiated with 1800mJ of UV-C for 100seconds. Cells harvested and washed with ice cold PBS before snap freezing in liquid nitrogen. RNA-VapC complexes wer purified over M2-anti-FLAG resin and Ni-NTA resin. Sequencing libraries were prepared from purified complexes essentailly as per Tree et al. Mol Cell 2014. Amplified  libraries were sequenced on an Illumina MiSeq instrument.

first: K

last: Winther

first: J

first: D

last: Tollervey

last: Gerdes


title: Combining chemical and genetic approaches to increase drought resistance in plants

first: Huang

last: Huan

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress  Biology

institute: Chinese Academy of Sciences

summary: Using RNA-Seq to analyse the gene expression pattern induced by ABA and two artificial analogs in wild type (Col-0) Arabidopsis plants

overall_design: RNA-Seq:  3-week-old Col-0 plants, sprayed with DMSO (control) or 10μM ABA/AMF1beta/AMF4 and sampled 6,24 or 72hours after treatment.

first: Min-jie

last: Cao

first: Yu-lu

last: Zhang

first: Xue

last: Liu

first: Huan

last: Huang

first: Jian-Kang

last: Zhu


title: Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

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

sample_organism:
Escherichia coli ETEC H10407
Escherichia coli HS
Escherichia coli O127:H6 str. E2348/69
Escherichia coli 102651
Escherichia coli 102712
Escherichia coli 401140
Escherichia coli 402290

overall_design: Refer to individual Series


title: Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli 102712

summary: Global transcriptional analysis of EPEC/ETEC hybrid isolates.

overall_design: RNA sequencing was performed on seven E. coli during growth in laboratory media and conditions that have been previously demonstrated to induce expression of virulence genes.

first: Tracy

last: Hazen

first: Amol

last: Shetty

first: David

last: Rasko


title: Comparison of biofilm formation and motility processes in five arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite

status: Public on Aug 13 2017

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Bacteria of the genus Thiomonas are found ubiquitously in arsenic contaminated waters such as Acid Mine Drainage (AMD), where they contribute to the precipitation and the natural bioremediation of arsenic. In these environments, these bacteria have developed a large range of resistance strategies, such as biofilm formation, which is one of the most ubiquitous adaptive response observed in prokaryotes to various stresses, such as those induced in the presence of toxic compounds. This study focused on the process of biofilm formation in several Thiomonas strains isolated from the same AMD. The results obtained here show that these bacteria are all capable of forming biofilms, but the architecture and the kinetics of formation of these biofilms differ depending on whether arsenic is present in the environment and from one strain to another. Indeed, two strains favored biofilm formation, whereas three others favored motility in the presence of arsenic. In order to identify the underlying mechanisms, the patterns of expression of some genes possibly involved in the process of biofilm formation were investigated in Thiomonas sp. CB2 in the presence and absence of arsenite, using a transciptomic approach (RNAseq). The findings obtained here shed interesting light on how the formation of biofilms and the motility processes contribute to the adaptation of Thiomonas strains to extreme environments.

overall_design: Characterisation of  genes that may be involved in biofilm formation and regulation in response to As(III)

first: Julien

last: Farasin

first: Sandrine

last: Koechler

first: Hugo

last: Varet

last: Deschamps

first: Marie-Agnès

last: Dillies

first: Caroline

last: Proux

first: Mathieu

last: Erhardt

first: Aline

last: Huber

first: Bernd

last: Jagla

first: Romain

last: Briandet

first: Jean-Yves

last: Coppée

first: Florence

last: Arsène-Ploetze


title: SynapTRAP on SNAP25 TRAP Cortex

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: SynapTRAP. Identification of Synaptic mRNA of neurons of the cortex. Technique combines sucrose percoll fractionation of a synaptically rich sample (SN) and TRAP tagged ribosome IP (PreIP and PostIP). This experiment uses pan neuronal SNAP25 mice and a cortical dissection.

overall_design: Three replicates of four samples.

first: Rebecca

last: Ouwenga


title: Evolutionary Principles Predict 3D Chromatin Organization

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TADs, CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C. elegans and A. thaliana. Architectural proteins insulate compartmental domains by reducing interaction frequencies between neighboring regions in Drosophila, but CTCF loops do not play a distinct role in this organism. In mammals, compartmental domains exist alongside CTCF loop domains to form topological domains. The results suggest that compartmental domains are responsible for domain structure in all eukaryotes, with CTCF playing an important role in domain formation in mammals.

overall_design: ChIP-seq, HiChIP, and ChIAPET, ATAC-seq

first: Jordan

first: Michael

last: Nichols

first: Xiaowen

last: Lyu

first: Masami

last: Ando-Kuri

first: Sarahi

middle: M

last: Rivera

first: Karen

last: Hermetz

first: Ping

last: Wang

first: Yijun

last: Ruan

first: Victor

middle: G

last: Corces


title: Next Generation Sequencing Facilitates Quantitative Analysis of Tg(hsp70:dn-xBrg1) and wild-type sibling hearts Transcriptomes

city: Beijing

first: Jing-Wei

last: Xiong

address: Peking University, No.5 Yiheyuan Road Haidian District

institute: Institute of Molecular Medicine, Peking University

summary: The goal of this study is to compare the NGS-derived heart transcriptome profiling (RNA-seq) between Tg(hsp70:dn-xBrg1) and wild-type sibling injured hearts.

overall_design: Total heart mRNA profiles of Tg(hsp70:dn-xBrg1) and wild-type sibling hearts after heat-shock daily from 5 to 14 dpa were caried out by using Illumina HiSeq 2500

first: Yu

last: Hou

first: Fuchou

last: Tang

first: Jingwei

first: Chenglu

last: Xiao


title: NFIA Controls the Brown Fat Gene Program by Co-Localizing with PPARgamma at Cell-Type-Specific Enhancers (RNA)

city: Tokyo

first: Hironori

last: Waki

address: Hongo 7-3-1, Bunkyo-ku

institute: The University of Tokyo

summary: Brown fat dissipates energy as heat and protects against obesity. Here, we identified nuclear factor I-A (NFIA) as a novel transcriptional regulator of brown fat by a genome-wide open chromatin analysis of murine brown and white fat followed by motif analysis of brown-fat-specific open chromatin regions. NFIA and the adipogenic master regulator, PPARγ, co-localize at the brown-fat-specific enhancers. Moreover, the binding of NFIA precedes and facilitates the binding of PPARγ, leading to increased chromatin accessibility and active transcription. Introduction of NFIA into myoblasts results in brown adipocyte differentiation. Conversely, the brown fat of NFIA knockout mice displays impaired expression of the brown-fat-specific genes and reciprocal elevation of muscle genes. Finally, expression of NFIA and the brown-fat-specific genes is positively correlated in human brown fat. These results indicate that NFIA is a key transcriptional regulator of brown fat and exerts its effects by co-localizing with PPARγ at cell-type-specific enhancers.

overall_design: RNA-seq analysis of ctrl- or NFIA-expressing C2C12 myoblasts, BAT of wild type or NFIA-KO mouse neonates.

first: Yuta

last: Hiraike

first: Masahiro

last: Nakamura

first: Ken

last: Suzuki

first: Ryo

last: Nakaki

first: Shogo

last: Yamamoto

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Toshimasa

last: Yamauchi

first: Takashi

last: Kadowaki


title: Gene expression profiling of MEFs with and without Mitf induction compared to wild type MEF and primaryt melanocytes

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: We performed a global mRNA expression profiling via RNA-seq. Genes differentially expressed in Mitf knock-in MEFs compared to vehicle-treated knock-in MEFs were clustered and compared to expression in untreated wild-type MEFs and primary mouse melanocytes. This clustering demonstrates a gradual transition in the expression profile of Dox-treated Mitf knock-in MEFs toward the melanocyte expression profile

overall_design: Cells were grown in monolayer on 10cm plates. Mitf knock-in MEFs were treated with Dox for 6 days Mitf induction. RNA was extracted from Trizol pellets of wild type MEFs, Dox treated Mitf knock-in MEFs for 6 days, untreated Mitf knock-in MEFs and primary mouse melanocytes, and utilized for RNA-seq by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instruction.

first: Asaf

last: Zviran

first: Itay

last: Maza

first: Carmit

last: Levy

first: Jacob

last: Hanna


title: A Sall1-NuRD interaction regulates multipotent nephron progenitors and is required for loop of Henle formation

status: Public on Aug 12 2017

city: St. Louis

first: Michael

last: Rauchman

state: MO

address: 1100 S. Grand Ave.

department: Internal Medicine- Nephrology

institute: Saint Louis University

summary: RNA expression was measured by RNA-seq in E17 wild type and Sall1-∆SRM mutant kidney.

overall_design: RNA expression in mutant kidney was compared to wild type stage matched kidney.


title: UV-induced DNA lesion mapping reveals that carcinogen susceptibility is regulated by genome architecture and dictates cancer mutagenesis

city: Stanford

first: Ashby

last: Morrison

address: 371 Serra Mall

department: Biology

institute: Stanford University

summary: In this study, we present the first quantitative human genome-wide map of DNA lesions induced by ultraviolet (UV) radiation, the ubiquitous carcinogen in sunlight that causes skin cancer. Remarkably, the pattern of carcinogen susceptibility across the genome of primary cells significantly reflects mutation frequency in malignant melanoma. Surprisingly, DNase-accessible euchromatin is protected from UV, while lamina-associated heterochromatin at the nuclear periphery is vulnerable. Many cancer driver genes have an intrinsic increase in carcinogen susceptibility, including the BRAF oncogene that has the highest mutation frequency in melanoma. These findings provide a genome-wide snapshot of DNA injuries in cells at the earliest stage of carcinogenesis. Furthermore, they identify carcinogen susceptibility as a previously unrecognized origin of mutagenesis that is regulated by nuclear architecture and dictates genome instability in cancer.

