title: Transcriptomic profiling of LPS-induced adrenal inflammation in WT mice

city: Dresden

first: Lan-Sun

last: Chen

address: Fetscherstraße 74

institute: TU Dresden

summary: Although of the utmost importance for our survival, the activation of the adrenal gland is often impaired during sepsis. Little is known about the mechanisms involved in this process. In the present study, we have used a robust RNA Sequencing (RNA-Seq) technology in a search for novel transcriptomic signatures in adrenal glands triggered by bacterial lipopolysaccharide-induced systemic inflammation. Our results demonstrate that LPS injection to mice induce a robust change in the adrenal transcriptome, significantly altering the expression of 8458 genes as compared to saline injected animals. The principal component analysis shows a clear separation between LPS and saline treatments, as well as show low variance between biological samples from each group. The functional analysis of 4312 upregulated and 4146 downregulated genes by LPS, demonstrate a strong induction of genes involved in inflammatory and steroidogenic responses, and inhibition of genes involved in DNA repair and stem/progenitor cell pathways. Gene enrichment set analysis (GSEA) further validated the functional data, and indicated a strong grouping of genes involved in LPS-mediated induction of interferon and innate immune responses, along with previously unexplored activation of the hypoxia and inhibition of Wnt/Shh pathways in the adrenal gland. These results were further validated by quantitative PCR analysis. Collectively, this is the first study demonstrating a global alteration of adrenal gene signatures during systemic inflammation, indicating the potential pathways that are involved in the adrenal gland dysregulation during sepsis.

overall_design: Examination of acute LPS-induced transcriptomic changes in mouse adrenal gland

first: Waldemar

last: Kanczkowski


title: Molecular Evaluation of Impacted Reproductive Physiology in Fathead Minnow Testes Provides Mechanistic Insights into Insensitive Munitions Toxicology (NTO)

status: Public on Jun 21 2019

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

country: USA

institute: US Army ERDC

summary:
Abstract —  Previous toxicological investigations of the insensitive munition (IM), 3-nitro-1,2,4-triazol-5-one (NTO), demonstrated histopathological and physiological impacts in mammalian testes.  The implications of these findings for fish was unknown, therefore we investigated the effects of chronic (21 day) exposures to NTO and an NTO-containing IM formulation called IMX-101 (composed of 2,4-dinitroanisole (DNAN), nitroguanidine (NQ), and NTO) in adult male fathead minnows to assess if impacts on testes were conserved.  The NTO exposure caused no significant mortality through the maximum exposure concentration (720 mg/L, measured), however NTO elicited testicular impacts causing significant asynchrony in spermatogenesis and necrosis in secondary spermatocytes at the two highest exposure concentrations (383 mg/L and 720 mg/L) and testicular degeneration at the highest exposure.  Microarray-based transcriptomics analysis identified significant enrichment of steroid metabolism pathways and mTORC-signal control of spermatogonia differentiation in NTO exposures each having logical connections to observed asynchronous spermatogenesis.  Additionally, NTO impaired transcriptional expression for genes supporting sperm structural and flagellar development including sperm-associated antigen 6 (Spag6).  These functional transcriptomic responses are logical contributors underlying impacted reproductive physiology in NTO exposures that ultimately lead to reductions in spermatozoa.  In contrast to NTO, the IMX-101 formulation elicited significant mortality at the two highest exposure concentrations of 25.2 and 50.9 mg/L (DNAN nominal + NTO measured + NQ measured).  Unlike NTO and NQ, the DNAN component of the IMX-101 formulation underwent significant transformation in the 21d exposure.  From previous investigations, neither NTO or NQ caused mortality in fish at >1000 mg/L suggesting that mortality in the present study arose from DNAN / DNAN-attributable transformation products.  The 12.6 mg/L IMX-101 exposure caused significant sublethal impacts on testes including sperm necrosis, interstitial fibrosis, and Sertoli-like cell hyperplasia.  Transcriptional profiles for IMX-101 indicated significant enrichment on multiple signaling pathways supporting spermatogenesis, mitosis / meiosis, and flagellar structure, all logically connected to observed sperm necrosis.  Additionally, pronounced transcriptional increases within the PPARα-RXRα pathway, a known DNAN target, has been hypothesized to correspond to Sertoli cell hyperplasia, presumably as a compensatory response to fulfill the nurse-function of Sertoli cells during spermatogenesis.  Overall, the transcriptional results indicated unique molecular responses for NTO and IMX-101.  Regarding chemical hazard, NTO impacted testes and impaired spermatogenesis, but at high exposure concentrations (≥ 192 mg/L), whereas the IMX-101 formulation, elicited mortality and impacts on reproductive physiology likely caused by DNAN and its transformation products present at concentrations well below the NTO-component concentration within the IMX-101 mixture formulation.
see previous row.

