title: Sialic acid relieves RetS-dependent inhibition of GacS to induce a chronic infection state of Pseudomonas aeruginosa

status: Public on Mar 30 2019

city: Cambridge

first: Benjamin

last: Wang

state: MA

address: 31 Ames Street

country: USA

institute: MIT

type: Expression profiling by high throughput sequencing

summary: The purpose of this experiment was to see if the addition of sialic acid activated the GacS-GacA regulon, which includes >300 genes.

overall_design: Cultures were grown to OD~0.6, and then split in half. 2 mM sialic acid was added to one culture but not to the other. After 20 minutes of incubation with sialic acid, RNA was extracted from the + or - sialic acid samples for RNA-seq.

middle: X

first: Kyle

middle: C

last: Cady

first: Katharina

last: Ribbeck

first: Michael

middle: T

last: Laub


title: Differential expression of miRNAs in a cellular model of MELAS.

status: Public on Mar 29 2019

city: Valencia

first: Joaquin

last: Panadero

state: Valencia

address: Avenida Fernando Abril Martorell, 106 Torre A

department: Genomics

country: Spain

institute: Instituto Investigación Sanitaria La Fe

type: Non-coding RNA profiling by high throughput sequencing

summary: We investigate the participation of miRNAs in the cell response to the mitochondrial dysfunction associated with m.3243A>G mutation in mitochondrial DNA (mtDNA), which is the most common cause of MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) syndrome.Through small-RNA sequencing and in silico analysis, we identified 246 differentially-expressed in a transmitochondrial cybrid model of MELAS (100% m.3243A>G mutant mitochondrial DNA), with 126 being up-regulated and 120 down-regulated. The enrichment analysis of Gene Ontology (GO) terms revealed that target genes for dysregulated miRNAs were involved in muscle and nervous system development, heart development, and signaling pathways controlling cardiac events.These data suggest that the miRNA program triggered by the MELAS m.3243A>G mutation could explain for some of the clinical manifestations of the MELAS syndrome.

overall_design: Examination of dysregulated miRNAs in MELAS.

first: Salvador

last: Meseguer

first: Carmen

last: Navarro-González

first: Marda

last: Villarroya

first: Rachid

last: Boutoual

first: Giacomo

middle: P

last: Comi

first: Maria

middle: E

last: Armengod


title: Transcriptomic study of soybean (Glycine max) in response to zinc deficiency

city: Hangzhou

first: Houqing

last: Zeng

address: NO.2318, Yuhangtang Rd, Yuhang District

country: China

institute: Hangzhou Normal University

summary: We conducted a genome-wide transcriptomic analysis in soybean leaves and roots treated with zinc (Zn) deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for Zn-sufficient leaves (ZSL), Zn-deficient leaves (ZDL), Zn-sufficient roots (ZSR), and Zn-deficient roots (ZDR). Therefore a total of eight libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified Zn-deficiency responsive genes. At least 20 genes that are potentially involved Zn homeostasis were significantly changed by Zn deficiency, including 7 ZIP (ZRT, IRT-related protein) transporter genes, 3 nicotianamine synthase genes, and 7 metallothionein genes. At least 48 genes encoding likely Zn-binding proteins were found to be responsive to Zn deficiency in leaves or roots. Eighty-five transcription factor genes were significantly changed by Zn deficiency in leaves or roots, including 5 bZIP members and 10 Golden 2-like members. In addition, some other groups of genes which are possibly related to reactive oxygen species scavenging, calcium and hormone signaling, and protein phosphorylation and dephosphorylation also differentially expressed under Zn deficiency.

overall_design: The first trifoliate true leaves and roots of soybean were harvested after 12 days treatment with or without zinc element in the nutrient solution, and RNA was extracted and sequenced by paired-end sequencing. RNA sequencing reads were aligned against the soybean reference genome and differentially expressed genes between treatments were detected.


title: Physiological and genome-wide expression analysis of cold-induced leaf rolling at the seedling stage in rice (Oryza sativa L.)

city: Guangzhou

first: Junliang

last: Zhao

address: 29 Jinying Road, Tianhe District

institute: Guangdong Academy of Agricultural Science

summary: Leaf rolling and discoloration are two chilling injury symptoms that are widely adopted as indicators for evaluation of cold tolerance at the seedling stage in rice, respectively. However, their relationship has not been well investigated, in particular the mechanism on how low temperature causes leaf rolling at a genome-wide level. In this study, a cold-tolerant japonica cultivar Lijiangxintuanheigu and a cold-sensitive indica cultivar Sanhuangzhan-2 were subjected to different low temperature treatments and physiological and genome-wide gene expression analysis were conducted. Our results showed that leaf rolling happened at temperatures lower than 11℃, but discoloration appeared at moderately low temperatures, such as 13℃. Chlorophyll contents of the two cultivars significantly decreased under 13℃, but didn’t change under 11℃. Contrastly, their relative water contents and the relative electrolyte leakages decreased significantly. Genome-wide gene expression profiling of LTH revealed that the calcium signaling related genes and the genes related to ABA degradation significantly changed under 11℃. Moreover, numerous genes in DREB, MYB, bZIP, NAC, Zin finger, bHLH, WRKY gene families were differently expressed. Furthermore, many aquaporin genes, the key genes in trehalose and starch synthesis were down-regulated under 11℃. These results suggest that the two chilling injury symptoms are controlled by different mechanisms. Cold-induced leaf rolling is associated with calcium and ABA signaling pathways, and subjected to regulation of multiple transcription regulators. The suppression of aquaporin genes and reduced accumulation of soluble sugars under cold stress result in reduction of water potential in cells and consequently, leaf rolling.

overall_design: mRNA profiles of Lijiangxintuanheigu (LTH) rice under 11℃,13℃ and 25℃ cold stresses for 24h were generated by deep sequencing, in two biological replicates, using Illumina Hiseq 2500 platform.

first: Jingfang

last: Dong

first: Shaohong

last: Zhang

first: Tifeng

last: Yang

first: Qing

last: Liu

first: Xingxue

last: Mao

first: Hua

last: Fu

first: Wu

first: Liu

last: Bin


title: RNA-Seq analysis of skin from bleomycin induced scleroderma murine models treated with EHP-101 or Ajulemic acid

status: Public on Mar 31 2019

city: Córdoba

first: Eduardo

last: Muñoz

address: Avda Menéndez Pidal s/n

institute: Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), University of Córdoba

summary: Several lines of evidence have shown that the endocannabinoid system (ECS) may play a role in the pathophysiology of systemic sclerosis (SSc). Thereby, structurally different dual PPARγ/CB2 agonists such as VCE-004.8 and Ajulemic acid (AjA) have been shown to alleviate skin fibrosis and inflammation in experimental models of SSc. Since both compounds are currently being tested in humans, we were interested to identify similarities and differences in a murine model of SSc. One method available to assess this is the pharmacotranscriptomic signature of the individual compounds. To analyze the pharmacotranscriptomic signature, we used RNA-Seq to analyze the skin gene expression changes from bleomycin-induced fibrosis in mice treated orally with either AjA or EHP-101, a lipidic formulation of VCE-004.8.  While both compounds prevented the upregulation of a common group of genes involved in the inflammatory and fibrotic components of the disease and the pharmacotranscriptomic signatures were similar for both compounds in some pathways, we found key differences between the compounds in several functional groups, including genes related the hypoxia, interferon-α and interferon-γ response. Additionally, we found 28 specific genes with translation potential by comparing our results with a list of intrinsic human scleroderma genes.  Inmunohistochemical analysis revealed that both EHP-101 and AjA prevented bleomycin-induced skin fibrosis, collagen accumulation, and TNC and VCAM expression. However, only EHP-101 normalized the reduced expression of vascular CD31, CD34 and Von Willebrand factor markers, which parallels skin fibrosis, while AjA did not affect these markers. Finally, clear differences were also found in the plasmatic biomarker analysis, in which we found that EHP-101, but not AjA, enhanced the expression of some factors related to angiogenesis and vasculogenesis. Altogether the results indicate that dual PPARγ/CB2 agonists qualify as a novel therapeutic approach for the treatment of SSc and other fibrotic diseases as well, and that EHP-101 has unique mechanisms of action related to the pathophysiology of SSc which could be beneficial in treatment of this complex disease with no current therapeutic options.

overall_design:
RNA-Seq profiles were generated for six- to eight-week-old female BALB/c mice in four conditions: Control, Bleomycin, Bleomycin + EHP-101 treatment and Bleomycin + Ajulemic acid treatment.

Please note that the "raw_counts_newsamples.txt" includes raw counts obtained from featureCounts for the samples included in this entry and the "raw_counts_merged.txt" includes raw counts obtained from merging the counts of the samples from this entry with the counts of the samples from the GSE115503 entry.

first: Adela

last: García-Martín

first: Martín

last: Garrido-Rodríguez

last: Navarrete

first: Danilo

last: del Prete

first: Belén

last: Palomares

first: Jim

last: DeMesa

first: Giovanni

last: Appendino


title: Comparison of Porphyromonas gingivalis 381 and W83 gene expression between surface translocation and biofilm mode

city: Gainesville

first: Fata

last: Moradali

state: FL

address: 1395 Center Drive

institute: University of Florida

summary: Porphyromonas gingivalis (P. gingivalis) 381 and W83 growing in motility condition (i.e. stabbed in soft agar culture) and on surface of solid agar culture (Biofilm) were prepared. Applied medium was BAPHK supplemented with hemin and menadione . The cultures were then permitted to grow anaerobically at 37°C for 24 hours, which corresponds to initial stages of surface translocation by P. gingivalis. At this point, RNA extraction was performed using the cultures, and these samples were processed and submitted for RNA sequencing using an Illumina platform. Significant changes in gene expression were observed in cells growing in motility and biofilm modes , and the majority of changes were associated with cell surface proteins, membrane proteins, biosynthesis of folates and bioenergetic pathways.

overall_design: Both sets of cultures were grown in triplicate and RNA extraction was performed inside anaerobic chamber.

first: Shirin

last: Ghods

first: Thomas

last: Angelini

first: Mary

last: Davey


title: RIP-CHIP data from CNOT6L WT and KO hepatocytes

city: San Antonio

first: Masahiro

last: Morita

state: Texas

address: 4939 Charles Katz Drive

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary:
mRNA poly(A) tail plays a key role in post-transcriptional regulation of gene expression, including mRNA decay and translation. Deadenylation is a rate-limiting step in mRNA decay, which is catalyzed by the CCR4-NOT complex.
To identify mRNAs associated with the CCR4-NOT complex, we have done RIP-CHIP (RNA-immunoprecipitation followed by DNA microarray) using primary hepatocytes from CNOT6L wild-type and knockout mice.