overall_design: IP of DNA lesions, followed by in-vitro repair and next-generation sequencing

first: Pablo

last: García-Nieto

first: Erin

last: Schwartz

first: Rafael

last: Herrera

first: Devin

middle: A

last: King

middle: J


title: Differential effects of FTY720 on the B cell compartment in a mouse model of multiple sclerosis

status: Public on Aug 11 2017

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

country: Germany

institute: University of Wuerzburg

summary: Oral FTY720 treatment of mice with experimental autoimmune encephalomyelitis leads to B cell-specific effects of the drug, which comprise the induction of apoptosis and the modulation of B cell receptor signaling.

overall_design: Examination of the influence of FTY720 on B cell function.

first: Stefanie

last: Kuerten

first: Kathrin

last: Bail


title: Effect of lactation on conceptus-maternal interactions at the initiation of implantation in cattle: Effects on the conceptus transcriptome

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary: The hypothesis tested was that the uterine environment of lactating cows would affect conceptus gene expression. Approximately 65-75 days post-partum (dpp) the estrous cycles of non-lactating (dried off immediately post partum: n=12) and lactating (n=13) cows were synchronized and on Day 7 a high quality blastocyst derived from superovulated heifers was transferred. A control group of maiden heifers (n=8) were synchronized, inseminated to a standing heat and slaughtered on the same day as non-lactating and lactating recipients (Day 19; estrus=Day 0). The ipsilateral uterine horn was flushed with 10 ml PBS and the conceptus, when present, and uterine luminal fluid (ULF) snap frozen in liquid nitrogen prior to analysis. Gene expression analysis of the conceptus was performed by RNA sequencing analysis while amino acid (aa) composition of ULF was determined by High Performance Liquid Chromatography (HPLC). Eight differentially expressed genes (DEGs) were identified between conceptuses recovered from non-lactating cows versus heifers while 269 DEGs (100 up-regulated and 169 down-regulated) were identified between conceptuses recovered from lactating cows compared to heifers. The aa, alanine, glycine, serine and threonine, arginine, leucine and valine, were significantly lower in abundance in ULF recovered from heifers compared to both non-lactating or lactating cows. Glutamic acid, glutamine and lysine concentrations were lowest in heifers compared to both cow groups. This study demonstrates that exposure of a grade one embryo to a uterine environment that has been exposed to the metabolic stresses associated with lactation modifies the transcriptome of the conceptus and aa composition of the ULF.

overall_design: Comparison of differences in mRNA in bovine conceptuses recovered from the uterus of dry and lactating dairy cows on Day 19 following embryo transfer of blastocysts from maiden heifers on Day 7 along with Day 19 conceptuses recovered from maiden heifers following AI.

first: Niamh

last: Forde

first: Constantine

last: Simintiras

first: Roger

last: Sturmey

first: Alexander

last: Graf

first: Eckhard

last: Wolf

first: Helmut

last: Blum

first: Pat

last: Lonergan


title: Transcriptome sequencing identified RNAs associated with renal fibrosis in UUO rat model (urine)

first: Jiazeng

last: Sun

state: None Selected

address: National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

summary: Renal fibrosis as the final outcome of many renal diseases, has always been paid more attention to by the researchers. To better understand whether lncRNAs could be a player in this process or be a biomarker for renal fibrosis diagnosis, we compared transcriptome sequencing data on renal tissues and urine respectively between UUO and shamed (Sham) rat model. Numerous genes including lncRNAs with significant changes in their expression were identified. 24 lncRNAs were up-regulated and 79 lncRNAs were down-regulated in the renal tissues of the UUO rats. 625 lncRNAs were up-regulated and 177 lncRNAs were down-regulated in urines of the UUO rats. Among the lncRNAs upregulated in renal tissue of UUO rats, 19 lncRNAs were predicted containing several conserved Smad3 binding motifs in the promoter. Among them, lncRNAs with putative promoter containing more than 4 conserved Smad3 binding motifs were demonstrated to be induced by TGF-β significantly in NRK-52E cells. We further confirmed that lncRNA TCONS_00088786 and TCONS_01496394 were regulated by TGF-β stimulation and also can influence the expression of some fibrosis-related genes through a feedback loop. Based on transcriptome sequencing data, bioinformatics analysis and qRT-PCR detection, we also demonstrated lncRNA in Urine are detectable and might be a novel biomarker of renal fibrosis. These data provide new information about the involvement of lncRNAs in renal fibrosis, indicating that they may serve as candidate biomarkers or therapeutic targets in the future.

overall_design: Rats' urine RNA profiles of 14-day wild type (WT) and unilateral ureteral occlusion rat model type were generated by deep sequencing, using Illumina HI-seq 2000.

first: Shang

last: Zhang

first: Bianhua

last: Shi

first: Dexian

last: Zheng

first: Juan


title: Transcriptome sequencing identified RNAs associated with renal fibrosis in UUO rat model (kidney)

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

overall_design: Rat RNA profiles of 14-day wild type (WT) and UUO rat model type were generated by deep sequencing, in triplicate, using Illumina HI-seq 2500.


title: Increased dermal collagen bundle alignment in Systemic Sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs [ECMs]

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

summary: Systemic sclerosis (SSc) is a devastating disease affecting the skin and internal organs. Dermal fibrosis manifests early and Modified Rodnan Skin Scores (MRSS) correlate with disease progression. Transcriptomics of SSc skin biopsies suggest the role of the in vivo microenvironment in maintaining the pathological myofibroblasts. Therefore, defining the structural changes in dermal collagen in SSc patients could inform our understanding of fibrosis pathogenesis. Here, we report a method for quantitative whole-slide image analysis of dermal collagen from SSc patients, and our findings of more aligned dermal collagen bundles in diffuse cutaneous SSc (dcSSc) patients. Using the bleomycin-induced mouse model of SSc, we identified a distinct high dermal collagen bundle alignment gene signature, characterized by a concerted upregulation in cell migration, adhesion, and guidance pathways, and downregulation of spindle, replication, and cytokinesis pathways. Furthermore, increased bundle alignment induced a cell migration gene signature in fibroblasts in vitro, and these cells demonstrated increased directed migration on aligned ECM fibers that is dependent on expression of Arhgdib (Rho GDP-dissociation inhibitor 2).  Our results indicate that increased cell migration is a cellular response to the increased collagen bundle alignment featured in fibrotic skin. Moreover, many of the cell migration genes identified in our study are shared with human SSc skin and may be new targets for therapeutic intervention.

overall_design: This experiment is to perform RNASeq on human fibroblasts cultured on engineered extracellular matrices (ECMs) with patterned surfaces. Dermal fibroblasts were cultured for 48 hours, on collagen-adsorbed aligned nanofibers vs. randomly oriented nanofibers coated with type I collagen. Total RNA was extracted, and analyzed by RNASeq.

first: Lizhi

last: Cao

first: Linda

last: Burkly

first: Robert

last: Lafyatis


title: Plasma and B cells from mice treated with GSK-LSD1

city: New York

first: Steven

last: Lipkin

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary: We treated mice daily with the GSK-LSD1 or vehicle for 21 days. B and plasma cells were isolated by FACS and RNA-seq performed. Pathway analysis showed that MYC targets, Unfolded protein  response, TNFalpha signaling, STAT3, STAT5 and other signaling pathways were significantly altered.

overall_design: Examination of mouse B and plasma cells treated with GSK-LSD1 or control.

first: Nieves

last: Calvo-Vidal

first: Leandro

last: Cerchietti


title: Increased dermal collagen bundle alignment in Systemic Sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: α7 nicotinic acetylcholine receptor signaling modulates the inflammatory phenotype of fetal brain microglia: first evidence of interference by iron homeostasis.

city: Montreal

first: Martin

last: Frasch

state: QC

address: 3175, Côte-Sainte-Catherine

department: Dépt. obstétrique-gynécologie

country: Canada

institute: Université de Montréal

summary: We sequenced mRNA from 7 microglia extracted from sheep fetuses exposed to LPS, agonist and antagonist of  α7 nicotinic acetylcholine receptor to determine signaling pathway through modeling of α7 during inflammation.

overall_design: Examination of genetic expression in microglia after α7 nicotinic acetylcholine receptor modeling with agonistic and antagonistic drug.