overall_design: Two separate microarray assays were conducted within this study.  The two experiments investigated 2 unique chemical exposures in dose-series assays including:  1. NTO and 2. the IMX-101 formulation which contains a mixture of NTO, DNAN and NQ.  This GEO entry represents analysis number 1. NTO:   Subchronic (21 day) toxicity tests employing adult male P. promelas were conducted as static renewal assays conducted at 23 °C.  Exposures were performed in 7.6 L glass fish tanks with a test solution volume of 6.0 L following ASTM general guidance.  Partial water renewals were conducted thrice weekly on Mondays, Wednesdays and Fridays by removing and replacing 3.0 L of exposure solution.  Two fish were exposed in each tank to NTO at 0 (control), 94, 192, 383, 720 mg/L (measured concentrations) where each experimental treatment included 5 replicate tanks.  All fish surviving until the conclusion of the 21d assay were euthanized by immersion in an overdose solution of MS-222 (300 mg/L) for at least 10 minutes after cessation of movement.  After euthanasia, each fish was weighed (g) and then necropsied where one testis was fixed in 10% neutral-buffered formalin for histopathological evaluation and the other fixed for transcriptomics by flash freezing in liquid nitrogen.  All animal testing was conducted using methods and protocols approved by the US Army, Engineer Research and Development Center’s Institutional Animal Care and Use Committee (IACUC Protocol #EL-6009-2014-1).

first: Guilherme

middle: R

last: Lotufo

first: Thiyagarajah

last: Arunthavarani

first: Natalie

middle: D

last: Barker

first: Qing

last: Ji

first: Karin

last: Marshall

first: Mitchell

middle: S

last: Wilbanks

first: Pornsawan

last: Chappell


title: Gene expression by BTF3 knocked down in Vcap cells

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

country: China

institute: Shandong University

summary: The aim of this research was to confirm the regulatory effect of BTF3 on gene expression in the development of prostate cancer.

overall_design: In this research, there were two samples examed including sample of negative control cells (Vcap-Scr) and sample of BTF3 knocked down cells (Vcap-shBTF3).

first: Bo

last: Han


title: Necroptosis of intestinal epithelial cells induces innate lymphoid cell-dependent lethal ileitis in preterm mice

city: Tokyo

first: Ryodai

last: Shindo

state: Ota-ku

address: 5-21-16 Omori-Nishi

country: Japan

institute: Toho univercity

summary: CFLARs encodes short form of cellular FLICE-inhibitory protein that blocks apoptosis, but promotes necroptosis in vitro. Here, we generate transgenic mice expressing CFLARs on the X-chromosome, designated as XCFY or XCFX mice. All XCFY mice die perinatally due to severe ileitis, whereas XCFX mice appear to be normal and fertile. Intestinal epithelial cell (IEC)s of XCFY mice die by necroptosis that subsequently induces massive apoptosis of IECs. Deletion of Ripk3 or Mlkl that are essential for necroptosis rescues embryonic lethality of XCFY mice by preventing both apoptosis and necroptosis of IECs. Surprisingly, deletion of RORγt+ ILC3s or Il22 rescues embryonic lethality of CFLARs Tg mice by preventing apoptosis, but not necroptosis of IECs. Thus, necroptosis of IECs triggered by cFLIPs activates RORγt+ ILC3s, resulting in induction of lethal ileitis in preterm mice.

overall_design: To identify the gene expression profiles of RNAs from the intestines of WT mice and CFLARs Tg mice, we compared gene expression of  the intestines of WT mice and CFLARs Tg mice by microarray.