overall_design: Primary hepatocytes were isolated from 8-week-old wild-type and Cnot6l knockout (KO) mice. Each sample was divided into two parts for input RNA extraction, and anti-CNOT6L immunoprecipitation followed by RNA extraction. Input mRNA and immunoprecipitated (IPed) mRNA were hybridized to separate Mouse Genome 430 2.0 Affymetrix microarrays. Cnot6l KO hepatocytes was used as a negative control. All experiments were done in triplicates, with immunoprecipitated and input RNA from wild-type and CNOT6L KO hepatocytes generated for a total of 12 microarrays.

first: Ola

last: Larsson

first: Takeshi

last: Nagashima

first: Mariko

last: Okada-Hatakeyama

first: Tadashi

last: Yamamoto

first: Nahum

last: Sonenberg


title: Transcriptome profiles of distinct mechanoreceptive somatosensory neuron subtypes

city: New York

first: Joriene

last: de Nooij

state: NY

address: 650 West 168th Street

department: Neurology

institute: Columbia University

summary: The objective of the study was to identify molecules that are selectively expressed in proprioceptive sensory neurons (pSNs) in DRG. To try to achieve this goal, we performed RNAseq on genetically identified and FACS purified cohorts that either contained i) pSNs and rapidly-adapting low threshold mechanoreceptors (RA-LTMRs), iI) pSNs and slowly-adapting (SA)-LTMRs, or RA-LTMRs only. Differential expression analysis between these different sensory neuron cohorts identified multiple proprioceptor enriched transcripts.

overall_design: We conducted a molecular analysis of pSN, RA-LTMR and SA-LTMR cohorts on the basis of their differential PV and RX3 expression pattern. To do so, we took advantage of a previously generated Runx3 mutant allele, a PV:Cre driver, and the Cre-dependent Ai9:tdTomato (tdT) reporter (Taniuchi et al., 2002; Kramer et al., 2006; Madison et al., 2010), and separately crossed PV:Cre and Ai9:tdT alleles into the Rx3 mutant background. Subsequent intercrosses between these two strains resulted in some wild type Rx3 PV:Cre;Ai9:tdT animals, and some Rx3 mutant PV:Cre;Ai9:tdT animals (hereafter referred to as Rx3+/+;PV:tdT and Rx3-/-;PV:tdT respectively). In Rx3 mutants, pSNs fail to survive, and all remaining PVon neurons correspond to RA-LTMRs sensory neurons (Kramer et al., 2006; de Nooij et al., 2013). We isolated neonatal PV:tdT+ sensory neurons from dissociated Rx3+/+ (comprising pSNs and RA-LTMRs) and Rx3-/- DRG (comprising only RA-LTMRs), using fluorescent activated cell sorting (FACS). In addition, we used TrkC:GFP BAC transgenic mice, in which the GFP reporter is selectively expressed in Rx3onTrkCon neurons but not in Rx3offTrkCon neurons, to isolate a mixed population of neonatal pSNs and SA-LTMRs (Lee et al., 2012; de Nooij et al., 2013). We performed global transcriptome analysis (RNAseq) on each of the three isolated mechanoreceptor populations: Rx3+/+;PV:tdT+,  Rx3-/-;PV:tdT+, and TrkC:GFP+.

first: Dawei

last: Wu

first: Ira

middle: S

last: Schieren

first: Yingzhi

last: Qian

first: Chaolin

last: Zhang

middle: M

last: Jessell


title: Nano genome altas (NGA) of body wide tissue specific responses

city: HangZhou

first: Bingbing

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

institute: Zhejiang University

summary:
Purpose: In order to detect the unpredictable risks of the cumulative nanoparticles infiltrated everywhere in the whole body after systematic administration

Methods: By using RNA-seq, we systematically studied the transcriptomic response of multi-organs from mice and tissue specific (stem) cells to the hydroxyapatite (HA) nano-delivery system.

Results: We show that HA could differentially influence gene expression, immune response, cell proliferation, stress, apoptosis, metabolic, ion transport activity, cell signaling and epigenetic activity across tissues and tissue specific (stem) cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We collected mouse tissues of heart, liver, spleen, kidney, skeletal muscle, peripheral blood mononuclear cells (PBMC) as well as tissue specific (stem) cells of mouse skeletal muscle derived stem cells (MUSC), Human bone marrow derived stem cells (hBMSC), Human primary umbilical vein endothelial cell lines (HUVEC) for RNA-seq after treated with the two groups (PBS control and HA solution) for 24hours, respectively.

first: Xiaohui

last: Zou

first: Hongwei

last: Ouyang


title: Investigation of Bach1 function by heme-iron homeostasis in bone marrow derived macrophage

city: Sendai

first: Kazuhiko

last: Igarashi

address: Seiryo 2-1

country: Japan

institute: Tohoku University

summary: Macrophages are central in regulating iron homeostasis. Transcription repressor Bach1 regulates by heme. Here we investigated the relationship between heme-regulated Bach1 and bone marrow derived macrophage. We found that Bach1 KO macrophage showed that up-regulated genes were the process that iron-heme homeostasis and maintenance related gene compared with WT.  Our results suggest that Bach1 expression is important to the heme homeostasis and maintenance in the bone marrow derived macrophage.

overall_design: Gene expression in bone marrow derived macrophages cells of WT and Bach1 KO mice was measured. 3 independent mice were used for each genotype.

first: Miki

last: Watanabe-Matsui


title: Diap3 (Dia2) knock-down in murine marrow-derived mesenchymal stem cells

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Control (non-targeting) and Dia2-targeting siRNA were transfected into murine-derived mesenchymal stem cells and mRNA-Seq analysis was performed two days after transfection.

overall_design:
Murine marrow‐derived mesenchymal stem cells (mdMSC) were isolated from murine marrow and maintained in IMDM as described (Peister et al., 2004).  Cells (passage 6-12) were seeded into 6-well plates at a density of 6,000 cells/cm2 in IMDM and allowed to adhere for 24 hours. Cells were then transfected overnight with control or Dia2 siRNA (50 nM, 5′-CAGAGTCCATGATTCAGAACTTAAT) by Lipofectamine RNAiMax (Invitrogen) and Opti-MEM. Next morning, transfection media was replaced with αMEM. RNA was harvested twenty four hours later (RNeasy mini kit, Qiagen).
Peister, A. et al. Adult stem cells from bone marrow (MSCs) isolated from different strains of inbred mice vary in surface epitopes, rates of proliferation, and differentiation potential. Blood 103, 1662-1668 (2004).

first: Amel

last: Dudakovic

first: Andre

middle: J

last: van Wijnen


title: Changes in miRNAs and miRNA-transcriptome networks in whole blood and monocytes during preterm labor [whole blood 2]

city: Seattle

first: alison

middle: g

last: paquette

state: WA

address: 401 Terry Avenue N

institute: Institute of Systems Biology

summary: The goal of this study was to define relationships between peripheral blood miRNAs and mRNAs of women undergoing idiopathic preterm labor (PTL) and compare network level changes to control women that deliver at term.Using RNA Sequencing we have performed global miRNA and mRNA profiling in both monocytes and whole blood leukocytes of women who underwent PTL (N=15) matched to non-pathological controls (N=30) as a part of the Ontario Birth Study cohort.  We have identified differentially expressed miRNAs, mRNAs and pathways associated with PTL.

overall_design: miRNA was quantified from whole blood and monocytes of women undergoing spontaneous preterm labor compared to nonlabor controls matched on gestational age

first: Stephen

last: Lye

first: Nathan

last: Price


title: Nutrient Sensing Programs Development and Differentiation of the Bovine Embryo

city: Wilrijk

first: Veerle

last: Van Hoeck

state: Antwerp

address: Campus Drie Eiken, Universiteitsplein 1

department: Department of Veterinary Sciences

country: Belgium

institute: University of Antwerp

summary: We aimed to verify whether and to which extent a perturbed nutrient environment during embryo development impact on the capacity of the resultant blastocyst to participate in initial embryo-maternal interactions. For this, in vitro-derived bovine zygotes were exposed to perturbed nutritional environments during the first days of their development. On Day 4 (post fertilization), groups of 5 morulas were transfered to sub-confluent Bovine Endometrial Epithelial Cell (BEEC) monolayers. Embryos were cocultured with BEEC until Day 8, when endometrial cells were recovered for transcriptome analysis.

overall_design: Transcriptomes of Bovine Endometrial Epithelial Cells exposed to distinct groups of embryos were sequenced (NGS) on the Illumina HiSeq2000 platform.

first: Mariana

last: Sponchiado

first: Meriem

last: Hamdi

first: Alfonso

last: Gutiérrez-Adán

first: Katrien

last: Sprangers

first: Gerrit

last: Beemster

first: Peter

last: Bols

first: Mario

last: Binelli

first: Jo

middle: R

last: Leroy


title: Transcriptome responses in wheat roots to colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis

city: Yangling

first: HUI

last: TIAN

institute: Northwest A&F University

summary: The influence of arbuscular mycorrhizal (AM) colonization on the expression of genes in the roots of wheat (Triticum aestivum L.) at the transcriptome level is largely unknown. A pot experiment was established to study the responses of the transcriptome profile in the roots of wheat to colonization by the AM fungus Rhizophagus irregularis using high through-put sequencing methods. The results indicated that the expression of 11,746 genes was regulated by AM colonization, and 64.7% of them were up-regulated genes. 1106 genes were only expressed in roots colonized by AMfungi, and 108 genes were only expressed in non- mycorrhizal roots. The differentially expressed genes (DEGs) were primarily distributed on the 2B, 3B, 2A, 2D, and 5B chromosomes of wheat. The DEGs (including both up- and down- regulated) mainly located on membranes, and functioned in nucleotide binding and transferase activity during cellular protein modification and biosynthetic processes. The data revealed that AMcolonization up-regulated genes involved in the phenylpropanoid biosynthesis pathway and transcription factors which play vital roles in protecting plants from biotic or abiotic stresses. A number of key genes involved in molecular signal biosynthesis and recognition, epidermal cell colonization and arbuscule formation, carbon and nutrients exchange during AM symbiosis were found. All the ammonium transporter (AMT), iron-phytosiderophore transporter, boron, zinc, and magnesium transporter genes found in our study were up-regulated DEGs. One new AM-specific induced AMT and three new AM-specific induced nitrate transporter (NRT) genes were found in the roots of wheat colonized by AMfungi, even though a negative growth response of wheat to AM colonization occurred. The present study provided new information which is important for under- standing the mechanisms behind the development and function of the symbiosis between wheat and AM fungi.

overall_design: 6 samples for the two treatments, and three biological replicates for each treatment

first: Mengjiao

last: Li

first: Runze

last: Wang

first: Hui

last: Tian

first: Yajun

last: Gao


title: Gene are regulated by Myocardin

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression data from 15-day-old mouse testes

city: Gliwice

first: Wiesława

middle: Elżbieta

last: Widłak

address: Wybrzeże Armii Krajowej 15

country: Poland

institute: Maria Sklodowska-Curie Institute – Oncology Center, Gliwice Branch

summary:
Activation of the Heat Shock Factor 1 (HSF1) in spermatogenic cells leads to apoptosis and infertility of males.
To elucidate a mechanisms of apoptosis induced by HSF1 we generated transgenic mice expressing mutated, constitutively active human HSF1 (with a deletion of amino acids 221–315) specifically in spermatocytes (under control of the rat Hspa2 promoter).  We carried  out genome-wide transcriptional analyses in testes of control, wild-type, and transgenic males. Genes that changed the expression due to activation of HSF1 have been identified.