first: Marina

last: Cortes

first: Mingju

first: Helen

last: Liu

first: CS

last: Moore

first: Lucien

last: Durosier

first: Patrick

last: Burns

first: Gilles

last: Fecteau

first: Andre

last: Desrochers

first: Luis

middle: B

last: Barreiro

first: Jack

middle: P

last: Antel


title: Single-cell transcriptomics of East-Asian pancreatic islets cells

city: Singapore

first: Rajkumar

last: Dorajoo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: Single-cell RNA-seq (scRNA-seq) of pancreatic islets have reported on α- and β-cell gene expression in mice and subjects of predominantly European ancestry. We aimed to assess these findings in East-Asian islet-cells. 448 islet-cells were captured from three East-Asian non-diabetic subjects for scRNA-seq. Hierarchical clustering using pancreatic cell lineage genes was used to assign cells into cell-types. Differentially expressed transcripts between α- and β-cells were detected using ANOVA and in silico replications of mouse and human islet cell genes were performed. We identified 118 α, 105 β, 6 δ endocrine cells and 47 exocrine cells. Besides INS and GCG, 26 genes showed differential expression between α- and β-cells. 10 genes showed concordant expression as reported in rodents, while FAM46A was significantly discordant. Comparing our East-Asian data with data from primarily European subjects, we replicated several genes implicated in nuclear receptor activations, acute phase response pathway, glutaryl-CoA/tryptophan degradations and EIF2/AMPK/mTOR signaling. Additionally, we identified protein ubiquitination to be associated among East-Asian β-cells. We report on East-Asian α- and β-cell gene signatures and substantiate several genes/pathways. We identify expression signatures in East-Asian β-cells that perhaps reflects increased susceptibility to cell-death and warrants future validations to fully appreciate their role in East-Asian diabetes pathogenesis.

overall_design: 448 islet-cells were captured from three East-Asian non-diabetic subjects for scRNA-seq. 223 islet-cells remained after samples QC, and these cells were used for subsequent analyses. Hierarchical clustering using pancreatic cell lineage genes was used to assign cells into cell-types. We identified 118 α and 105 β endocrine cells in our dataset.

first: Yusuf

last: Ali

first: Bernhard

middle: O

last: Boehm

first: Jianjun


title: Targeting neuronal activity-regulated neuroligin-3 dependency for high-grade glioma therapy

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

summary: Neuronal activity promotes high-grade glioma (HGG) growth. An important mechanism mediating this neural regulation of brain cancer is activity-dependent cleavage and secretion of the synaptic molecule and glioma mitogen neuroligin-3 (Nlgn3), but the therapeutic potential of targeting Nlgn3 in glioma remains to be defined. We demonstrate a striking dependence of HGG growth on microenvironmental Nlgn3 and determine a targetable mechanism of secretion. Patient-derived orthotopic xenografts of pediatric glioblastoma, diffuse intrinsic pontine glioma and adult glioblastoma fail to grow in Nlgn3 knockout mice. Glioma exposure to Nlgn3 results in numerous signaling consequences, including early focal adhesion kinase activation upstream of PI3K-mTOR. Nlgn3 is cleaved from both neurons and oligodendrocyte precursor cells via the ADAM10 sheddase. Administration of ADAM10 inhibitors robustly blocks HGG xenograft growth. This work defines the therapeutic potential of and a promising strategy for targeting Nlgn3 secretion in the glioma microenvironment, which could prove transformative for treatment of HGG.

overall_design: RNA-seq patient-derived pediatric GBM cell cultures in two replicates. Libraries were sequenced on Illumina NextSeq 500, 1x75.

first: Surya

last: Nagaraja


title: Transcriptome sequencing identified RNAs associated with renal fibrosis in UUO rat model

first: Jiazeng

last: Sun

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

overall_design: Refer to individual Series


title: A Novel Alzheimer's Disease Drug Candidate Targeting Inflammation and Fatty Acid Metabolism

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: CAD-31 has potent neuroprotective properties in six distinct nerve cell assays that mimic toxicities observed in the old brain. Pharmacological and preliminary toxicology studies show that CAD-31 is brain penetrant and likely safe. When fed to old, symptomatic transgenic Alzheimer's disease (AD) mice starting at ten months of age for three additional months in a therapeutic model of the disease, there was a reduction in the memory deficit and brain inflammation, and an increase in the expression of synaptic proteins. Small molecule metabolic data from the brain and plasma showed that the major effect of CAD-31 is centered on fatty acid metabolism and inflammation. Pathway analysis of gene expression data showed that CAD-31 had major effects on synapse formation, AD and energy metabolism.

overall_design: Cortical RNA from AD, wild type, and drug-treated mice was isolated and sequenced.

first: Daniel

last: Daugherty

first: Dave

last: Schubert


title: Role of STA-1 and SID-3 upon Orsay virus infection in C. elegans (RNA-Seq)

first: Eric

middle: Alexander

last: Miska

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Across metazoans, innate immunity is vital in defending organisms against viral infection. In mammals, antiviral innate immunity is orchestrated by interferon signaling, activating the STAT transcription factors downstream of the JAK kinases to induce expression of antiviral effector genes. In the nematode C. elegans, which lacks the interferon system, the major antiviral response so far described is RNA interference but whether additional gene expression responses are employed is not known. Here we show that, despite the absence of both interferon and JAK, the C. elegans STAT homologue STA-1 orchestrates antiviral immunity. Intriguingly, mutants lacking STA-1 show increased resistance to antiviral infection. Using gene expression analysis and chromatin immunoprecipitation we show that, in contrast to the mammalian pathway, STA-1 acts as a transcriptional repressor. Thus STA-1 might act to suppress a constitutive antiviral response in the absence of infection. Using a reverse genetic screen we identify the SID-3 as a kinase upstream of STA-1 in the response to infection. Together, our work identifies a novel STAT regulatory cascade controlling its activity in antiviral resistance, illustrating the complex evolutionary trajectory displayed by innate immune signaling pathways across metazoan organisms.

overall_design: In this study, 3 different strains of C. elegans were analysed. Each strain was analysed after infection by the Orsay virus or not. Each condition for each strain were performed in biological triplicate.

first: Mélanie

last: Tanguy

first: Peter

last: Sarkies


title: Genome-wide Identification and Characterization of Natural Antisense Transcripts by Strand-specific RNA Sequencing in Ganoderma lucidum

first: junjie

last: shao

state: --- Select a state ---

address: Rm 409, Ke-Yan-Lou, No. 151 Malianwa North Road, Haidian District, Beijing 100093, P.R.China

institute: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

type: Non-coding RNA profiling by high throughput sequencing

summary: We have identified and characterized the natural antisense transcripts using strand-specific (ss) RNA-seq technology.

overall_design: Identification and Characterization of natural antisense transcripts (NATs) from three development stages in G.lucidum.

first: Junjie

last: Shao

first: Haimei

last: Chen

first: Dan

last: Yang

first: Mei

last: Jiang

first: Hui

last: Zhang

first: Bin

last: Wu

first: Jianqin

last: Li

first: LiChai

last: Yuan

first: Chang

last: Liu


title: Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function [miRNA-seq]

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrück Center for Molecular Medicine

summary: Hundreds of circular RNAs (circRNAs) are highly abundant in the mammalian brain, often with conserved expression. Here we show that the circRNA Cdr1as is massively bound by the microRNAs (miRNAs) miR-7 and miR-671 in human and mouse brains. When the Cdr1as locus was removed from the mouse genome, knockout animals displayed impaired sensorimotor gating-a deficit in the ability to filter out unnecessary information-which is associated with neuropsychiatric disorders. Electrophysiological recordings revealed dysfunctional synaptic transmission. Expression of miR-7 and miR-671 was specifically and posttranscriptionally misregulated in all brain regions analyzed. Expression of immediate early genes such as Fos, a direct miR-7 target, was enhanced in Cdr1as-deficient brains, providing a possible molecular link to the behavioral phenotype. Our data indicate an in vivo loss-of-function circRNA phenotype and suggest that interactions between Cdr1as and miRNAs are important for normal brain function.

overall_design: We performed miRNA sequencing for three knockout and three wild type replicates in four brain regins - cerebellum, cortex, hippocampus (2 KO replicates) and olfactory bulb.

first: Monika

last: Piwecka

last: Glažar

first: Luis

last: Hernandez-Miranda

first: Sebastian

last: Memczak

first: Andrei

last: Filipchyk

first: Filippos

last: Klironomos

first: Ralf

last: Kühn

first: Christine

last: Kocks

first: Carmen

last: Birchmeier

first: Nikolaus

last: Rajewsky


title: RNA profiling Analysis of the Serum Exosomes Derived from Active and Latent M.tuberculosis infectious Patients

first: Fei

last: Chen

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics

summary: We performed RNA-seq analysis on exosomes derived from the clinical specimens of healthy control (HC), active tuberculosis (ATB) and latent tuberculosis infection (LTBI) individuals. Our results revealed the distinguished gene expression panels and patterns of the exosomes for the LTBI and ATB patients: We identified many up-regulated and down-regulated differentially expressed genes (DEGs) in the LTBI and ATB samples, and further screened the top-20 DEGs, which might provide a clue to differentiate HC, LTBI and ATB;  We classified all the DEGs into six expression patterns, screened the top-20 genes in each pattern, and mainly focused on those highly expressed in LTBI and ATB; A lot of Mtb genes were only expressed and enriched in the exosomes of LTBI patients; Pathway and functional analysis further indicated the gradually increased deteriorated healthy signals in LTBI and ATB samples, including down-regulated signaling pathways/immune response, and up-regulated apoptosis/necrosis. Our findings not only add new data to tuberculosis clinical studies, but also facilitate the development of potential targets for the diagnosis, prevention and treatment of tuberculosis.

overall_design: Examined three samples and each has two repeats


title: Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function [RNA-seq]

overall_design: We performed polyA-selected RNA sequencing for three knockout and three wild type replicates in four brain regins - cerebellum, cortex, hippocampus and olfactory bulb.


title: An integrative analysis of different histone acetylation in ethylene response in Arabidopsis