first: Hiroyasu

last: Nakano


title: Genome-wide expression analysis of EPCAM+ epithelial cells from 3-dimensional lung organoids harboring Hermansky-Pudlak Syndrome-associated mutations

status: Public on Jun 25 2019

city: New York

first: Hans-Willem

last: Snoeck

state: NY

address: 650 W. 168th Street, BB816

department: Medicine

institute: Columbia University Medical Center

type: Expression profiling by high throughput sequencing

summary: Introduction of Hermansky-Pudlak Syndrome-associated mutations with CRISPR/Cas9 genome editing, allows for disease modeling in 3D cultures of hPSC-derived lung organoids.

overall_design: Wild-type human pluripotent stem cells (hPSCs) or hPSCs harboring Hermansky-Pudlak Syndrome-associated mutations introduced by CRISPR/Cas9 genome-editing were differentiated to Day40 3D lung organoids and EPCAM+ epithelial cells were sorted. mRNA profiles from these cells were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Hans

middle: W

first: Alexandros

last: Strikoudis


title: Analyses of a panel of transcripts and construction of RNA networks in hepatocellular carcinoma

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify HCC-related RNAs, we used four HCC patients’ fresh tumor tissues and paired adjacent non-tumor tissues for RNA sequencing. Differential expression of mRNAs, lncRNAs, circRNAs and miRNAs were then analyzed

overall_design: lncRNA, circRNA and miRNA profiles of 4 paired tumor and paratumor tissues of HCC patients.

first: Sheng

last: Zhiyong


title: Resin tapping transcriptome in adult slash pine (Pinus elliottii var. elliottii)

status: Public on Jun 22 2019

city: Porto Alegre

first: Arthur

last: Fett-Neto

state: Rio Grande do Sul

address: Av. Paulo Gama, 110 - Bairro Farroupilha

department: Center for Biotechnology

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

summary: To better understand the molecular bases of resin production, a major source of terpenes for industry, the transcriptome of adult Pinus elliottii var. elliottii (slash pine) trees under field commercial resinosis was obtained.

overall_design: Samples were collected from the cambium after 5 and 15 days of treatment application, which included tapping followed by application of commercial resin stimulant paste or control wounding without paste application.

middle: G

first: Janette

middle: P

last: Fett


title: Neuronal Methylome in Multiple Sclerosis

city: Solna

first: Maria

last: Needhamsen

address: Solnavagen 1

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling of NeuN+sorted neuronal nuclei from post-mortem brain tissue of Multiple Sclerosis (MS) patients (n=10) (MS) and non-neurological controls (n=7) (non-MS). Genomic DNA was subjected to conventional BS-treatment as well as oxidative BS (oxBS)-conversion using TrueMethylTM 96 kit of CEGXTM (Cambridge Epigenetix Limited) to allow for subsequent detection of hydroxymethylation (5hmC = BS - oxBS).

overall_design: Detection of DNA methylation differences (oxBS, BS and 5hmC) in NeuN+ sorted from white matter brain tissue of MS patients and non-neurological controls

first: Lara

last: Kular

first: Maja

last: Jagodic

first: Ewoud

last: Ewing

first: David

last: Gomez-Cabrero


title: Molecular insights into an ancient bone disorder

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

country: United Kingdom

institute: Cambridge University

summary: DE microRNAs between normal bone and ancient osteosarcoma

overall_design: Profiling of normal tissue versus disorder tissue to generate DE of miRNA

first: Darrell

last: Green


title: Defining genetic variation in widely used congenic and backcrossed mouse models reveals varied regulation of genes important for immune responses [ChIP-seq]

status: Public on Jun 24 2019

city: Birmingham

first: Amy

last: Weinmann

state: AL

address: 1825 UNIVERSITY BLVD

department: Department of Microbiology

institute: University of Alabama at Birmingham

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In our study, we developed an alternative next-generation sequencing dataset processing strategy to identify genetic variation in backcross mouse models.  We used this approach to define SJL genetic content in B6.SJL-CD45.1 mice from different vendor sources.