overall_design: On Affymetrix gene chip arrays we analyzed RNA isolated from testes of 15-day-old FVB/N mice (corresponding to the first wave of the meiotic division and beginning of the transgene expression), wild-type and transgenic with active HSF1 transcription factor.

first: Wieslawa

last: Widlak

first: Joanna

last: Polanska

first: Katarzyna

last: Lisowska


title: Genome-wide maps of chromatin state in Ba/F3 cell with PAX5-KIDINS220 fusion protein

city: Kyoto

first: Takuyo

last: Kanayama

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Pediatrics

institute: Kyoto Prefectural University of Medicine

summary: PAX5-KIDINS220 (PAX5-K220) is a novel chimeric fusion gene identified in a pediatric Philadelphia chromosome (Ph)-like acute lymphoblastic leukemia (ALL) patient, but the function of the encoded fusion protein has not yet been analyzed. Here, using in vitro murine assays and ChIP-sequencing, we demonstrate that PAX5-K220 is a nuclear protein that inhibits PAX5 transcriptional activity in a dominant-negative fashion, resulting in a B-cell differentiation block. Gene expression analysis and ChIP-sequencing revealed that PAX5-K220 is associated with multiple pathways related to chemotaxis and migration.

overall_design: Examination of histone modification (H3K4me2) in Ba/F3 cell (murine pro-B cell)

last: kanayama

first: Toshihiko

last: Imamura

first: Kenichi

last: Sakamoto

first: Fumihiko

last: Hayakawa

first: Akihiko

last: Tanizawa

first: Nobutaka

last: Kiyokawa

first: Hajime

last: Hosoi


title: Transcriptome profiling  (RNA-seq) of wild type and MYOCD overexpression in human lung cancer cell line A549.

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of wild type and MYOCD overexpression in human lung cancer cell line A549.
Methods: mRNA profiles of wild type（WT） and MYOCD overexpression (MYOCD)  human lung cancer cell line A549 were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR.

overall_design: mRNA profiles of human lung cancer cell line A549 with no treatment (WT) and MYOCD overexpression (MYOCD) were generated by deep sequencing using Illumina HiSeq 4000.

first: Haixia

last: Yang

first: Liang

last: Chen


title: Transcriptome profiling  (RNA-seq) of wild type and MYOCD Knockdown in human lung cancer cell line A549.

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of wild type and MYOCD Knockdown in human lung cancer cell line A549.
Methods: mRNA profiles of wild type（WT） and Dox inducible MYOCD Knockdown (MYOCD−/−)  human lung cancer cell line A549 were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR.

overall_design: mRNA profiles of human lung cancer cell line A549 with no treatment (WT) and MYOCD knockdown (MYOCD−/−) were generated by deep sequencing using Illumina HiSeq 4000.


title: 16p11.2 Reciprocal Genomic Disorder Tissue-Specific Mouse Molecular Signatures

city: Boston

first: Michael

last: Talkowski

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Transcriptome analyses of 16p11.2 reciprocal genomic disorder (RGD) deletion and wild type mouse across cortex, striatum and cerebellum tissues.

overall_design: RNA sequencing analysis of mice harboring syntenic 7qF3 deletions, and wild-type controls, across cortex, striatum, and cerebellum (8 16p11.2 Deletion, 8 matching WT controls)

first: Parisa

last: Razaz


title: Role of AtMLKLs in response to powdery mildew fungus

city: Cologne

first: Takaki

last: Maekawa

address: Carl-von-Linne Weg 10

country: Germany

institute: Max-Planck Institute for Plant Breeding Research

summary: We performed RNA-sequencing of Golovinomyces orontii-infected Arabidopsis leaves of wild type, the double or triple mutants of AtMLKLs to examine the role of AtMLKLs in response to the powdery mildew fungus.

overall_design: Leaf samples from at least three independent plants were collected at 48 hours post inoculation of conidia of the powdery mildew fungus Golovinomyces orontii. Mock samples were collected from plants without conidia inoculation.

first: Lisa

middle: K

last: Mahdi


title: Gene expression signatures for GSC2 after treated by clofoctol for 6 hours

city: beijing

first: Yan

last: Hu

state: beijing

address: dongdan san tiao No 5

department: Department of Molecular Biology and Biochemistry

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

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

summary: To address the mechanisms by which clofoctol suppresses growth of GSCs, we performed gene expression profiling using mRNA microarray analysis. GSC2 were incubated with 1‰ DMSO or clofoctol at 3 μM and 10 μM for 6 h before RNA was isolated. Unsupervised hierarchical clustering revealed a high level of consistency across biological replicates. To gain insight into the pathways regulated by clofoctol, we investigated the changes in genes treated with 10 μM clofoctol vs. control using Ingenuity Pathway Analysis (IPA). Diseases and biofunction analysis suggested that clofoctol altered the expression of genes primarily associated with cell apoptosis. Then, to find the crucial genes involved in decreasing cellular growth or inducing cell apoptosis after clofoctol treatment, we analyzed differentially expressed genes. Seventy-six upregulated genes (P <0.05, fold-change >2, FC absolute (10 µM) / FC absolute (3 µM) >3) and 63 downregulated genes (P <0.05, fold-change >2) were differentially expressed in both 3 μM and 10 μM clofoctol treatment groups. To narrow the range of candidates, we then analyzed the differentially expressed genes that showed a relationship with patient survival, according to CGGA (Chinese Glioma Genome Atlas) database, followed by real-time PCR analysis of the expression change in three glioma stem cell lines, GSC2, GSC5, U251 SLC. Only the 5 upregulated genes, LDHB, FGD5-AS1, PDZRN1, KLF13 and NRSN1 were ultimately selected.

overall_design: Gene expression of GSC2 cells was measured at 6 hours after exposure to 0 μM, 3 μM, 10 μM of clofoctol. Three independent experiments were performed at each concentrations.

first: Xiaozhong

last: Peng


title: Changes in miRNAs and miRNA-transcriptome networks in whole blood and monocytes during preterm labor [monocytes 2]

first: alison

last: paquette

first: Stephen

last: Lye

first: Nathan

last: Price


title: RNA-sequencing of chicken primary myoblasts and myotubes

city: Guangzhou

first: chen

last: genghua

address: WuShan

institute: South China Agricultural University

summary: Chick is an ideal model system for myogenesis study. Lots of genes would change their expression during myogenesis, however, is there any difference about gene expression between chick and mice? Our study represents the first detailed analysis of the transcriptomes of chicken primary myoblasts and myotubes, with biologic replicates, generated by RNA-seq technology. The data reported here may provide an important understanding of the genes involved in the regulation of chicken myogenesis.

overall_design: Examination of differentially expressed genes in chicken myoblasts versus myotubes

first: Wen

last: Luo

first: Xiquan

last: Zhang


title: Transcriptome analysis of electroporated/GFP+ cells from embryonic mouse cortex E15.5 (E13.5 + 48 h), shRNA against circSlc45a4, mRNA Slc45a4 and scramble KD

city: Berlin

first: Nikolaus

last: Rajewsky

state: Berlin

address: Robert-Rössle-Str. 10

department: Systems Biology of Gene Regulatory Elements

institute: Max-Delbrück Center for Molecular Medicine / Berlin Institute for Medical Systems Biology

summary: We perturbed the expression levels of circSlc45a4 and mRNA Slc45a4 in developing mouse cortex (E15.5) by RNAi/shRNAs. 48 h post-electroporation the cells were isolated by FACS (GFP+), RNA was extracted with Trizol and polyA+ libraries were generated with Illumina TruSeq Stranded mRNA LT Sample Prep Kit. We find many significant changes in the transcriptomic profile after knockdown of circSlc45a4 and mRNA Slc45a4, that are distinct from each other.

overall_design: Examination of 3 different shRNAs against circSLC45A4 and 2 different shRNAs against mRNA Slc45a4 vs. 1 scrambled siRNAs, 3 biological replicates per shRNA mix.

first: Christin

last: Suenkel


title: HDAC Inhibitor-Induced Acetylation of KRAS Confers A Pro-Oncogenic Effect Limiting Treatment Response in Colorectal Cancer

first: Florian

last: Uhlitz

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

summary: The limited clinical utility of HDAC inhibitors for the treatment of colorectal cancer (CRC) has until now remained an unresolved conundrum. Our findings provide comprehensive mechanistic insight into the ineffectiveness that defines HDAC inhibitors as a monotherapy for CRC. We identified that inhibition of HDAC2 promotes the emergence of a super-oncogenic KRAS by inducing K5 acetylation that fosters a previously undiscovered electrostatic interaction with R67 conserved in RAF kinases. This post-translational modification facilitates an increase in the binding affinity to this family of downstream RAS effectors, which translates into an immediate and persistent hyperactivation of the downstream MAPK-signaling. The concomitant instability of its co-conspirator c-MYC enables cells selectively harboring oncogenic KRAS to enter a protective state of reversible cell cycle arrest characterized by a senescence-like phenotype. Demonstratively, preventing this phenomenon from taking place provides a compelling alternative strategy for improving the prospects of HDAC inhibitor treatment for CRC.

overall_design: CaCO-2et KRAS G12V and CaCO-2et KRAS WT were treated with doxycycline to induce an ectopic expression of KRAS G12V and WT respectively. Cells were also treated with either DMSO or MS-275 for the specified duration (1, 6, 24 and 72hrs).

first: S

last: Ispasanie

last: Kistler

first: A

last: Heberle

first: F

first: K

last: Kasack

last: Klotz-Noack

first: L

last: Wang

middle: H

last: Lee

first: B

last: Gastl

last: Boehme

first: N

last: Kuhn

first: R

last: Schäfer

first: D

last: Horst

first: X

first: G

last: Dittmar

last: Blüthgen

last: Thedieck

last: Campbell

first: C

last: Sers


title: High-Fructose Corn Syrup Enhances Intestinal Tumor Growth in Mice

first: Charles

last: Murphy

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Excessive consumption of beverages sweetened with high-fructose corn syrup (HFCS) is associated with obesity and with an increased risk of colorectal cancer. Whether HFCS contributes directly to tumorigenesis is unclear. We investigated the effects of daily oral administration of HFCS in APC mutant mice, which are predisposed to develop intestinal tumors. The HFCS-treated mice showed a dramatic increase in tumor size and tumor grade in the absence of obesity or metabolic syndrome. HFCS increased the levels of fructose and glucose in the intestinal lumen and serum, respectively, and the tumors absorbed  both sugars. Within the tumors, fructose was converted to fructose-1-phosphate, leading to activation of glycolysis and increased synthesis of fatty acids that support tumor growth. These mouse studies support the hypothesis that the combination of dietary glucose and fructose, even at a moderate dose, can enhance tumorigenesis.