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

summary: We reported that ethylene specifically elevated acetylation of histone H3 at K14 and the non-canonical acetylation of histone H3 at K23,but not H3K9ac.Thus, we further performed Chip-sequencing of H3K9Ac, using chromatins isolated from 3-day old etiolated ein2-5 seedlings treated with ethylene or air gas.

overall_design: Examination of 1 histone modification (H3K9Ac) in 1 Arabidopsis line which under 2 different treatment.

first: Fan

last: Zhang

first: Likai

last: Wang


title: Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein

city: HOUSTON

first: Jianzhong

last: Su

address: 1 Baylor Plaza

institute: Baylor college of Medicine

type: Methylation profiling by high throughput sequencing


title: Role of STA-1 and SID-3 upon Orsay virus infection in C. elegans (ChIP-Seq)

first: Eric

last: Miska

overall_design: In this experiment, the DNA binding capacity of a GFP::STA-1 fusion protein was assessed by chip-sequencing with GFP immunoprecipitation followed by DNA sequencing.

first: Mélanie

last: Tanguy

first: Peter

last: Sarkies


title: Differential gene expression of WT vs THAP1 KO and a THAP1 C54Y mutation in mouse ES cells

first: Rajal

last: Sharma

state: NY

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

summary: We report the differences in mRNA profiles of WT mouse cells in comparison to both THAP1 -/- cells and cells in which a disease causing C54Y mutation was introduced.

overall_design: RNA was extracted from wild type, THAP1 KO, and THAP1 C54Y mouse ES cells derived from C57Bl/6 blastocysts, followed by library preparation and sequencing on the illumina platform.

first: Michelle

last: Ehrlich


title: Increased dermal collagen bundle alignment in Systemic Sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs [bleomycin]

first: Suzanne

last: Szak

overall_design: For bleomycin experiments, 8 week old C57Bl/6 female mice were used.The bleomycin model was established with daily subcutaneous injections of bleomycin (100uL at 1U/mL) into the back skin. Experimental timepoints include: saline, 2 weeks bleo, 4 weeks bleo, 6 weeks recovery, and 10 weeks recovery.

first: Lizhi

last: Cao

first: Linda

last: Burkly

first: Robert

last: Lafyatis


title: cFos-Sox9 Axis Reprograms Bone Marrow-derived Mesenchymal Stem Cells into Chondroblastic Osteosarcoma [RNA-seq]

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

summary: The goal is to profile cFos binding sites in an p53 knockout mouse bone marrow-derived stem cells (mBMSCs).

overall_design: Four single clones (clone2, 4, 8, 12) of p53 knockout (p53KO) mouse bone marrow-derived mesenchymal stem cells were transduced with retroviruses expressing either luciferase (Luc) or cFos cDNAs. RNA was extracted from cells and subject to RNAseq.


title: Role of STA-1 and SID-3 upon Orsay virus infection in C. elegans


title: cFos-Sox9 Axis Reprograms Bone Marrow-derived Mesenchymal Stem Cells into Chondroblastic Osteosarcoma [ChIP-seq]

overall_design: Fifty million of p53 knockout (p53KO) mBMSCs expressing cFos were fixed and subjected to ChIP-seq assay using 10 ug anti-cFos antibody (Santa Cruz, Cat:sc-253).


title: Binding to SMN2 pre-mRNA-Protein complex elicits specificity for small molecule splicing modifiers

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

summary: Small molecule splicing modifiers have been extensively described which target the generic splicing machinery and thus have low target specificity. We have identified potent splicing modifiers with unprecedented high selectively, correcting the splicing deficit of the SMN2 (survival motor neuron 2) gene in Spinal Muscular Atrophy (SMA). Here we show that they directly bind to two sites of the SMN2 pre-mRNA, thereby stabilizing a novel ribonucleoprotein (RNP) complex in the SMN2 gene that is critical for the high target specificity of these small molecules over other genes. In addition to the therapeutic potential of these molecules for treatment of SMA, our work may have wide-ranging consequences for further research to identify small molecules that target splicing correction of specific genes by interacting with tertiary RNA structures.

overall_design: mRNA profiling of type I SMA fibroblasts treated with NVS-SM1

first: Manaswini

last: Sivaramakrishnan

first: Kathleen

last: McCarthy

first: Sylwia

last: Huber

first: Sebastièn

last: Campagne

first: Sonja

last: Meier

first: Angélique

last: Augustin

first: Tobias

last: Heckel

first: Hélène

last: Meistermann

first: Melanie

last: Hug

first: Pascale

last: Birrer

first: Ahmed

last: Moursy

first: Sarah

last: Khawaja

first: Nicolas

last: Giroud

first: Sabrina

last: Golling

first: Manuel

last: Tzouros

first: Balazs

last: Banfai

first: Gonzalo

last: Duran-Pacheco

first: Jens

last: Lamerz

first: Ying

last: Hsiu Liu

first: Thomas

last: Luebbers

first: Hasane

last: Ratni

first: Antoine

last: Clery

first: Martin

last: Ebeling

first: Sergey

last: Paushkin

first: Adrian

middle: R

last: Krainer

first: Frédéric

last: Allain

first: Friedrich

last: Metzger

first: Nikolaos

last: Berntenis


title: Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein (RRBS)

first: Jianzhong

last: Su

summary: Comprehensive studies have shown that DNA methylation plays vital roles in both loss of pluripotency and governance of the transcriptome during embryogenesis and subsequent developmental processes. Aberrant DNA methylation patterns have been widely observed in tumorigenesis, aging, and neurodegenerative diseases, highlighting the importance of a systematic understanding of DNA methylation and the dynamic changes of methylomes during disease onset and progression. Here we describe a facile and convenient approach for efficient targeted DNA methylation by fusing inactive Cas9 (dCas9) with an engineered prokaryotic DNA methyltransferase MQ1. Our study presents a lentivirus-free strategy to achieve locus-specific cytosine modifications in the genome within 24 hours. Finally, we demonstrated our tool can induce targeted CpG methylation in mice by zygote microinjection, thereby facilitating the dissection of the functional relevance of specific CpG methylation marks at endogenous loci.

overall_design: I)  ChIP-seq of plasmid electroporated K562 cells using Illumina Nextseq sequencing system. II) Reduced representation bisulfited sequencing (RRBS) of plasmid transfected HEK 293T cells using Illumina Hiseq2000 sequencing system. III) PCR amplicon deep sequencing of HEK 293T cells, K562 cells or mice tissue using Illumina Nextseq sequencing system.

first: Yong

last: Lei


title: MED12cKO heart ventricles from male mice [RNA-seq]

city: Dallas

first: Kedryn

middle: K

last: Baskin

state: TX

address: 6000 Harry Hines

department: Molecular Biology

institute: UT Southwestern

summary: The Mediator complex regulates gene transcription by linking basal transcriptional machinery with DNA-bound transcription factors. The activity of the Mediator complex is mainly controlled by a kinase submodule that is comprised of four proteins, including MED12. Although ubiquitously expressed, Mediator subunits can differentially regulate gene expression in a tissue-specific manner. Here, we report that MED12 is required for normal cardiac function such that mice with conditional cardiac-specific deletion of MED12 display progressive dilated cardiomyopathy. Loss of MED12 perturbs expression of calcium handling genes in the heart, consequently altering calcium cycling in cardiomyocytes and disrupting cardiac electrical activity. We identified transcription factors that regulate expression of calcium-handling genes that are downregulated in the heart in the absence of MED12, and found that MED12 localizes to transcription factor consensus sequences within calcium handling genes. We showed that MED12 interacts with one such transcription factor, MEF2, in cardiomyocytes, and that MED12 and MEF2 co-occupy promoters of calcium handling genes. Furthermore, we demonstrated that MED12 enhances MEF2 transcriptional activity and overexpression of both increases expression of calcium handling genes in cardiomyocytes. Our data support a role for MED12 as a coordinator of transcription through MEF2 and other transcription factors. We conclude that MED12 is a regulator of a network of calcium handling genes, consequently “mediating” contractility in the mammalian heart.

overall_design: Ventricle mRNA profiles of 1-day old control (CTL, CreNEG) and cardiac-specific Med12 knockout mice (Med12cKO, CrePOS) were generated by deep sequencing, in triplicate, using Illumina.

first: Beibei

last: Chen

first: Eric

middle: N

last: Olson


title: Expression data from Enterovirus 71 and Coxsackievirus A16 infected SK-N-SH cells

city: wilayah persekutuan

first: THINESSHWARY

last: YOGARAJAH

address: kuala lumpur

department: PATHOLOGY

country: Malaysia

institute: university of malaya

summary:
Both viruses differently express genes at 48 and 72 hours involving cell cycle, cellular damage and inflammatory response
We used microarrays to detail the total gene expression underlying two virus infection in neuronal cells and identified distinct classes of up-regulated genes during this process at specific time.

overall_design: Enterovirus 71 and Coxsackievirus A16 infected SK-N-SH cells at 48 hours and 72 hours were selected for RNA extraction and hybridization on Affymetrix microarrays, respectively. We sought to obtain high number of infected cell populations of SK-N-SH cells at each time point in order to increase the temporal resolution of expression profiles. To that end, we ensured using flow cytometry data for confirmation of more than 60% of SK-N-SH cells are infected by the viruses.

first: Thinesshwary

last: Yogarajah


title: Discovery of first-in-class reversible dual small molecule inhibitors against G9a and DNMTs with in vivo activity in hematological malignancies

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

overall_design: Refer to individual Series


title: RNA-Seq of subcutaneous inguinal white fat of Hlx transgenic mice and littermate controls.