overall_design: We performed H3K27Ac ChIP-seq experiments with CD4+ Th1 cells isolated from C57BL/6 or B6.SJL-PtprcaPepcb/Boy mice from different vendor sources.  We also performed H3K27Ac ChIP-seq experiments with CD4+ Th1 cells or CD8+ Tc1 cells isolated from conventional or germ-free mice.

first: Danielle

last: Chisolm

first: Wayne

last: Cheng

first: Shelby

last: Colburn

first: Aaron

last: Silva-Sanchez

first: Selene

last: Meza-Perez

first: Troy

last: Randall


title: Transcriptome profiling of wild type and ΔabaI::Km mutant

city: Lembah Pantai

first: Chung Kiat

last: Ng

address: Jalan Universiti

country: Malaysia

institute: University of Malaya

summary: Transcriptome profiling of quorum sensing regulated genes in Acinetobacter baumannii 863

overall_design: mRNA profiles of quorum sensing mutant vs wild type

first: Chung-Kiat

first: Kok-Gan

last: Chan


title: Gene expression of subtypes of neocortical projection neurons over developmental time is correlated with cell class-specific chromatin accessibility

city: Bethesda

first: Whitney

middle: E

last: Heavner

state: MD

address: Building 35 Rm 2B-203

department: NINDS

institute: National Institutes of Health

summary: Excitatory projection neurons of the neocortex can be classified as occupying the upper layers, layers 2-4, or the deep layers, layers 5 and 6. It is still unclear which transcription factors are required to specify one cell fate versus another and which downstream targets confer specific aspects of neuronal identity over developmental time. To identify transcription factors that specify upper layer versus deep layer fate, we analyzed cell type specific gene expression and differential chromatin accessibility over three defined stages of development. We found that transcription factor expression can distinguish upper layers from deep layers, and cell type specific transcription factor genes have differentially accessible chromatin in their regulatory domains, which tends to be correlated with gene expression.

overall_design: Total mRNA was isolated from two specific populations of FACS-purified projection neurons at three defined stages of mouse development.


title: The role of TERF2IP (Telomeric repeat binding factor 2-interacting protein) in regulating disturbed flow-induced changes of gene expression

city: Houston

first: Jun-ichi

last: Abe

state: Texas

address: 2121 W Holcombe Blvd. IBT8 803e

institute: University of Texas MD Anderson Cacer Center

summary: To understand the function of TERF2IP in ECs, we isolated total RNAs from human aortic endothelial cells (HAECs) transfected with control or TERF2Ip siRNA and transcriptionally profiled them.

overall_design: HAECs were transfected by control siRNA or TERF2IP siRNA, and after 48 hrs of transfection HUVECs were exposed to disturbed flow (d-flow). After 24 hrs of disturbed flow RNA was extracted for futher microarray processing. We have the following four groups (1. Control siRNA under static condition (siCont), 2. Control siRNA under d-flow (siCont + DF), 3. TERF2IP siRNA under d-flow (siTERF2IP), and 4. TERF2IP siRNA under d-flow (siTERF2IP + DF), and each group have three samples and total twelve samples were analyzed.

first: Nhat-Tu

last: Le

first: Aldons

middle: J

last: Lusis


title: Gene expression profiling of prostate basal cells at proximal and distal ducts

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We have noticed that the proliferative potential of epithelial cells in the mouse proximal prostatic ducts is less than those at the distal prostatic ducts. To determine whether specific signaling is differentially activated in distal and proximal prostate basal cells, we isolated respective basal cells in the two regions and performed an RNA-seq analysis.

overall_design: Two group comparison

first: Yiqun

last: Zhang

first: Li

last: Xin


title: Importance of Transcriptional coactivator PC4 in p53-dependent Genotoxic Stress Response

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: In order to get an idea of involvement of PC4 in regulation of p53-dependent gene expression, we carried out global gene expression profiling upon treatment with R6-NLS-p53(380–386-3Ac). R6-NLS-p53(380–386-3Ac) is a small peptide of 20 residues derived from p53 C-terminal domain. This peptide can successfully block the cellular p53-PC4 interactions. Lung cancer line A549 which contain both wild type p53 and PC4 were used for this study. The cells were treated with 25µM R6-NLS-p53(380–386-3Ac) for two different time points (12 h and 24 h) and the gene expression profile was analyzed by microarray analysis.