overall_design: We investigated tumor and small intestines in APC mutant mice, which are predisposed to develop intestinal tumors.

first: Marcus

middle: D

last: Goncalves

first: Jihye

last: Yun


title: Gene expression regulated by CSA and CSB in neuroblastoma cell line

first: Yuming

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

summary: Mutations in the CSA and CSB genes are causative of Cockayne syndrome neurological disorder. Since the identification of the indispensable functions of these two proteins in transcription-coupled repair and restoring RNA synthesis following DNA damage, the paradoxical milder clinical spectrum in CS-A patients has been puzzling. In this study we compared the effect of a CSA and a CSB defect at the levels of the cell and the intact organism. We showed that CSA-deficient zebrafish embryos exhibited modest hypersensitive to UV damage than CSB depletion. We found that loss of CSA can effectively release aggregation of mutant crystallin proteins in vitro. We described the distinct effect of CSA and CSB on neuritogenesis and elucidated the differentiated gene expression pathways regulated by these two proteins. Our data demonstrate convergent and divergent roles for CSA and CSB in DNA repair and transcription regulation and provide explanations for the reported differences between CS-A and CS-B patients.

overall_design: mRNA profiles of CSA-depleted, CSB-depleted and WT SH-SY5Y cells were generated by deep sequencing, using Illumina HiSeq X Ten in paired-end mode.

first: Zhenzhen

last: Wu

first: Qian

last: Yu

first: Xun

last: Zhu

first: Yingying

last: Xu


title: Transition state dynamics during a stochastic fate choice

status: Public on Mar 28 2019

city: London

first: Vlatka

last: Antolovic

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

country: United Kingdom

institute: University College London

summary: A stochastic differentiation programme shows stepwise separation of cell fate, with initiation of cell-type specific gene expression coupled to global transcriptome changes shared by all cells.

overall_design: Single cell transcriptomes of disaggregated mound cells were determined using the Fluidigm C1 system. An average of around 3 million reads were generated from each single cell library. We excluded seven cells (marked in Supplementary file Dd_Mound_RawCounts.csv) based on the following criteria: total number of reads was lower than 5 x 10^5, percentage of mitochondrial reads was higher than 15%, or the data was missing a contiguous part of the transcriptome.  We obtained a total of 116 cells, from 3 experimental replicates.

first: Jonathan

last: Chubb

first: Tchern

last: Lenn

first: Agnes

last: Miermont


first: huanwei

last: huang

summary: Purpose: Genome-wide DNA-binding analysis for Myocardin in human lung cancer cell line A549

overall_design: MYOCD was stably overexpressed in lung cancer cell line A549 by pWPI vector. The stable cell line was harvested and simultaneously immune precipititated by IgG or anti-Myocardin antibody.

first: Haixia

last: Yang

first: Liang

last: Chen


title: Transient stabilization, rather than inhibition of MYC amplifies extrinsic apoptosis and therapeutic responses in refractory B-cell lymphoma

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

state: PA

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Identification of gene expression changes following inhibition of GSK-3 in Burkitt lymphoma

overall_design: We profiled cells treated for 0, 3, and 6 hours with the GSK-3 inhibitor CHIR99021 in biological triplicates

first: Colleen

last: Harrington

first: Elena

last: Sotillo


title: Chemical conversion of human fetal astrocytes into neurons through modulation of multiple signaling pathways

city: University Park

first: Gong

address: Old Main

institute: Penn State University

summary: To characterize the transcriptome of our cultured human astrocyte cell line, RNA-seq was performed and the data were compared with other available datasets.

overall_design: RNA profiles of HA1800 human astrocyte , 3 replicates.

first: Jiuchao

last: Yin

first: Ningxin

last: Ma


title: HOIL-1/RBCK1 promotes p53 degradation in Renal cancer cells

first: Sifan

address: Fucheng Road 52#

institute: Peking University Cancer Hospital & Institute

summary: We performed RBCK1 depletion in renal cancer cells along with RNA sequencing. The expression profiling showed p53 signaling as a potential RBCK1 target and the conclusions were also verified in clinical samples.

overall_design: RNA sequencing in 1 renal cell lines with si-Control or si-HOIL-1/RBCK1

first: Jun

last: Guo


title: The miRNome in CFBE41o- cells stably transduced with F508del-CFTR and WT-CFTR

city: Charlottesville

first: Agnieszka

last: Swiatecka-Urban

state: VA

address: 409 Lane Road

department: Pediatrics

institute: University of Virginia School of Medicine

summary: The purpose of this study was to explore baseline expression of miRNome in Cystic Fibrosis Bronchial Epithelial (CFBE41o-) cells stably transfected with wild type (WT) Cystic Fibrosis Transmembrane Conductance regulator (CFTR) and F508del-CFTR. To fulfill this goal miRNA sequencing was done to see miRNA landscape in CFBE41o- Cells with homozygous F508del mutated CFTR and in CFBE41o- Cells with homozygous WT-CFTR, without any treatment condition.

overall_design: Sequencing microRNAs in WT-CFBE41o- and F508delCFBE41o- cells without any treatment

first: Nilay

last: Mitash

first: Fangping

last: Mu


title: A heterochromatin-specific RNA export pathway facilitates piRNA production

city: Aarhus

first: Peter

last: Andersen

state: Denmark

address: Universitetsbyen 83

department: MBG

country: Denmark

institute: Aarhus University

summary: PIWI-interacting RNAs (piRNAs) guide transposon silencing in animals. The 22-30nt piRNAs are processed in the cytoplasm from long non-coding RNAs. How piRNA precursors, which often lack RNA processing hallmarks of export-competent transcripts, achieve nuclear export is unknown. Here, we uncover the RNA export pathway specific for piRNA precursors in the Drosophila germline. This pathway requires Nxf3-Nxt1, a variant of the hetero-dimeric mRNA export receptor Nxf1-Nxt1. Nxf3 interacts with UAP56, a nuclear RNA helicase essential for mRNA export, and CG13741/Bootlegger, which recruits Nxf3-Nxt1 and UAP56 to heterochromatic piRNA source loci. Upon RNA cargo binding, Nxf3 achieves nuclear export via the exportin Crm1, and accumulates together with Bootlegger in peri-nuclear nuage, suggesting that after export, Nxf3-Bootlegger delivers precursor transcripts to the piRNA processing sites. Our findings indicate that the piRNA pathway bypasses nuclear RNA surveillance systems to achieve export of heterochromatic, unprocessed transcripts to the cytoplasm, a strategy also exploited by retroviruses.

overall_design: This study characterizes an RNA export pathway that drives expression of small RNAs (piRNAs) from heterochromatin in Drosophila

first: Julius

last: Brennecke

first: Mostafa

last: ElMagrabhy

first: Katharina

last: Meixner

first: Thomas

last: Lendl

first: Florian

last: Puehringer

first: Laszlo

last: Tirian


title: 5-hydroxymethylcytosine Promotes Productive Transcription and Inhibits Spurious Promoters

city: Oxford

first: Skirmantas

last: Kriaucionis

address: Old Road Campus Research Building

institute: Ludwig Institute for Cancer Research

type: Methylation profiling by high throughput sequencing

summary: Covalent DNA modifications play vital roles during animal development. While 5-methylcytosine (5mC) is important for imprinting, X chromosome inactivation and transcriptional repression, the function of 5-hydroxymethylcytosine (5hmC) is less well defined. Recent studies indicate that 5hmC can be stable and long-lived in some cell types, suggesting roles beyond a DNA demethylation intermediate. Here we show that oxidation of 5mC to 5hmC enhances transcription of a specific repertoire of genes. 5hmC upregulates transcription by counteracting the repressive effects of promoter-proximal 5mC, while supressing the ability of gene body resident spurious transcription initiation sites to produce mature transcripts. By contrast, the equivalent hypomethylation results in chaotic gene expression potentiating a broad collection of genes and cryptic promoters. Our observations provide an explanation why some post-mitotic cell types favour high 5hmC in the genomes, while equivalent global hypomethylation is rarely observed.

overall_design: 94 samples in total. 4 hmC-Seal: 2 conditions, 2 biological replicates, total genomic DNA as an input DNA. 4 MeDIP: 2 conditions, 2 biologial replicates, total genomic DNA as an input DNA. 4 EpiJET: 2 conditions, 2 biologial replicates, total genomic DNA as an input DNA. 63 RNA-Seq: 6 conditions, pair-wise comparison was performed within one experiment containg 3 replicates. 9 PRO-Seq: 3 conditions, 3 biologial replicates. 9 PRO-Cap: 3 conditions, 3 biologial replicates.

first: Pijus

last: Brazauskas

first: Hiromi

last: Tagoh

first: Olena

last: Yavorska


title: Alteration of the gene expression profile in the Hox13dKO

city: Nagoya

first: Atsushi

last: Kuroiwa

state: Aichi

address: Furo-cho, Chkusa-ku

department: Graduate School of Science

institute: Nagoya University

summary:
The free limb is subdivided into three anatomical domains along the proximodistal axis: the stylopod, zeugopod and autopod. These domains possess a specific number and pattern of the bones and each bone possesses unique morphology and length. During limb development, the mesenchymal cells of limb bud first forms precartilaginous aggregates which eventually grow and differentiate into the limb cartilage. Expression of Hox genes belonging to the Abd-B family, Hox9-13, is closely related to the anatomical domains of the limb bones and crucial for controlling morphogenesis and patterning of the limb cartilage. Hoxa13 and Hoxd13 are expressed in the autopodal mesenchyme and double KO mice have smaller autopods during the embryonic stage and a fan-shaped cartilage develops instead of the normal five digits. Thus, Hoxa13 and Hoxd13 are crucial for the cartilage patterning in the autopod. Since Hox encodes a transcription factor, Hox target genes function in region/compartment-specific formation of the precartilaginous condensation, cellular differentiation and proliferation of the cartilage.
We used microarray to identified downstream genes of Hox13 in the autopod as exhibiting changes in the expression in the Hox13dKO mutant embryos.

overall_design: Hoxa13 and Hoxd13 show overlapping expression in the autopodal mesenchyme and cooperatively function in autopodal cartilage pattern formation. Hoxd11 and Hoxd12 are also expressed in the autopodal mesenchyme and cooperate in autopodal cartilage pattern formation in a gene dosage-dependent manner together with Hoxa13 and Hoxd13. Specifically, homozygote with simultaneous deletion of Hoxd11,12,13 (HoxDdel) exhibited more severe adult cartilage phenotypes than Hoxd13 KO homozygotes. To increase the sensitivity in analyzing the Hox function we used Hoxa13-/- ; HoxDdel/del double homozygotes (Hox13dKO). We isolated RNA from the autopod around E11.25 wild type and Hox13dKO embryos and quantified the transcript levels by Genechip. In the wild-type autopod at E11.25, Hoxa13 and Hoxd13 are expressed in the mesenchyme. At this stage, the precartilaginous condensation of the carpal/tarsal region is visible and the precartilaginous condensation of metacarpal/metatarsal region begin to form as protrusions from the carpal/tarsal condensation. We isolated the autopodal tissue corresponding to the Hoxd13 expressing region from both fore- and hindlimb buds.