city: Worcester

first: Yongxu

last: Wang

address: 364 Plantation Street

department: Program in Gene Function and Expression

institute: UMass Medical School

first: Lei

last: Huang

first: Dongning

last: Pan

first: Jianhong

last: Ou

first: Yong-Xu


title: Discovery of first-in-class reversible dual small molecule inhibitors against G9a and DNMTs with in vivo activity in hematological malignancies [RNA-Seq]

summary: The indisputable role of epigenetics in cancer and the fact that epigenetic alterations can be reversed have favored development of epigenetic drugs. In this study, we have designed and synthesized potent novel, selective and reversible chemical probes that simultaneously inhibit the G9a and DNMTs methyltransferase activity. In vitro treatment of hematological neoplasia (Acute Myeloid Leukemia-AML, Acute Lymphoblastic Leukemia-ALL and Diffuse Large B-cell Lymphoma-DLBCL) with the lead compound CM-272, inhibited cell proliferation and promoted apoptosis, inducing interferon stimulated genes and immunogenic cell death. CM-272 significantly prolonged survival of AML, ALL and DLBCL xenogeneic models. Our results represent the discovery of first-in-class dual inhibitors of G9a/DNMTs and establish this chemical series, as a promising therapeutic tool for unmet needs in hematological tumors.

overall_design: Transcriptome analysis of ALL and DLBCL cell lines before and after treatment with a dual inhibitor against G9a and DNMTs.

first: Edurne

last: San José-Eneriz

first: Felipe

last: Prósper

first: Victor

last: Segura


title: The Nucleoid Protein Dps Binds Genomic DNA of Escherichia coli in a Non-random Manner

status: Public on Aug 10 2017

city: Pushchino

first: Olga

last: Ozoline

state: Moscow Region

address: Institutskaya

department: Functional Genomics and Cellular Stress

country: Russia

institute: Institute of Cell Biophysics of Russian Academy of Sciences

summary: Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. Ferroxidase activity of Dps is rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. Using the ChIP-seq data presented here, we found a non-random distribution of Dps binding sites in the bacterial chromosome of exponentially growing cells and showed their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. The transcription activity of several Dps-targeted genes evaluated by qRT-PCR, showed dependence on the presence of Dps. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA or, vice versa, competing with inhibitors to activate transcription.

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

overall_design: ChIP-Seq for Dps from Escherichia coli K12 MG1655

first: Sergey

middle: S

last: Antipov

first: Maria

last: Tutukina

first: Elena

last: Preobrazhenskaya

first: Fedor

last: Kondrashov

first: Maxim

last: Patrushev

first: Stepan

last: Toshchakov

first: Irina

last: Dominova

first: Uliana

last: Shvyreva

first: Veronika

last: Vrublevskaya

first: Oleg

last: Morenkov

first: Natalia

last: Sukharicheva

first: Valeriy

last: Panyukov


title: ChIP-seq data of RedN-venus from asynchronous and swarmer populations of Caulobacter crescentus NA1000

city: West Haven

first: Christine

last: Jacobs-Wagner

state: CT

address: 840 West Campus Drive, PO BOX 27388

department: Molecular, Cellular and Developmental Biology

institute: Yale University

summary: Goal: We have discovered and charactherized a new Nucleoid Associated Protein in Caulobacter crescentus, that we named RedN. To determine its global binding on C.crescentus chromosome we have performed a ChIP-seq using a strain with a RedN-Venus fusion expressed at gene loci and as single copy on the chromosome.

overall_design: We analyzed 2 replicates for the asynchronous population and 1 replicate for the swarmer population after synchrony of RedN-venus expressed in wild type samples (Caulobacter crescentus NA1000). We also performed 1 replicate using Venus protein expressed at xylose locus as control for non-specific binding at regions of high expression, this sample was named Mock. The total DNA before Immunoprecipitation was also extracted and sequenced and used as the control for peak detection for every biological sample, this samples were called Input.

first: Rodrigo

last: Arias-Cartin

first: Genevieve

last: Dobihal

first: Sameet

last: Mehta


title: Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein (ChIP-Seq)

first: Jianzhong

last: Su

overall_design: I)  ChIP-seq of plasmid electroporated K562 cells using Illumina Nextseq 500 sequencing system. II) Reduced representation bisulfited sequencing (RRBS) of plasmid transfected HEK 293T cells using Illumina Hiseq2000 sequencing system. III) PCR amplicon deep sequencing of HEK 293T cells, K562 cells or mice tissue using Illumina Nextseq sequencing system.

first: Yong

last: Lei


title: IL-22 inhibits allergic airway inflammation in house dust mite-induced asthma models

city: Chiba

first: Takashi

last: Ito

state: Chiba

address: Inohana

institute: Chiba university

summary: While the pathogenesis of asthma is mainly orchestrated by antigen-specific Th2 cells and their cytokines, recent findings indicate the involvement of other subsets of helper T cells including Th17 cells. Previous studies have shown that IL-22, one of Th17 cell-related cytokines, plays multiple roles in regulating allergic airway inflammation; however, the mechanism underlying the Il-22-mediated regulation remains unclear. Here, we show that allergic airway inflammation upon intratracheal administration of house dust mite extract (HDM), a representative allergen, were exacerbated in IL-22-deficient mice.  To address the molecular mechanisms by which IL-22 inhibits the development of HDM-induced allergic airway inflammation, we next performed an unbiased comprehensive screening of genes induced by IL-22 administration in the lung by RNA-seq analysis.

overall_design: Lung total RNA profiles of wild type (WT) and IL-22 knock out mice were generated by deep sequencing, using Illumina Hiseq.

first: Koichi

last: Hirose

first: Hiroshi

last: Nakajima


title: Distinct cellular mechanisms underlie anti-CTLA-4 and anti-PD-1 checkpoint blockade [RNA-seq]

city: Houston

first: Spencer

last: Wei

address: 7455 Fannin St.

department: Immunology

institute: MD Anderson Cancer Center

summary: Immune checkpoint blockade is able to achieve durable responses in a subset of patients, however we lack a satisfying comprehension of the underlying mechanisms of anti-CTLA-4 and anti-PD-1 induced tumor rejection. To address these issues we utilized mass cytometry to comprehensively profile the effects of checkpoint blockade on tumor immune infiltrates in human melanoma and murine tumor models. These analyses reveal a spectrum of tumor infiltrating T cell populations that are highly similar between tumor models and indicate that checkpoint blockade targets only specific subsets of tumor infiltrating T cell populations. Anti-PD-1 predominantly induces the expansion of specific tumor infiltrating exhausted-like CD8 T cell subsets. In contrast, anti-CTLA-4 induces the expansion of an ICOS+ Th1-like CD4 effector population in addition to engaging specific subsets of exhausted-like CD8 T cells. Thus, our findings indicate that anti-CTLA-4 and anti-PD-1 checkpoint blockade induced immune responses are driven by distinct cellular mechanisms.

overall_design: RNA profiles of a subset of tumor infiltrating T cell populations in anti-PD-1, anti-CTLA-r and control mice were generated by RNA sequencing, using Illumina HiSeq 4000. Mouse mutation background was assessed by whole exome sequencing data

middle: C

first: Jacob

middle: H

last: Levine

first: Alexandria

last: Cogdill

first: Yang

last: Zhao

first: Nana-Ama

last: Anang

first: Miles

last: Andrews

first: Padmanee

last: Sharma

first: Jing

last: Wang

first: Jennifer

last: Wargo

first: Dana

last: Pe’er

first: James

last: Allison


title: Vammin induces a highly efficient angiogenic response through VEGFR-2/NRP-1 and bypasses the regulatory function of VEGFR-1

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

summary:
Rationale: VEGF family members mediate their effects through cell surface receptors VEGFR-1, VEGFR-2 and NRP. Specific ligands were used to stimulate specific combinations of the receptors to evaluate ligand and receptor properties.
Objective: The properties of a novel VEGF family member Vammin were studied in level of receptor binding, gene expression in HUVECs by RNAseq and in vivo using adenoviral gene trasfers.
Methods: HUVECs were trasduced using adenoviral vectors encoding VEGF-A109, VEGF-A165 and Vammin and with an empty vector as a control. Gene expression was measured using RNA sequencing. Adenoviral intramuscular gene transfers were performed into rabbit hindlimbs. Confocal and multiphoton microscopy were used for blood vessel imaging.
Results and conclusions: Vammin is a highly effective VEGFR2 ligand that induces differential gene expression of genes related to proliferation, survival, angiogenesis and blood vessel development in HUVECs. The effect is stronger than ones induced by VEGF-A165 and VEGF-A109.  Vammin induces highly efficient angiogenic responses when delivered into rabbit skeletal muscles using adenoviral gene transfers.

overall_design: HUVEC mRNA profiles after adenoviral vector gene transfers in duplicate.