overall_design: Organism : Homo sapiens, Agilent's Human Gene Expression  8x60k Array (AMADID: 039494)

first: Priya

last: Mondal

first: Siddhartha

last: Roy

first: Bipin

last: Chand


title: Specific chromatin accessibility in subtypes of neocortical projection neurons over developmental time is correlated with cell class-specific gene expression

summary: Excitatory projection neurons of the neocortex can be classified as occupying the upper layers, layers 2-4, or the deep layers, layers 5 and 6. It is still unclear which transcription factors are required to specify one cell fate versus another and which downstream targets confer specific aspects of neuronal identity over developmental time. To identify transcription factors that specific upper layer versus deep layer fate, we analyzed cell type specific gene expression and differential chromatin accessibility over three defined stages of development. We found that transcription factor expression can distinguish upper layers from deep layers, and cell type-specific transcription factor genes have differentially accessible chromatin in their regulatory domains, which tends to be correlated with gene expression.

overall_design: Accessible chromatin of two specific populations of FACS-purified projection neurons at three defined stages of mouse development was measured.


title: Subtypes of neocortical projection neurons over developmental time

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

overall_design: Refer to individual Series


title: Gene expression profiling of mouse prostate stromal cells with beta-catenin S37A mutation

summary: To identify such inhibitory signaling mediated by the stromal cells with active Wnt activity, we performed an RNA-seq analysis comparing the gene expression profiles of primarily cultured adult mouse prostate stromal cells that express S37A β-Catenin and the control cells that only express GFP. We identified 783 genes that were differentially expressed by at least 1.2 fold (Fig. 4A). Genes associated with the Wnt receptor signaling pathway were enriched in the S37A β-catenin group, corroborating the higher Wnt activity in this group.


title: FACS-isolated Lin-CD24-CD49f-Sca-1+stromal cells from adult mouse proximal and distal prostatic ducts

summary: We have noticed that the proliferative potential of epithelial cells in the mouse proximal prostatic ducts is less than those at the distal prostatic ducts. We were curious whether the tissue microenvironment in the two anatomic regions play a role in the distinct epithelial proliferative indices. So we isolated respective stromal cells in the two regions and performed an RNA-seq analysis.

overall_design: To identify such signaling, we performed an RNA sequencing(RNA-seq) analysis using fluorescence-activated cell sorting(FACS)-isolated Lin-CD24-CD49f-Sca-1+stromal cells from adult mouse proximal and distal prostatic ducts


title: Mechanism of Induction of Mouse Breast Cancer by Non-coding Heterochromatic RNAs

city: Charlottesville

first: Eugene

last: Ke

state: Virginia

address: P.O. Box 800734, 1340 Jefferson Park Avenue

department: MIC

institute: University of Virginia

summary: Heterochromatic non-coding RNAs induce breast tumor formation in mice by interacting with BRCA1-associated proteins functioning in the DNA damage response.

overall_design: mouse tumor mRNA profiles using ribosomal mRNA depletion

first: Quan

last: Zhu

first: Inder

last: Verma


title: Human mesenchymal stem cells prevent neurological complications of radiotherapy

city: SEVILLA

first: Vivian

last: Capilla-Gonzalez

state: Sevilla

address: Avda. Americo Vespucio 24

country: Spain

institute: CABIMER

summary: Radiotherapy is a highly effective tool for the treatment of brain cancer. However, radiation also causes detrimental effects in the healthy tissue, leading to neurocognitive sequelae that compromise the quality of life of brain cancer survivors. Despite the recognition of this serious complication, no satisfactory solutions exist at present. Here we investigated the effects of intranasal administration of human mesenchymal stem cell (hMSCs) as a neuroprotective strategy for cranial radiation in mice. Our results demonstrated that intranasally delivered hMSCs promote radiation-induced brain injury repair, improving neurological function. The molecular analysis revealed that hMSC administration reduces persistent activation of damage-induced c-AMP response element-binding signaling in the irradiated neurogenic niches. Furthermore, hMSC treatment did not compromise survival of glioma-bearing mice. Our findings encourage the therapeutic use of hMSCs as an effective and non-invasive approach to prevent neurological complications of radiotherapy, improving the quality of life of brain tumor survivors.