first: Kuroiwa

last: Atsushi


title: Genome-wide mapping of Hoxa11 and Hoxa13 binding sites in the limb bud

summary: Hox genes control domain specific cartilage pattern formation along the proximodistal axis. Hoxa11 and Hoxd11 (Hox11) show overlapping expression in the mesenchyme of the zeugopod and regulate cartilage growth and differentiation. Hoxa13 and Hoxd13 (Hox13) are expressed in the autopodal mesenchyme and are crucial for the autopodal cartilage patterning. Since both Hox11 and Hox13 are involved in the limb cartilage development, they may share the target genes. To identify common target genes among the Hoxa11 and Hoxa13, we performed ChIP-Seq analysis using specific antibody.

overall_design: Soluble chromatin was prepared from mouse limb bud and the Hox binding DNA was recovered by immune-precipitation. Then the enriched sequence was determined by NGS analysis.

first: Nayuta

last: Yakushiji-Kaminatsui


title: Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [microarray]

city: Medford

first: Eric

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

summary: In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher.  We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq and microarray, as well as another low-cost highly multiplexed technique known as 3’ digital gene expression (3’ DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens.  SFL demonstrated improved performance over 3’ DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from in vivo lung cancer mutation signatures.

overall_design: Microarray RNA expression for immortalized human bronchial epithelial cells (AALE) exposed to chemical and genotypic perturbations

first: Elizabeth

last: Moses

first: Xiaohui

last: Xiao

first: Gang

last: Liu

first: Joshua

last: Campbell

first: Catalina

last: Perdomo

first: Stefano

last: Monti


title: GALNT10 knockdown in  A549 cell line and over-expressing in the H322 cell line

status: Public on Mar 27 2019

first: Jian

last: Zhang

address: 1838 Guangzhou Blvd North

department: Department of Medical Genetics

institute: Southern Medical University

summary: Aberrant mucin-type O-glycosylation affects many cellular properties and is associated with many cancers. N-acetylgalactosaminyltransferase 10 (GALNT10) is a GalNAc-transferase that initiates protein O-glycosylation. The aim of this study was to explore the role of GALNT10 in lung adenocarcinoma. Immunohistochemistry was performed to study the expression of GALNT10 in an lung adenocarcinoma tissue microarray. We found that GALNT10 is frequently down-regulated in lung adenocarcinoma tissues and is associated with pathological classification and TNM stage. Additionally, we demonstrated that knockdown of GALNT10 with small interference (si) RNA promoted cell proliferation, cell colony formation and cell invasion capacity in A549 cells by using CCK8 assay, flow cytometry, cell colony formation, and transwell invasion assay.Moreover, whole genome microarray analysis showed that 287 genes were up-regulated and 137 were down-regulated in A549 cells upon GALNT10 knockdown. Functional enrichment analysis reveal that GALNT10 knockdown in A549 cells leads to differential gene expression in pathways, including TNF signaling pathway. These findings suggest that down-regulation of GALNT10 plays an important role in the cell proliferation and invasive behavior of lung adenocarcinoma via modifying O-glycosylation and activity of TNF pathway. In addition, we suggest that GALNT10 may be a tumor suppressor gene in lung adenocarcinoma and that targeting GALNT10 could be a promising approach for lung adenocarcinoma therapy.

overall_design: Gene expression analysis was carried out as previously described (Wang et al., 2014; Huang et al., 2015). Briefly, total RNA from control and GALNT10 siRNA knockdown A549s cells were extracted in triplicates using GeneJET RNA Purification kit (Thermo Scientific) following the manufacturer’s protocol and quantified by NanoDrop spectrophotometer. The quality of the RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent). Fluorescently labeled cDNA targets were generated from 10 μg of total RNA from each corresponding A549s cell clone following user’s manual. Agilent Gene Expression Hybridization Kit was used for hybridization according to the manufacturer’s instruction. Array hybridization, washing, scanning, data extraction and analyses were performed as previously described (Keita et al., 2013). Furthermore, we investigated the function GALNT10 of by over-expressing GalNAc-T10 in the H322 cell line and by down-regulating GalNAc-T10 expression by shRNA interference in the A549 cell line, and by evaluating proliferation, invasion and apoptosis in the corresponding cells. These in vitro experiments showed that increased gene expression of GalNAc-T10 could inhibit the growth, invasion and promote H322 cell apoptosis. On the contrary, reduced expression of the GalNAc-T10 gene can promote the growth, invasion, and inhibit A549 cell apoptosis.

first: Yuan

last: Gao


title: RNA seq analysis of TEs in L1RP-expressing HEK293T cells

city: Baltimore

first: Kathleen

middle: Helen

last: Burns

state: MD

address: 733 N. Broadway, MRB 447

department: Pathology

institute: Johns Hopkins University School of Medicine

summary: Transfection of HEK293T with L1RP or control plasmid

overall_design: 3 independent transfections of HEK293T cells transfected with pCEP puro L1RP plasmid or pCEP puro empty plasmid

first: Wan

last: Yang

first: Daniel

last: Ardeljan


title: The long noncoding RNA lnc-ob1 facilitates bone formation by upregulating Osterix in osteoblasts

first: Gong

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

summary: Long noncoding RNAs (lncRNAs) have emerged as integral regulators of physiology and disease, but specific roles of lncRNAs in bone disease remain largely unknown. Here, we show that lnc-ob1 regulates osteoblast activity and bone formation in mice by upregulating the osteogenic transcription factor Osterix. Expression of lnc-ob1 is enriched in osteoblasts and upregulated during osteoblastogenesis. We demonstrate that osteoblast-specific knock-in of lnc-ob1 enhances bone formation and increases bone mass. Pharmacological overexpression of lnc-ob1 specifically in osteoblasts confers resistance to ovariectomy-induced osteoporosis in mice. In humans, expression of the homologue, lnc-OB1, decreases with age in osteoblasts of patients with osteoporosis. Mechanistically, lnc-ob1 upregulates the expression of Osterix in mouse and human osteoblasts, probably via inhibition of H3K27me3 methylation. Our data indicate that lnc-OB1 regulates bone formation and might be a drug target for the treatment of osteoporosis.

overall_design: High throughput RNA-seq was performed on human and mouse undifferentiated BMSCs (0 week) and osteoblastic differentiated BMSCs (2 weeks). RNA-seq was also performed on the osteoblast isolated from lnc-OB1 knockdown KI mice and N.C control KI mice.

first: Yao

last: Sun

first: Mingxiang

last: Cai

first: Jiayong

last: Zhong

first: Li

first: Jia

first: Fujun

last: Jin

first: Hui

last: Xue

first: Xiangning

first: Huisheng

first: Yongbiao

first: Dong

last: Jiang

first: An

last: Hong

first: Xunming

last: Ji

first: Zuolin

last: Wang

first: Xiaogang


title: Janus kinase 1 plays a critical role in mammary cancer progression

city: Detroit

first: Kay-Uwe

last: Wagner

state: MI

address: 421 East Canfield, EL01TM

department: Department of Oncology

institute: Barbara Ann Karmanos Cancer Institute  Wayne State University School of Medicine

summary: Janus kinases (JAKs) and their downstream STAT proteins play key roles in cytokine  signaling, tissue homeostasis, and cancer development. Using a novel breast cancer  model that conditionally lacks the Janus kinase 1, we show here that JAK1 is essential  for IL-6 class inflammatory cytokine signaling and plays a critical role in metastatic  cancer progression. JAK1 is indispensable for the oncogenic activation of STAT1,  STAT3, and STAT6 in ERBB2-expressing cancer cells, suggesting that ERBB2  receptor tyrosine kinase complexes do not directly activate these STAT proteins in  vivo. A genome-wide gene expression analysis revealed that JAK1 signaling has  pleiotropic effects on several pathways associated with cancer progression. We  established that FOS and MAP3K8 are targets of JAK1/STAT3 signaling that promote  tumorsphere formation and cell migration. The results highlight the significance of  JAK1 as a rational therapeutic target to block IL-6 class cytokines that are master  regulators of cancer-associated inflammation.

overall_design: Total RNA was extracted from JAK1 deficient mammary tumor cell lines and wildtype controls expressing JAK1 using the RNeasy Mini Kit (Qiagen).

first: Patrick

last: Rädler

first: Barbara

middle: L

last: Wehde

first: Hridaya

last: Shrestha

first: Stevi

last: Johnson

first: Aleata

middle: A

last: Triplett


title: Transcriptome landscape during tenderization in sea cucumber Apostichopus japonicus

city: Dalian

first: Xiufang

last: Dong

state: Liaoning

address: No.1st Qinggongyuan, Ganjingzi district

institute: Dalian Polytechnic University

summary: The gene expression profiles associated with tenderization in body wall of sea cucumber (Apostichopus japonicus) were determined

overall_design: Examination of the transcript from the body wall treated at 37°C for 0 h (CON), 1 h (T_1h) and 3 h (T_3h) using Illumina HiSeq™ 4000 platform.

first: Hang

last: Qi


title: Light releases the TCP4-SAUR16/50 transcription module from the repression of PIF3 to facilitate cotyledon opening during de-etiolation

city: New Haven

first: jie

last: dong

state: Connecticut

address: 165 prospect st, OML 257

department: MCDB

institute: yale university

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

overall_design: Refer to individual Series


title: Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [SFL]

first: Eric

last: Reed

state: MA

overall_design: Highly-multiplexed RNA-seq for immortalized human bronchial epithelial cells (AALE) exposed to chemical and genotypic perturbations

first: Elizabeth

last: Moses

first: Xiaohui

last: Xiao

first: Gang

last: Liu

first: Joshua

last: Campbell

first: Catalina

last: Perdomo

first: Stefano

last: Monti


title: Light releases the TCP4-SAUR16/50 transcription module from the repression of PIF3 to facilitate cotyledon opening during de-etiolation [ChIP-Seq]

summary: Etiolated Arabidopsis seedlings open their cotyledons and halt rapid elongation of hypocotyl when exposed to light (de-etiolation). Major light responsive components in this process have been identified and signaling pathways revealed, yet how the organ-specific light responses are achieved remains unknown. Here we report that a developmental regulator TCP4 (TEOSINTE BRANCHED1, CYCLOIDEA, and PCF) participates in photomorphogenesis and facilitates light-induced cotyledon-opening. We demonstrate that TCP4-like transcriptional factors, which predominantly express in cotyledons of both light and dark seedlings, activate SAUR16 and SAUR50 in response to light. Light repressor PIF3 (or PIFs, phytochrome-interacting factors), which accumulates in etiolated seedlings and rapidly declines upon light exposure, inhibits TCP4 promoter-binding and prevents activation of SAUR16/50 in darkness. Our study reveals how an interplay between light responsive factors and developmental regulators leads to signal-dependent and tissue-specific regulation of gene expressions, which ultimately resulted in organ-specific light responses during de-etiolation.