first: Pyry

middle: I

last: Toivanen

first: Tiina

last: Nieminen

first: Johanna

last: Laakkonen

first: Tommi

last: Heikura

first: Seppo

last: Ylä-Herttuala


title: cFos-Sox9 Axis Reprograms Bone Marrow-derived Mesenchymal Stem Cells into Chondroblastic Osteosarcoma

last: Huang

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


title: Comparison of transcriptionnal changes in Petunia hybrida WT and ram1-2 induced by mycorrhiza

city: Castanet-Tolosan

first: Christophe

last: Roux

address: Chemin de Borde Rouge

institute: University of Toulouse/CNRS

summary:
Aim: compare the transcriptionnal responses induced by mycorrhiza in wild type and GRAS transcription factor RAM1 mutant ram1-2 in roots.
Results: 650 genes were upregulated in mycorrhized WT (fold change >5; FDR<0,05, experiment difference>10) and 201 in the ram1 mutant. 182 genes were induced in both WT and ram1. 468 and 19 genes were induced only in WT or ram1-2 respectively. 91 genes were downregulated in mycorrhized WT (fold change <5; FDR<0,05, experiment difference>10) and 51 in ram1-2. There was no overlap in the downregulated genes.
Conclusion: The transcriptionnal response to mycorrhiza is more important in WT than in ram1-2. Gene induction in ram1 mostly overlap with wild type. Our results confirm that ram1 plays a central role in the root response  to mycorrhization.

overall_design: mRNA profile comparition of control (NM) and mycorrhized (M) roots in wild type (WT) and ram1-2 Petunia, generated by deep sequencing, in triplicate, using Illumina.

first: Mélanie

last: Rich

first: Pierre-Emmanuel

last: Courty

first: Didier

last: Reinhardt


title: Microsatellite expansion RNA visualization, elimination, and reversal of molecular pathology by RNA-targeting Cas9

city: La Jolla

first: Ranjan

last: Batra

state: California

address: 2880 Torrey Pines Scenic Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: In this Study, we used RNA-targeting Cas9 (RCas9) to reverse characteristic Myotonic Dystrophy (DM1) cellular phenotypes such as elimination of RNA foci, MBNL relocalization, and reversal of transcriptome-wide splicing.

overall_design: We performed RNA-seq for control and myotonic dystrophy (DM1) myoblasts and myotubes with various treatments including lentivirus mediated expression of either non-targeting (NT) or CTG-targeting (CTG) single guide RNA (sgRNA) and PIN-dCas9.Lentivirus mediated GFP expression was used as control.

first: Gene

last: Yeo


title: A sequence-specific core promoter binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes

city: University Park

first: David

last: Gilmour

state: Pennsylvania

address: 465 North Frear

institute: Penn State University

summary: Ribosomal protein (RP) genes must be coordinately expressed for proper assembly of the ribosome yet the mechanisms that control expression of RP genes in metazoans are poorly understood. Recently, TATA-Binding Protein-related factor 2 (TRF2) rather than the TATA-Binding Protein (TBP) was found to function in transcription of RP genes in Drosophila. Unlike TBP, TRF2 lacks sequence-specific DNA binding activity, so the mechanism by which TRF2 is recruited to promoters is unclear. We show that the transcription factor M1BP, which associates with the core promoter region, activates transcription of RP genes. Moreover, M1BP directly interacts with TRF2 to recruit it to the RP gene promoter. High resolution ChIP-exo was used to analyze in vivo the association of M1BP, TRF2, and the TFIID subunit, TAF1. Despite recent work suggesting that TFIID does not associate with RP genes in Drosophila, we find that TAF1 is present at RP gene promoters and that its interaction might also be directed by M1BP. Although M1BP associates with thousands of genes and TRF2 associates with hundreds, their colocalization is largely restricted to RP genes, suggesting that this combination is key to coordinately regulating transcription of the majority of RP genes in Drosophila.

overall_design: ChIP-exo was performed using S2R+ cells. The datasets include replicates for TRF2, TAF1 (TAF250), and Preimmune samples and a single dataset for M1BP.

first: Douglas

last: Baumann


title: RNA-seq analysis of WT vs. Reck vascular KO P0 mouse brains

city: Baltimore

first: Jeremy

last: Nathans

address: 725 North Wolfe Street, 805 PCTB

institute: Johns Hopkins University School of Medicine

summary: We examined, compared, and analyzed the transcriptome profile (RNA-seq) of WT vs Reck vascular KO (Reck flex2/Δex1; Tie2Cre) P0 mouse brains. Specifically, cortical transcriptomic differences (between WT and mutant genotypes) were compared separately from subcortical transcriptomic changes.

overall_design: Cortical and subcortical mRNA profiles from P0 mice, in triplicates, for WT and Reck vascular KO animals (12 samples total).

first: Chris

last: Cho


title: Global mRNA polarization regulates translation efficiency in the intestinal epithelium [RNAseq of LCM subcellular tissue fragments]

first: Andreas

last: Moor

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

institute: ETH Zurich

summary:
Asymmetric mRNA localization facilitates efficient translation in cells such as neurons and fibroblasts. However, the extent and significance of mRNA polarization in epithelial tissues is unclear. Here, we used single molecule transcript imaging and subcellular transcriptomics to uncover global apical-basal intracellular polarization of mRNA in the mouse intestinal epithelium. The localization of mRNAs did not generally overlap protein localization. Instead, ribosomes were more abundant on the apical sides, and apical transcripts were consequently more efficiently translated. Refeeding of fasted mice elicited a basal to apical shift in polarization of mRNAs encoding ribosomal proteins, which was associated with a
specific boost in their translation. This lead to increased protein production, required for efficient nutrient absorption. These findings reveal a post-transcriptional regulatory mechanism involving dynamic polarization of mRNA and polarized translation.

overall_design: RNAseq of laser capture microdissected subcellular tissue fragments of the murine intestinal epithelium.

middle: E

first: Shalev

last: Itzkovitz


title: Global mRNA polarization regulates translation efficiency in the intestinal epithelium


title: Long non-coding control of pericyte function

city: Frankfurt am Main

first: Christoph

middle: Michael

last: Zehendner

address: Theodor Stern Kai 7

institute: Goethe University


title: Global mRNA polarization regulates translation efficiency in the intestinal epithelium [Ribo-Seq]

overall_design: RNAseq and RiboSeq of the murine duodenum.


title: Loss of the SUMO Protease Ulp2 Triggers a Specific Multi-Chromosome Aneuploidy

city: New Haven

first: Hong-Yeoul

last: Ryu

address: 266 Whitney Ave

department: MB&B

institute: Yale

summary: Post-translational protein modification by the small ubiquitin-related modifier (SUMO) protein regulates numerous cellular pathways, including transcription, cell division and genome maintenance. The SUMO protease Ulp2 modulates many of these SUMO-dependent processes in budding yeast. To investigate changes to the transcriptome of cells lacking Ulp2, whole-genome RNA sequencing (RNA-seq) was employed. Unexpectedly, ulp2Δ cells display a general two-fold increase in transcript levels across two particular chromosomes, Chromosome I (ChrI) and Chromosome XII (ChrXII). Quantification of relative DNA levels showed that ChrI and ChrXII are present at twice their normal copy number in ulp2Δ cells. This double disomy occurs in mutants in multiple genetic backgrounds and does not require passage through meiosis. An abnormal number of chromosomes in a cell, termed aneuploidy, is usually deleterious. However, development of specific aneuploidies allows rapid adaptation to cellular stresses in yeast and other species, and aneuploidy characterizes most tumors. Extra copies of ChrI and ChrXII appear quickly following loss of active Ulp2, suggesting aneuploidy is an adaptive mechanism in cells lacking the functional SUMO protease. The specific aneuploidy in ulp2Δ cells highlights a unique example of a homogeneous, multi-chromosome aneuploidy in response to mutation of a single gene.

overall_design: three mutants and one WT control each with 3 replicates

first: Nicole

last: Wilson

first: Sameet

last: Mehta

first: Soo

last: Hwang

first: Mark

last: Hochstrasser


title: Impact of HypERrlnc Knockdown on the human pericyte transcriptome

summary: Pericytes are essential for vessel maturation and endothelial barrier function. Long non-coding RNAs (lncRNAs) regulate endothelial cell function, but their role in pericyte biology remains unexplored. Here we characterize the human pericyte transcriptome following knockdown of lncRNA HypERrlnc (RP11-65J21.3).

overall_design: To investigate the impact of the knockdown of long noncoding RNA HypERrlnc on the pericyte transcriptome. HypERrlnc was silenced by LNA GapmeRs, controls were treated with scramble LNA GapmeR control. HypERrlnc was silenced in 3 independent experiments and total, ribosomal depleted RNA was subsequently analyzed via RNA deep sequencing. Mouse pericytes were kept in pre-equilibrated culture medium in a hypoxic incubator (Labotect) with humidified atmosphere at 5% CO2, 1% O2, 37°C. Mouse Pericytes were subjected to hypoxia for 24 h. Hypoxia was verified with measurement of culture medium pO2 levels with a hypoxia sensing probe (Oxford Optronix) as described elsewhere (Zehendner et al Plos One 2013).

middle: M

first: Stefanie

last: Dimmeler


title: Long non-coding RNA TYKRIL controls pericyte function and survival in the cardiovascular and central nervous system through regulation of p53 activity and PDGFRß expression

summary: Vessel maturation is dependent on platelet derived growth factor (PDGF), which signals via tyrosine kinase receptors and facilitates recruitment of pericytes. Long noncoding RNAs (lncRNAs) regulate endothelial and smooth muscle cell properties, but their role in pericyte function is unclear. Using RNA sequencing, we identify the hypoxia induced lncRNA “Tyrosine kinase receptor inducing lncRNA” (TYKRIL) as a species conserved lncRNA which regulates pericyte function by controlling PDGF receptor beta (PDGFRß) expression in vitro, in vivo and in human disease. TYKRIL preferentially binds to the N-terminus of p53, thereby acting as a p53 decoy molecule that prevents the interaction with its co-activator p300, which augments the expression of the known p53 target PDGFRß. In summary, our results identify TYKRIL as a key regulator of pericyte function by acting as a previously unknown modulator of p53 activity which may enable to develop novel therapeutic concepts in PDGFRß and p53 dependent disease states.