overall_design: To identify the potential targets of TCP4 in Arabidopsis at seedling stage.

first: JIE

last: DONG

first: NING

last: SUN

first: JING

last: YANG

first: ZHAOGUO

last: DENG

first: GENJI

last: QIN

first: HANG

last: HE

first: XING

middle: W

first: VIVIAN

last: IRISH

first: HAODONG

last: CHEN

last: WEI


title: Protein Tyrosine Phosphatase Non-receptor 3 Acts as a Tumor Suppressor and Boosts TGF-b Signaling Independent of its Phosphatase Activity

city: Hang Zhou

first: BO

last: YUAN

address: Zijingang Campus

institute: Zhejiang University

summary: Transforming Growth Factor  b (TGF-b) controls a variety of cellular functions during development. Abnormal TGF-b responses are commonly found in human diseases such as cancer, suggesting that TGF-b signaling must be tightly regulated. Here we report that Protein Tyrosine Phosphatase Non-receptor 3 (PTPN3) profoundly potentiates TGF-b signaling independent of its phosphatase activity. PTPN3 stabilizes TGF-b type I receptor (TbRI) through attenuating the interaction between Smurf2 and TbRI. Consequently, PTPN3 facilitates TGF-b-induced R-Smad phosphorylation, transcriptional responses and subsequent physiological responses. Importantly, the leucine-to-arginine substitution at amino acid residue 232 (L232R) of PTPN3, a frequent mutation found in intrahepatic cholangiocarcinoma (ICC), disable the role to enhance TGF-b signaling and abolishes its tumor suppressive function. Our findings have revealed a vital role of PTPN3 in regulating TGF-b signaling during normal physiology and pathogenesis.

overall_design: mRNA profiles of HaCaT siControl and siPTPN3 cells with or without TGF-beta were generated by deep sequencing, using Illumina HiSeq X Ten. There are four samples for transcriptome sequencing (RNA-Seq).

first: Bo

last: Yuan

first: Jin

middle: Q

last: Cao

first: Han

middle: C

last: Zhang

first: Fei

last: Wang

first: Ye

middle: Z

last: Zhu

first: Mu

first: You

last: Ye

first: Le

last: Ma

first: De

last: Xu

first: Ning

middle: Y

first: Yi

last: Li

first: Bin

last: Zhao

first: Ping

first: Jian

last: Jin

first: Xi

last: Chen

first: Li

last: Shen

first: Xia

last: Lin

first: Xin

last: Feng


title: Expression data from U266 MM cells untreated or treated with trabectedn

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

summary:
Trabectedin triggered apoptosis in primary MM cells and MM cell lines in both 2D and 3D in vitro assays
To shed light on molecular mechanisms underlying the anti-MM activity of trabectedin, modifications in the gene expression profile of U266 cells, untreated or treated with 2.5 nM of trabectedin for 24 h were evaluated.

overall_design: 3x10^6 U266 MM cells obtained from two different experiments were treated with PBS or 2.5 μM of trabectedin for 24 h. RNA extraction was then performed transcriptome profiles were evaluated by using Human transcriptom arrays from Affymetrix.

first: Maria

last: Cucè

first: Francesca

last: Scionti

first: Teresa

last: Di Martino

first: Pierosandro

last: Tagliaferri

first: Pierfrancesco

last: Tassone


title: Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [3pDGE]

first: Eric

last: Reed

overall_design: 3' Digital Gene Expression (3'DGE) for immortalized human bronchial epithelial cells (AALE) exposed to chemical and genotypic perturbations

first: Elizabeth

last: Moses

first: Xiaohui

last: Xiao

first: Gang

last: Liu

first: Joshua

last: Campbell

first: Catalina

last: Perdomo

first: Stefano

last: Monti


title: Influence of substrate stiffness on chemotherapeutic response in breast cancer

city: Bethesda

first: Margaret

last: Cam

institute: NIH

summary:
Mechanical feedback from the tumor microenvironment regulates an array of processes underlying cancer biology. Routine culture and adaptation of cancer cell lines to unnaturally rigid plastic or glass substrates leads to profound changes in their growth, metastatic potential and potentially chemotherapeutic response. Microarray studies were conducted to probe the impact of substratum stiffness on the regulation of genetic pathways in mammary tumor cells, and immortalized cancer cell lines, that modulate sensitivity and resistance towards clinically-approved chemotherapeutics
We used microarrays to detail the global programme of gene expression underlying cellular response to substrates of different mechanical stiffness.

overall_design: mammary tumor cells, isolated from FVB/N-Tg(MMTV-PyVT)634Mul/J transgenic mice (referred to as MMTV-PyVT), or an immortalized human breast cancer cell line (MDA-MB-453) were seeded onto fibronectin-coated polyacrylamide gels of 5 and 30 kPa stiffness, or glass as a control. After 5 days of culture, cellular RNA was extracted from cells seeded onto gels of varying stiffness in the array and utilized for hybridization on Affymetrix mouse or human gene microarrays. Four replicates from each condition were analyzed, and data referenced against cells seeded onto glass as controls. Array data were processed using the affy and limma bioconductor packages.

first: Scott

last: Medina

first: Brian

last: Bush

first: Maggie

first: Emily

last: Sevcik

first: Frank

last: DelRio

first: Kaustav

last: Nandy

first: Joel

middle: P

last: Schneider


title: miRNA expresion data from human induced pluripotent stem cells

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

institute: National Institute of Health and Sciences

summary: We used miRNA array to detail the global miRNA expression of human induced pluripotent stem cells

overall_design: 10 human induced pluripotent stem cell lines (201B7, 253G1, 409B2, HiPS-RIKEN-1A, HiPS-RIKEN-2A, HiPS-RIKEN-12A, Tic, mc-iPS, ATCC-DYR0100hiPSc, ATCC-DYR0103hiPSc)

first: T

first: F

last: Oohashi

first: S

last: Yasuda

first: Y

last: Sato


title: Prediction of VEGF-C as a key target of pure total flavonoids from Citrus against NAFLD in mice via network pharmacology

city: Hangzhou

first: Chen

last: Zhiyun

address: No. 9, Street 9, Xiasha economic development zone, Jianggan district

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

summary: Pure total flavonoids from Citrus (PTFC) effectively reduce the symptoms of non-alcoholic fatty liver disease (NAFLD). Our previous microarray analysis uncovered the alterations of important signaling pathways in the treatment of NAFLD with PTFC. However, the underlying core genes that might be targeted by PTFC, which play important roles in the progression of NALFD are yet to be identified. In this study, we predicted the vascular endothelial growth factor-C (VEGF-C) as potential key molecular target of PTFC against NAFLD via network pharmacology analysis. The network pharmacology approach presented here provided important clues for understanding the mechanisms of PTFC treatment in the development of NAFLD.

overall_design: 12 samples were analyzed. The samples included 4 groups, each group including three replicates. The control group is named ND.

first: Wei

last: Hong

first: Songsong

last: Li

first: Liyan

last: Wu

first: Beihui

last: He

first: Jianping

last: Jiang

first: Zhiyun

last: Chen


title: Light releases the TCP4-SAUR16/50 transcription module from the repression of PIF3 to facilitate cotyledon opening during de-etiolation [RNA-seq]

first: jie

last: dong

overall_design: Cotyledon mRNA profiles of 4-day-old dark grown Col, mTCP4#4 and mTCP4#10 seedlings were generated by deep sequencing.

first: Jie

last: Dong

first: Ning

last: Sun

first: Jing

last: Yang

first: Zhaoguo

last: Deng

first: Genji

last: Qin

first: Hang

first: Xing

first: Vivian

last: Irish

first: Haodong

last: Wei


title: Evaluation of Transcriptomic Change in Late-Delayed Radiation following Fractionated Whole Brain Irradiation and High Dose Total Body Irradiation in Non-Human Primates

city: Winston-Salem

first: Rachel

middle: N

last: Andrews

state: North Carolina

address: Medical Center Boulevard

department: Pathology, Section on Comparative Medicine

institute: Wake Forest University

summary: Fractionated whole-brain irradiation for the treatment of intracranial neoplasia causes progressive neurodegeneration and neuroinflammation. The long-term consequences of high single dose brain irradiation are unknown. In order to assess the late effects of brain irradiation we have compared transcriptomic gene expression profiles from nonhuman primates (rhesus macaques, Macaca mulatta) receiving single dose total body irradiation to those given fractionated whole brain radiotherapy and control comparators. Gene expression profiles from the dorsolateral prefrontal cortex (Brodmann area 46), hippocampus, and deep white matter (centrum semiovale) were compared. The goals of this study were to identify novel potential molecular effects of radiation-induced brain injury, to evaluate regional differences in the cerebral radiation response, and to assess whether animals receiving high dose total body irradiation demonstrated similar transcriptomic patterns as those observed in animals receiving fractionated whole brain irradiation.

overall_design: 3x3 design in which 3 brain regions [dorsolateral prefrontal cortex (brodmann area 46), hippocampus, and deep whiter matter (centrum semiovale)] were evaluated from three treatment groups: thorax-only irradiated control animals (10 Gy, estimated dose to the brain < 0.1 Gy), animals receiving fractionated whole brain irradiation (n=5, 40 Gy, 8x5 Gy fractions; 12 months prior to necropsy) and animals receiving high, single dose, total body irradiation (n=5, 6.75 - 8.05 Gy, 6-9 years prior to necropsy). The effects of brain region and irradiation status on differential gene expression were evaluated.

first: Greg

middle: O

last: Dugan

first: Ann

middle: M

last: Peiffer

first: Gregory

last: Hawkins

first: David

middle: B

last: Hanbury

first: J

last: Bourland

first: Robert

middle: E

last: Hampson

first: Samuel

last: Deadwyler


title: Bach1 Regulates the Self-renewal and Mesendodermal Differentiation of Human Embryonic Stem Cells

city: Shanghai

first: Dan

last: Meng

address: 138 Yixueyuan Rd, P.O.Box: 224

department: Department of Physiology and Pathophysiology

institute: Fudan University

summary: Transcription factor Bach1 is a member of the alkaline leucine zipper protein family. Our results therefore highlight a critical role for Bach1 proteins in a regulatory network that integrates essential Wnt/β-catenin and nodal-Smad signaling to repress mesendodermal differentiation of pluripotent cells

overall_design: Taking the advantage of Crispr/Cas9 technique, we establish Bach1 knockout human embryonic stem cell line (Bach1-KO hESCs).The RNA were extracted from WT and Bach1-KO cell lines respectively to detect the markers of the pluripotent gene and three germs layers after spontaneous differentiation . Combined with the results from RNA-seq and CHIP-seq, the role and mechanism of Bach1 in self-renewal and differentiation of human embryonic stem cells were clarified.