overall_design: To identify the hypoxia regulated transcriptome in human pericytes, cells were exposed towards 24 hours of hypoxia (1%O2, 5% CO2, humidified atmosphere). Normoxic controls were kept at 20% O2, 5% CO2, humidified atmosphere. Hypoxia was performed in 3 independent experiments. Total, ribosomal depleted RNA was analyzed by RNA deep sequencing following hypoxia. To investigate the impact of the long noncoding RNA TYKRIL on the pericyte transcriptome, TYKRIL was silenced by LNA GapmeRs, controls were treated with scramble LNA GapmeR control. TYKRIL was silenced in 3 independent experiments and total, ribosomal depleted RNA was subsequently analyzed via RNA deep sequencing.

first: Dimmeler

last: Stefanie


title: Choline kinase alpha (CHKA) as a therapeutic target in pancreatic ductal adenocarcinoma: Expression, predictive value, and sensitivity to inhibitors

city: Madrid

first: Victor Javier

last: Sanchez-Arevalo Lobo

address: Melchor Fernandez Almagro, 3

department: Cancer Biology

institute: CNIO

summary: Choline kinase alpha (CHKA) plays a crucial role in the regulation of membrane phospholipid synthesis and has oncogenic properties in vitro. We have analyzed the expression of CHKA in cell lines derived from pancreatic ductal adenocarcinoma (PDAC) and have found increased CHKA expression and a good correlation between protein expression and sensitivity to MN58b, a CHKA inhibitor that reduced cell growth through the induction of apoptosis. Accordingly, CHKA knockdown led to reduced drug sensitivity. In addition, we found that gemcitabine-resistant PDAC cells displayed enhanced sensitivity to CHKA inhibition and, in vitro, MN58b had synergistic effects with gemcitabine, 5-fluorouracil and oxaliplatin, three active drugs in the treatment of PDAC. Using tissue microarrays, CHKA was found to be overexpressed in 90% of pancreatic tumors. While cytoplasmic CHKA did not relate to survival, nuclear CHKA distribution was observed in 43% of samples and was associated with survival, especially among patients with well/moderately differentiated tumors. To identify the mechanisms involved in resistance to CHKA inhibitors, we cultured IMIM-PC-2 cells with continuous incremental concentrations of MN58b and isolated a subline with a 30-fold higher IC50. RNA-Seq analysis identified up-regulation of ABCB1 and ABCB4 multidrug resistance transporters and functional studies confirmed that their up-regulation is the main mechanism involved in resistance. Overall, our findings support the notion that CHKA inhibition merits further attention as a therapeutic option in patients with PDAC.

overall_design: RNA profile from parental and MN58b-resistant IMIM-PC-2 were generated by deep sequencing were done in triplicates using illumina GAIIx

first: Jose

last: Mazarico

first: Victor

first: Enrique

last: Carrillo de Santa Pau

first: Francisco

middle: X

last: Real


title: Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm

first: Mattia

last: Brugiolo

state: Connecticut

address: 333 Cedar Street

department: Molecular biophysics and biochemistry

summary: We report a new method which combines subcellular fractionation to advance sequencing technique iCLIP. In this way we identified the spectrum of interactions of two SR-proteins (SRSF3 and SRSF7) to their target RNAs in different subcellular compartments

overall_design: Examination of 4 replicates for Cytoplasm, Nucleoplasm and Chromatin fractions using Fr-iCLIP technique for SRSF3-GFP; examination of 3 replicates for Cytoplasm, Nucleoplasm and Chromatin fractions using Fr-iCLIP for SRSF7-GFP

first: Valentina

last: Botti

last: Liu

first: Michaela

last: Müller-McNicoll

first: Karla

last: Neugebauer


title: Gene expression changes upon drug withdrawal

status: Public on Aug 09 2017

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

overall_design: Refer to individual Series


title: Gene expression changes upon drug withdrawal (Mel888 cell line)

summary: In this study we investigate the mechanism of drug addiction

overall_design: Drug was withdrawn from wt / MAPK1 KO / JUNB KO double drug resistant mel888 (DR Mel888) cells, and gene expression profiling was performed upon drug withdrawal

first: Xiangjun

last: Kong

first: Daniel

last: Peeper


title: PPARγ in DCs and T cells drives pathogenic type-2 effector responses in lung inflammation

status: Public on Aug 08 2017

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

institute: ETH Zürich

summary: We compare GW9662 (PPARg antagonist) treated CD4+ T cells under Th2 coculture conditions with vehicle controls

first: Samuel

last: Nobs


title: Gene expression changes upon drug withdrawal (A375/451Lu cell lines)

overall_design: Drug was withdrawn from several cell lines, and gene expression profiling was performed over time


title: Regulation of gene expression in serotype M1 group A Strep (GAS, aka S. pyogenes) by RocA

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

summary: We used RNA-Seq to assess whether the rocA gene regulates gene expression in M1 GAS

overall_design: Parental M1 isolate MGAS2221, rocA mutant derivative 2221ΔrocA, and the chromosomally complemented derivative 2221ΔrocAComp were compared following THY growth by RNA-Seq

first: Ira

last: Jain


title: SPLICING FACTOR FOR PHYTOCHROME SIGNALING promotes photomorphogenesis by regulating alternative splicing in Arabidopsis

city: Austin

first: Enamul

last: Huq

address: 205 West 24th

department: IB

institute: University of Texas at Austin

summary:
Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis.

Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. Except for gene expression, we also discovered 788 differentially spliced bins between Col-0 and mutant dark samples; 827 differentially spliced bins between Col-0 and mutant red light treated samples; 610 differentially spliced bins between Col-0 dark and red light treated samples; and 405 differentially spliced bins between mutant dark and red light treated samples. Altered splicing of 9 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method.

Conclusions: Our study represents the first detailed analysis of SFPS mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that SFPS regulates photomorphogenesis in Arabidopisis through regulating the splicing activity of light signaling genes, which helps us.

overall_design: Methods: Total RNA (rRNA was depleted) is extracted from 4-day-old Col-0 wild-type (WT) and SFPS knockout mutant (sfps-2) dark grown seedlings with or without 3hrs continuous red light irradiation (7μmolm-2s-1). The RNA-seq libraries are generated according to the commercial handbook from the Illumina kit (TruSeq Stranded Total RNA with Ribo-Zero Plant). The transcriptome and alternative splicing profiles are generated from Col_D, Col_Rc, mut_D, and mut_Rc samples, in triplicate. The sequence reads were analyzed to find the differentially expressed genes or differentially spliced bins by the following packages: TopHat, Cufflinks, and ASpli. qRT–PCR validation was performed using TaqMan and SYBR Green assays.


title: Integrated analyses of high throughput sequencing on the regulatory mechanism of abscisic acid in strawberry fruit ripening

city: Hangzhou

first: Dongdong

last: Li

state: Zhejiang

address: Yuhangtang Road

department: Food Science and Nutrition

institute: Zhejiang University

summary: By employing the high-throughput sequencing technology, we comprehensively analyzed the transcriptomic and miRNA expression profiles simultaneously in ABA- and nordihydroguaiaretic acid (NDGA, an ABA biosynthesis blocker)-treated strawberry fruits with a temporal resolution. The miRNAs target genes were validated by degradome sequencing.

overall_design: Sample 1: CK0.1, CK0.2 (Strawberry fruit two weeks after athesis treated with distilled water, set as day 0); Sample 2: CK5.1, CK5.2 (fruit treated with water, samples collected 5 days later after the treatment); Sample 3: CK8.1, CK8.2 (fruit treated with water, samples collected 8 days later after the treatment); Sample 4: ABA5.1, ABA5.2 (fruit treated with ABA, samples collected 5 days later after the treatment); Sample 5: ABA8.1, ABA8.2 (fruit treated with ABA, samples collected 8 days later after the treatment); Sample 6: NDGA5.1, NDGA5.2 (fruit treated with NDGA, samples collected 5 days later after the treatment); Sample 7: NDGA8.1, NDGA8.2 (fruit treated with NDGA, samples collected 8 days later after the treatment).

first: Zisheng

last: Luo


title: A noncoding function of TYRP1 mRNA promotes melanoma growth

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Competition among RNAs to bind miRNA is proposed to influence biological systems. However, the role of this competition in disease onset is unclear. Here, we report that TYRP1 mRNA, in addition to encoding tyrosinase-related protein 1 (TYRP1), indirectly governs cell proliferation by sequestering miR-16 to non-canonical miRNA response elements (MREs). Consequently, the sequestered miR-16 is no longer able to repress its mRNA targets, such as RAB17, which is involved in melanoma cell proliferation and tumor growth. Restoration of miR-16 tumor suppressor function can be achieved in vitro by silencing TYRP1 or increasing miR-16 expression. Importantly, TYRP1-dependent miR-16 sequestration can also be overcome in vivo by using small oligonucleotides that mask miR-16 binding sites on the TYRP1 mRNA. Together, our findings assign a pathogenic noncoding function to the TYRP1 mRNA and highlight miRNA displacement as a new targeted therapeutic approach in melanoma.

overall_design: Total RNA isolated from 4 distinct human melanoma cell lines (SK-MEL-28; ME1402; M234; 501Mel) was subjected to multiplexed small RNA-sequencing using the NEBNext Small RNA Library Prep Set for SOLiD sequencing technology.

first: D

last: Gilot

first: B

last: Mari

first: N

last: Nottet

first: K

first: P

last: Barbry


title: Innate to adaptive: Human IFN-gamma producing CD4+ T cells can derive directly from CXCL8-producing recent thymic emigrants.

city: London

first: Deena

middle: L.

last: Gibbons

address: Great Maze Pond

department: Dept. Immunology

institute: Kings College London

summary: An unanticipated feature of the human neonatal CD4 T cell response is a robust capacity to produce CXCL8. However, this 'innate-like' function dissipates with age and is scarce in the adult. Here, we investigated the fate of CD4+CXCL8+ cells and their transition into conventional adaptive T cells. We show that CXCL8 is imprinted on immature thymocytes prior to TCR signalling and is maintained in T cell committed thymic progenitors and recent thymic emigrants (RTEs) of adults as well as neonates. Hence, rather than being unique to neonates, CXCL8-producing CD4+ T cells decrease with age in humans (and in humanised mice) owing to the decline in thymic output, coupled with the cells’ peripheral expansion. By cloning of CXCL8+CD4+ cells from cord blood, we were able to track effector function within daughter cells and demonstrate that these cells can convert to IFN-g producing cells. In sum, we provide direct evidence that ‘innate like’ CXCL8-producing CD4+ T cells emerge from the thymus and can transition into conventional adaptive Th1 cells

overall_design: Examination of RNA-Seq count data from 96 single cells

first: A

last: Das

last: Rouault-Pierre

first: I

last: Gomez-Tourino

last: Wood

last: Donaldson

first: C

middle: A

last: Mein

last: Bonnet

last: Hayday

middle: L


title: RocA regulates gene expression in serotype M1 group A Strep (GAS, aka S. pyogenes)

last: Sumby

overall_design: Parental M1 isolate MGAS2221, rocA mutant derivative 2221ΔrocA, and the complemented mutant derivative 2221ΔrocA + pRocA-M1 were compared following THY growth by RNA-Seq

first: Eric

last: Miller


title: Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment

city: Bethesda

first: Songjoon

last: Baek

address: 41 Library Drive

department: CCR

institute: NCI / NIH

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


title: Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment [ChIP-seq]

summary: Despite the widespread use of glucocorticoids (GCs) for treating inflammatory conditions, the underlying mechanisms of their anti-inflammatory effects are not understood.  Moreover, the majority of molecular investigations have examined the effects of glucocorticoid receptor (GR) activation prior to inflammatory challenges.  However, clinically relevant situations are emulated by a GC intervention initiated in the midst of rampant inflammatory responses.  To characterize the effects of a late GC treatment, we performed systematic profiling of macrophage transcriptional and regulatory landscapes with Dexamethasone (Dex) treatment either before or after stimulation by lipopolysaccharide (LPS).  GR activation by Dex following LPS stimulation had a similar anti-inflammatory profile in comparison to GR pre-activation, while ameliorating the disruption of metabolic genes.  Unexpectedly, the chromatin occupancy pattern of GR is not predictive of the Dex-regulated expression changes and shows little evidence for the widely accepted ‘trans-repression by tethering’ model.  Rather, we find that GR activation results in global blockade of NF-κB binding to chromatin.  Integrative analyses of gene expression, transcription factor occupancy, and chromatin accessibility data highlight distinct mechanisms through which GR controls inflammatory macrophages: prevention of NF-κB chromatin occupancy and activation of negative regulators such as Nfkbia, Dusp1, Tnfaip3, and Tsc22d3.  Our investigation with differentially timed GC treatments reveals molecular mechanisms underlying therapeutic actions of GR for modulating the ‘inflamed epigenome’.

overall_design:
RNA-seq time course (0h, 4h, 10h) and DNase-seq sample replicates from macrophages; RelA/GR ChIP-seq time course sample replicates and input control DNA
This is the ChIP-seq dataset.

first: Kyu-Seon

last: Oh

first: Heta

last: Patel

first: Rachel

last: Gottschalk

first: Wai

last: Lee

first: Iain

middle: D

last: Fraser

first: Gordon

last: Hager

first: Myong-Hee

last: Sung


title: Drosophila Cbp80 is needed for the expression of piRNA components and piRNAs

city: Bern

first: Rémy

last: Bruggmann

address: Baltzerstrasse 6

institute: University of Bern

summary: piRNAs expression analysis in dissected Drosophila ovaries, focused on the 42ab and flamenco locus

overall_design: Germline tissue expressing reduced levels of Cbp80 (shRNA treatment knocked down Cbp80 specifically in the germline) was used to isolate small RNAs. Small RNA reads were compared to small RNA reads after knock down treatment of a control gene / mRNA (mCherry-Jupiter)

first: Ravish

last: Rashpa

first: Paula

last: Vazquez-Pianzola

first: Martino

last: Colombo

first: Beat

last: Suter


title: A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation

city: Portsmouth

first: Samuel

last: Robson

address: St Michael's Building

department: School of Pharmacy & Biomedical Science

institute: University of Portsmouth

summary: Execution of pluripotency requires progression from the naïve status represented by mouse embryonic stem cells (ESCs) to a state capacitated for lineage specification. This transition is coordinated at multiple levels. Non-coding RNAs may contribute to this regulatory orchestra. We identified a rodent-specific long non-coding RNA (lncRNA) linc1281, hereafter Ephemeron (Eprn), that modulates the dynamics of exit from naïve pluripotency. Eprn deletion delays the extinction of ESC identity, an effect associated with perduring Nanog expression. In the absence of Eprn, Lin28a expression is reduced, resulting in persistence of let-7, and up-regulation of de novo methyltransferases Dnmt3a/b is delayed. Dnmt3a/b deletion retards ES cell transition, correlating with delayed Nanog promoter methylation and phenocopying loss of Eprn or Lin28a. The connection from lncRNA to miRNA and DNA methylation facilitates the acute extinction of naïve pluripotency, a pre-requisite for rapid progression from preimplantation epiblast to gastrulation in rodents. Eprn illustrates how lncRNAs may introduce species-specific network modulations.

overall_design: RNA Seq expression profiling mouse ES cells was conducted to compared the expression of transcripts in mES wild-type (WT) and mES cells with knockout of the lncRNA ephemeron (KO). Cells were grown in PD/LIF medium, or following 8 hours withdrawal from PD/LIF. All conditions were conducted using three indepedent cell lines served as biological triplicates. ChIRP seq of ephemeron targets was also conducted in WT and KO cells (in duplicate), along with WT and KO input controls and 7SK ChIRP seq.

first: Meng-Amy

last: Li

first: Paulo

last: Aramal

first: Priscilla

last: Cheung

first: Jan

last: Bergmann

first: Masaki

last: Kinoshita

first: Tüzer

last: Kalkan

first: Meryem

last: Ralser

first: Maike

last: Paramor

first: Fengtang

last: Yang

first: Caifu

last: Chen

first: Jennifer

last: Nichols

first: David

last: Spector

first: Tony

last: Kouzarides

first: Lin

last: He

first: Austin

last: Smith


title: The transcription factor Sp3 cooperates with HDAC2 to regulate synaptic function and plasticity in neurons

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary: The histone deacetylase HDAC2, which negatively regulates neuronal plasticity and synaptic gene expression, is upregulated both in Alzheimer’s disease (AD) patients and mouse models (Graff et al., 2012). Therapeutics targeting HDAC2 are speculated to be a promising avenue for ameliorating AD related cognitive impairment. However, attempts to generate HDAC2-specific inhibitors have not been successful. Here, we take a novel approach utilizing integrative genomics to identify proteins that mediate HDAC2 recruitment to synaptic plasticity genes. Functional screening revealed that knockdown of the transcription factor Sp3 phenocopied HDAC2 knockdown, and that Sp3 facilitated the recruitment of HDAC2 to synaptic genes. Importantly, like HDAC2, Sp3 expression was elevated in AD patients and mouse models, where Sp3 knockdown ameliorated synaptic dysfunction. Furthermore, exogenous expression of an HDAC2 fragment containing the Sp3 binding domain fully restored synaptic plasticity and memory in a mouse model with severe neurodegeneration. Our findings indicate that targeting the HDAC2-Sp3 complex could enhance synaptic and cognitive function, without affecting HDAC2 function in other processes.

overall_design: We profiled gene expression levels in primary neurons treated with HDAC2 or Sp3 shRNAs through RNA-Seq to examine whether HDAC2 and Sp3 cooperatively regulate a set of genes.

first: Hidekuni

last: Yamakawa

first: Fan

last: Gao


title: Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment [DNase-seq]

first: Songjoon

last: Baek

overall_design:
RNA-seq time course (0h, 4h, 10h) and DNase-seq sample replicates from macrophages; RelA/GR ChIP-seq time course sample replicates and input control DNA
This is the DNase-seq dataset.

first: Kyu-Seon

last: Oh

first: Heta

last: Patel

first: Rachel

last: Gottschalk

first: Wai

last: Lee

first: Iain

last: Fraser

first: Gordon

last: Hager

first: Myong-Hee

last: Sung


title: Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment [RNA-Seq]

overall_design:
RNA-seq time course (0h, 4h, 10h) and DNase-seq sample replicates from macrophages; RelA/GR ChIP-seq time course sample replicates and input control DNA
This is the RNA-seq dataset.