first: Xiangxiang


title: Chromatin occupancy by Tralpha in mouse heart

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

summary: ChipSeq from transgenic mouse heart

overall_design: Heart was obtained HSA-Cre x ThraTag transgenic mice at post-natal day 15. This transgenic model expresses a tagged version of the TRalpha1 nuclear receptor only in cardiomyocytes.

last: FLAMANT

first: Romain

last: GUYOT


title: Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells

city: Cambridge

first: Cornelia

last: Kroeger

address: 455 Main St

institute: Whitehead Institute

summary: Using the recently described CD104+/CD44hi antigen combination we demonstrate that tumorigenicity depends on individual cells residing in a hybrid E/M state. Acquisition of this E/M hybrid state is facilitated by the differential expression of EMT- TFs, like Snail accompanied by the expression of adult stem-cell programs. Transition from the highly tumorigenic E/M state to a fully mesenchymal phenotype, achieved by constitutive ectopic expression of Zeb1, is sufficient to drive cells out of the E/M hybrid state into an extreme mesenchymal (xM) state, which is accompanied by a substantial loss of tumorigenicity and a switch from canonical to non-canonical Wnt signaling.

overall_design: Performing RNASeq with HMLE (immortalized human mammary epithelial cells) in different EMT stages, either in the E state the hybrid E/M state or the extreme mesenchymal (xM) state as determined by sorting for CD104 and CD44. And performing RNASeq with HMLE cells locked in the xE state by Zeb1KO (xE-SCC-Zeb1KO), from there transferred to the hybrid E/M state by Snail overexpression (E-SCC-Zeb1KOSn) or rescued and transitioned to an xM state with CRISPR resistant Zeb1 wobble mutant (mt) (E-SCC-Zeb1KOSnZmt).

last: Kröger

last: Weinberg


title: NK cell-derived GM-CSF potentiates autoantibody-induced inflammatory arthritis and is negatively regulated by CIS

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: To examine the effect of CIS-deficiency on neutrophil inflammation-associated transcriptional profile in response to GM-CSF signalling

overall_design: Bone marrow neutrophil mRNA profiles of 10 week old wild type (WT) and CIS-/- mice were generated by deep sequencing, in triplicate, using Illumina NextSeq 500

first: Cynthia

last: Louis

first: Soroor

last: Hediyeh-Zadeh


title: Phenotypic and transcriptomic characterization of canine myeloid-derived suppressor cells

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

institute: Wellcome Trust Centre for Human Genetics

summary: Myeloid-derived suppressor cells (MDSCs) are key players in immune evasion, tumor progression and metastasis. MDSCs accumulate under various pathological states, and fall into two functionally and phenotypically distinct subsets: polymorphonuclear (PMN)-MDSCs and monocytic (M)-MDSCs. These subsets have been studied extensively in humans and mice, yet to date no study has identified MDSC subsets in dogs with spontaneous tumors. As dogs are an excellent model for human tumor development and progression, we set out to identify PMN-MDSCs and M-MDSCs in clinical canine oncology patients. We identified MDSCs as hypodense MHC class II-CD5-CD21-CD11b+ cells and show for the first time that they can also be subdivided into polymorphonuclear (CADO48A+CD14-) and monocytic (CADO48A-CD14+) subsets. The transcriptomic signatures of PMN-MDSCs and M-MDSCs are distinct from each other and from those of conventional polymorphonuclear (PMN) and monocytic cells, respectively. Notably, bioinformatic analyses reveal a statistically significant similarity between canine and previously published human MDSC gene expression patterns. As in humans, peripheral blood frequencies of canine PMN-MDSCs and M-MDSCs are significantly different in dogs with cancer compared to healthy control dogs (PMN-MDSCs: p < .001; M-MDSCs: p < .01). Furthermore, a comparison of our canine MDSC RNA-seq data with transcriptomic results previously published for human and murine MDSCs highlights five commonly upregulated genes in PMN-MDSCs in all species, suggesting that these genes are evolutionarily conserved and functionally important. Interestingly, one gene has previously been implicated in PMN-MDSC function (MMP8), but four genes (LTF, LCN2, CAMP, EBP41L3) are novel in the context of PMN-MDSCs. Our findings therefore demonstrate for the first time that dogs have two distinct populations of MDSCs, characterized by specific phenotypic and transcriptomic signatures that share key features of human MDSC subsets. Importantly, by leveraging the power of evolution, we have identified additional conserved genes in PMN-MDSCs of multiple species which may play a role in MDSC function. Our findings therefore validate the dog as a model for studying MDSCs in the context of cancer.

overall_design: RNA was extracted from a) neutrophils isolated from control healthy (n=5) and tumor-bearing (n=9) dogs, b) monocytes isolated from control healthy (n=3) and tumor-bearing (n=8), c) PMN-MDSCs isolated from tumor-bearing dogs (n=8), and d) M-MDSCs isolated from tumor-bearing dogs (n=5) and sequenced for transcriptional analyses.

first: Michelle

last: Goulart

first: Oliver

last: Garden

first: Sabina

last: Hlavaty


title: Targeting of specific miR-145-5p or miR-223-3p binding sites restores CFTR activity in CF BECs

city: Dublin

first: Sebastian

last: Vencken

address: Catherine McAuley Centre, Nelson Street

department: Clinical Research Centre

country: Ireland

institute: University College Dublin

summary: Background. Accumulating evidence indicates that CFTR modulators can be effective for CF sufferers. However, in vivo the microRNAs that regulate CFTR are increased in the CF lung milieu and this can nullify the beneficial effects of CFTR modulators.    Methods. A panel of target site blockers (TSBs) designed against the CFTR 3’untranslated region (UTR) were tested for their ability to increase CFTR expression by CFTR 3’UTR luciferase assay and western blot. The effect of two lead TSBs on CFTR activity were tested alone or in combination with selected CFTR modulators in four separate p.Phe508del/p.Phe508del in vitro and ex vivo models (CFBE41o-, Cufi-1, primary bronchial epithelial cells, iPSC-derived lung organoids). Respirable poly-lactic-co-glycolic acid (PLGA) nanoparticles encapsulating the TSBs were formulated and tested.  Findings. TSBs that target the miR-145-5p or miR-223-3p binding sites at positons 298-305 and 166-173 in the CFTR 3’UTR, respectively, increased CFTR expression and CFTR anion channel activity, and enhance the effects of Lumacaftor/Ivacaftor or Lumacftor/Tezacaftor in CF BECs. PLGAs encapsulating the TSBs promote CFTR expression in primary BECs and retain their biophysical characteristics following nebulization.   Interpretation. Alone or in combination with CFTR modulators, CFTR-targeting TSBs encapsulated in PLGA nanoparticles and nebulized to the lung could overcome microRNA-mediated inhibition of CFTR in CF bronchial epithelium. This strategy represents a promising drug-device combination therapy for the treatment for CFTR dysfunction in the lung.

overall_design: 12 samples of primary bronchial epithelial cells were analysed, six from children with cystic fibrosis and six from children without cystic fibrosis. Each sample was treated as a separate biological replicate and microRNAome expression was compared between cystic fibrosis and non-cystic fibrosis groups. Analysis was performed on all samples by RT-PCR with single technical replicates.

first: Chiara

last: De Santi

first: Elena

middle: F

last: Fernandez

first: Rachel

last: Gaul

first: Arlene

last: Glasgow

first: Marne

last: Hagemeijer

first: Juliet

last: Lefferts

first: Jeffrey

last: Beekman

first: Irene

middle: K

last: Oglesby

first: Killian

last: Hurley

first: Nilay

last: Mitash

first: Fangping

last: Mu

first: Rana

last: Raoof

last: Henshall

first: Jenny

last: O'Rourke

first: Meritxell

last: Cutrona

first: Jeremy

last: Simpson

first: Brian

middle: J

last: Harvey

first: Barry

last: Linnane

first: Paul

last: McNally

first: Sally

last: Cryan

first: Ronan

last: MacLoughlin

first: Agnieszka

last: Swiatecka-Urban

first: Catherine

last: Greene


title: Single Cell RNA Sequencing Identifies TGFβ as a Key Regenerative Cue following LPS-induced Lung Injury

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Many lung diseases result from a failure of efficient regeneration of damaged alveolar epithelial cells (AECs) after lung injury. During regeneration, AEC2s proliferate to replace lost cells, after which proliferation halts and some AEC2s transdifferentiate into AEC1s to restore normal alveolar structure and function. Although the mechanisms underlying AEC2 proliferation have been studied, the mechanisms responsible for halting proliferation and inducing transdifferentiation are poorly understood. To identify candidate signaling pathways responsible for halting proliferation and inducing transdifferentiation, we performed single cell RNA sequencing on AEC2s during regeneration in a murine model of lung injury induced by intratracheal LPS. Unsupervised clustering revealed distinct subpopulations of regenerating AEC2s: proliferating, cell cycle arrest, and transdifferentiating. Gene expression analysis of these transitional subpopulations revealed that TGFβ signaling was highly upregulated in the cell cycle arrest subpopulation and relatively downregulated in transdifferentiating cells. In cultured AEC2s, TGFβ was necessary for cell cycle arrest but impeded transdifferentiation. We conclude that during regeneration after LPS-induced lung injury, TGFβ is a critical signal halting AEC2 proliferation but must be inactivated to allow transdifferentiation. This study provides insight into the molecular mechanisms regulating alveolar regeneration and the pathogenesis of diseases resulting from a failure of regeneration.

overall_design: Single cell RNA-Seq analysis of naïve and LPS-injured adult murine lung

first: Jay

middle: R

last: Hesselberth

first: Rachel

last: Zemans


title: HantavaxTM vaccinated peripheral blood mononuclear cells (PBMCs) and sera analyses by transcriptomic and metabolomic profilings

city: Sejong-ro,

first: Adnan

last: Khan

state: Please select

address: Jochiwon-eup, Yeongi-gun, Chungnam 30019

country: South Korea

institute: Korea University

summary:
Purpose: To annotate vaccine-induced protective immunity following vaccination and identify the dynamics of enriched modules over time, and determine whether and how transcriptomics and metabolomics data correlates.
charge ratio) within a range of ions set from 50 to 1,000 from mass spectral data. The data from triplicate run were averaged and statistically analysed using SIMCA 14.1
Results: Based on neutralizing antibody titers, subjects were subsequently classified into three groups; non responders (NRs), low responders (LRs) and high responders (HRs). Post vaccination differentially expressed genes (DEGs) associated with innate immunity and cytokine pathways were highly upregulated. DEG analysis revealed a significant induction of CD69 expression in the HRs. High resolution metabolomics (HRM) analysis showed that correlated to the antibody response, cholesteryl nitrolinoleate and octanoyl-carnitine were significantly elevated in HRs, while chenodeoxycholic acid and methyl palmitate were upregulated in NRs and LRs, but not HRs. Additionally, gene-metabolite interaction revealed upregulated gene-metabolite couplings in, folate biosynthesis, nicotinate and nicotinamide, arachidonic acid, thiamine and pyrimidine metabolism in a dose dependent manner in HR group.
Conclusions: Our data provide new insight into the underlying mechanisms of the HantavaxTM-mediated immunogenicity in humans. Our study illustrate the potential for transcriptomics and untargeted metabolomics to identify genes and metabolites involved in immune responses which may propose a targeted vaccine design in future.

overall_design:
Systems vaccinology analyses were performed based on two different approaches: vaccination instance and responsiveness to the vaccine.
In our study we vaccinated a total of 20 subjects with 4 doses. However, 1 subject (subject or sample # 3) was excluded from transcriptomic study after first vaccination due to abnormal antibody titer.  Hence, we have 19 subjects vaccinated 4 time but the samples were collected before 1st and after 2nd, 3rd and 4th vaccination (i.e., sample collections was performed at 4 time points).  This Series contains a total of 76 samples (19 x 4).

first: Ok

middle: S

last: Shin


title: Differential gene expression in uterosacral ligament from patients with recurrent and primary pelvic organ prolapse

city: Vermillion

first: Kathleen

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

summary:
Objective: The objective of this study was to profile differential gene expression in three distinct patient groups.
Study Design: The groups consisted of women with recurrent POP, women with primary POP and women without POP. Whole human genome DNA microarrays were used to evaluate differential gene expression in uterosacral ligament (USL) tissues.
Results: 10 genes of interest were identified in USL. Eight genes were over expressed 30-fold or greater, and two genes were under expressed. Confirmation of differential gene expression used the technique of real-time RT-PCR.  Five of the substantially over expressed genes functioned in the distribution, metabolism or deposition of adipose tissue. Homeobox genes D10 and D11 were under expressed.
Conclusions: The differential gene expression seen in the USL tissues in women with recurrent POP suggests that USLs are weakened by changes directed by these genes.

overall_design:
Experimental factors:  presence of disease (recurrent pelvic organ prolapse)

Experimental design:  Three groups of human subjects were used for the study.  Group1(n=4) were women undergoing surgery with no evidence or history of POP.  Group 2  (n=5) were women undergoing surgical repair for primary POP.  Group 3 (n=5) were women with recurrent and symptomatic POP undergoing surgical repair.  USL tissue was obtained at surgery.  Total RNA was extracted from USL tissue and processed for hybridization to Codelink Whole Human Genome microarrays.

Quality control steps:  The cRNA that was synthesized from each USL was used for hybridization to a single CodeLink (Applied Microarrays) whole human genome microarray.  Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary.  Bacterial control spikes were used as per manufacturer's instructions.

Samples used, extract preparation and labelling:
The origin of each biological sample:  The samples were uterosacral ligament tissue from women.

Manipulations of biological samples and protocols used:  The subjects were samples of convenience, patients undergoing surgery.  Group1 were women undergoing surgery with no evidence or history of POP.  Group 2 were women undergoing surgical repair for primary POP.  Group 3 were women with recurrent and symptomatic POP undergoing surgical repair.  The stage of POP was established by physical examination using the standard POP-Q scoring system.

Experimental factor:  presence of recurrent pelvic organ prolapse vs. primary POP or no prolapse

Technical protocols:  The USL samples were minced and soaked in 600 µl TRI reagent for one hour then homogenized in TRI reagent.  The homogenization probe was rinsed in 400 µl fresh TRI reagent and the two aliquots of TRI reagent were mixed. Bromochloropropane and sodium acetate were added and the samples were centrifuged to separate the phases.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of RNA were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip.

	Labelled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion).  0.75 micrograms of total USL RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on QIAquick columns (Qiagen) and the eluent was dried down in a SpeedVac concentrator.  The double-stranded cDNA was resuspended in a mixture containing T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on RNA extraction columns.  The concentration of cRNA was determined by spectrophotometry.

Hybridization procedures and parameters:  10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the CodeLink Whole Human Genome microarray slides, and hybridized for 18 hours at 37C.
	The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

Keywords:  pelvic organ prolapse, recurrent pelvic organ prolapse

first: Michael

last: Fiegen

first: Kevin

last: Benson

first: Peter

last: Van Eerden

first: Keith

middle: A

last: Hansen


title: Mammary Gland transcriptome modifications by nutrient restriction in early lactation Holstein cows challenged with intramammary lipopolysaccharide

city: Saint Genes Champanelle

first: Celine

last: BOBY

address: Centre INRA Auvergne-Rhône-Alpes

institute: INRA

summary: The objective was to evaluate the effect of nutrient restriction and intramammary lipopolysaccharide (LPS) challenge on mammary gland (MG) gene expression in early lactation cows. At 24 ± 3 d in milk, multiparous cows were either allowed to continue ad libitum intake of a lactation diet (CON, n = 6), or the ration was diluted with barley straw (48% DM) for 4 d (RES, n = 6). On d 3, one healthy rear mammary quarter was infused with 50 µg of LPS. Mammary biopsies were performed 24 h after LPS challenge. RNA and proteins analyzed using bovine 44K microarrays (Agilent Technologies) and micro-LC-MS/MS, respectively. Transcriptomic data were analyzed using GeneSpring (moderated-t-test with Westfall-Young correction, P < 0.05). Proteins were analyzed with Progenesis LC-MS software v4.1 (Nonlinear Dynamics). Production and energy balance did not differ prior to diet change. Negative energy balance was aggravated in RES (41 vs 97 ± 15 % of requirements, mean ± SD; P < 0.001). A total of 87 differentially expressed genes (DEG) were highlighted through the comparison of RES vs CON group. Among the 33 DEG identified in the transcriptomic analyses, 11 and 22 were down- and upregulated by restriction, respectively. Among the upregulated DEG, there were PDK4 and CPT1A which are involved in the regulation of fatty acid, ketone, and glucose metabolism. CPT1A is the key enzyme in the carnitine dependent fatty acid transport, promoting fatty acid oxidation. Genes involved in immune response such as PGLYRP3 and TRIB2 were upregulated, suggesting a higher inflammatory response in RES than CON. Proteomic analysis identified 54 proteins with 14 up- and 40 downregulated in RES cows.  Upregulated proteins were mostly involved in gene expression mechanisms such as translation, RNA splicing and cellular protein modification. The downregulated proteins (e.g., EIF3H, RS27A, RS15) take part in protein metabolism. This is coherent with transcriptomic results, namely the downregulation of RPL 37A, a component of ribosomal complex, which catalyzes protein synthesis and may partially explain the lower milk protein yield in RES (834 vs 1163 g/d; P = 0.02). Proteins involved in antigen processing and presentation were downregulated in RES compared to CON, suggesting an impaired ability to counteract inflammation in RES MG.  Preliminary transcriptomics and proteomics analyses show that undernutrition may influence the MG response to inflammation at each level of gene expression.

overall_design: one-color experiment, two groups of cows, one restricted (n=6) and one control (n=6). All animals were submited to LPS challenge after 3 days since the begining of restriction of restricted group.

first: Karol

last: Pawłowski

first: Jose

last: Pires

first: Yannick

last: Faulconnier

first: Christophe

last: Chambon

first: Pierre

last: Germon

last: Boby

first: Christine

last: Leroux


title: Gene expression data of ascites from Singapore

status: Public on Mar 26 2019

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: A collection of ascites and ovarian cancer gene expression data from Singapore.

overall_design: Frozen archival epithelial ovarian cancer tumors samples, as well as cells from ascites fluid were collected and subjected to microarray analysis. The samples were from  Department of Obstetrics & Gynecology, National University of Singapore dated from 2006 to 2014.

first: Yun-Ju

last: Huang

first: Jieru

last: Ye

first: Jeffrey

last: Low

first: Tuan


title: Transcriptomic impact of IMA-08401, a novel AHR-agonist resembling laquinimod, on rat liver

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

summary: IMA-08401 (C2) represents a novel AHR agonist and selective AHR modulator (SAHRM) that is structurally similar to laquinimod (LAQ). Although both compounds produce an identical AHR-active metabolite, IMA-06201 (DELAQ) in vivo, C2 generates it to a far greater degree. SAHRMs have been proposed as therapeutic options for autoimmune disorders, including multiple sclerosis. So far, clinical trials on LAQ have not reported any significant toxic outcomes and C2 has shown low toxicity in rats; however, more research is required due to the functional resemblance of these compounds to the highly toxic AHR agonist, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Here, we report transcriptomic profiling of rat liver following acute (single-dose) and sub-acute exposure (repeated dosing for 5 days followed by a 5-day recovery period) to high doses of C2. Exposure to C2 leads to activation of the AHR, as shown by changes in mRNA abundance of the prototypical AHR-response gene Cyp1a1. We identify a heightened response early after exposure (1 day) that drops off considerably by day 10. Acute exposure to C2 produces a significant immune response, with a focus on antiviral and antibacterial responses that highlights the dual effects of AhR agonists as immunomodulators. Sub-acute exposure leads to an increase in oxidative stress in the liver, the consequences of which require further study on sensitive tissues, such as the CNS and immune system which may be compromised in patients with the target autoimmune disorders.

overall_design: Young adult male Sprague-Dawley rats were treated by gavage with with either a single dose of C2 (100 mg/kg dissolved in PEG-400at a total volume of 5 ml/kg) or vehicle control alone (PEG-400; 5ml/kg) on day 0 and euthanized on day 1, or repeated doses of C2 (100 mg/kg/day, as above) or vehicle control (PEG-400, 5ml/kg/day) daily for 5 consecutive days (days 0-4) and euthanized on day 9. Liver tissue was harvested for analysis. RNA was isolated and the transcriptome for each animal assayed on separate microarrays.

middle: D

first: Raimo

last: Pohjanvirta

first: Selma

last: Mahiout

first: Lars

last: Pettersson

first: Paul

last: Boutros


title: Gene expression alterations induced by recombinant CPS1 in mouse hepatic macrophages

city: Ann Arbor

first: M. Bishr

last: Omary

state: Michigan

address: Rm 7720 Medical Science II, 1137 E. Catherine St.

department: Molecular and Integrative Physiology

institute: University of Michigan

summary: Gene expression alterations induced by recombinant CPS1 in hepatic macrophages of mice with acetaminophen-induced liver injury

overall_design: Mice were administered recombinant CPS1 or transferrin 12 hours prior to acetaminophen injection. Then, hepatic macrophages were isolated from mice with acetaminophen-induced liver injury and total RNAs were analyzed.

first: Min-Jung

last: Park