overall_design: The periventricular tissue of the brain lateral ventricles (PLv) and the hippocampus (Hipp) of irradiated and non-irradiated nude mice transplanted or not with human mesenchimal stem cells (MSC) was used for microarray analyses.

first: Bernat

last: Soria

first: Alejandro

last: Martin-Montalvo

first: Yolanda

last: Aguilera

first: Nuria

last: Mellado-Damas

first: Javier

last: López-Beas

first: Isabel

last: Herrera-Herrera

first: María

last: López

first: Juan

last: Barcia-Albacar

first: Manuel

last: Alvarez-Dolado

first: Abdelkrim

last: Hmadcha

last: Capilla-González


title: RNAseq data for chicken liver cells under mycotoxin treatment

city: Guangzhou

first: Yu

last: Sun

address: Tianhe Qu, Wushan

institute: South China Agricultural University

overall_design: RNAseq data for chicken liver cells, one control sample and three mycotoxin-treated (AFB1, OTA and ZEN) samples. Each sample sequenced with three biological replicates.


title: Transcriptome analysis of a PRRSV-infected and control PAMs

status: Public on Jun 20 2019

city: Wuhan

first: Junjing

last: Wu

address: No.1 Nanhu Yaoyuan, Nanhu Road

institute: Hubei Provincial Academy of Agricultural Sciences

summary: Transcriptomes analysis of long noncoding RNA (lncRNA) and mRNA expression profiles of the porcine alveolar macrophages (PAMs) after porcine reproductive and respiratory syndrome virus (PRRSV) infection in vitro. We obtained 105,627,026 clean reads from 109,443,286 raw reads. A total of 951 annotated and 751 novel lncRNAs were identified. PAMs showed distinct transcriptome profiles after PRRSV infection. It was observed that 126 lncRNAs and 753 mRNAs were differentially expressed between PRRSV-infected and control group PAMs.

overall_design: PAMs from the six pigs were divided into six groups (1×107 cells per group), three groups were infected with PRRSV-WUH3 at a multiplicity of infection (MOI) of 0.1, and the other three groups were treated separately with RPMI-1640 culture medium separately. At 30 h after treatment, cells were washed twice with PBS and harvested by scrapers and centrifugation. Aftrt RNA extraction, six RNA libraries (PRRSV1,2,3 and Mock1,2,3) of PAMs were sequenced on a Hiseq2500 platform.

first: Shuqi

last: Mei


title: RNA sequence of mRNA in HUVEC cells after depleting EGFL6

city: Shanghai

first: Chao-Tao

last: Tang

address: Shan Dong Middle road 145

institute: Renji hospital

summary: Total RNA was isolated from each thymic sample using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA). RNA quality was examined by gel electrophoresis and with a Nanodrop spectrophotometer (Thermo, Waltham, MA, USA). For RNA sequencing, RNA samples from 9 biological replicates were separated into three independent pools, each comprised of three distinct samples at equal amounts. Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out using the Illumina HiSeq X Ten instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China). The raw data was delieved into NCBI’s Gene Expression Omnibius, and was handled by Perl and data quality was checked by FastQC v0.11.2. Clean reads were aligned to the chicken genome (release: Gallus gallus 4.0) from NCBI using Bowtie, with one mismatch allowed. As shown by previous study[2], the expression of the transcript was calculated by FPKM using Perl. Differentially expression transcripts (DETs) were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package between different time points. The thresholds for determining DETs are P < 0.05 and absolute fold change ≥ 2. Then DETs were chosen for function and signaling pathway enrichment analysis using GO and KEGG database.

overall_design: 3 samples of control group and 3 samples of knock-down group


title: Genome-Wide RNA Pol II Initiation and Pausing in Neural Progenitors of the Rat.

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

summary:
We prepared and sequenced Start-seq libraries from rat (Rattus norgevicus) primary neural progenitor cells. Over 48 million uniquely mappable reads from two independent biological replicates allowed us to define the TSSs of 7,365 known genes in the rn6 genome, reannotating 2,503 TSSs by more than 5 base pairs, characterize promoter-associated antisense transcription, and profile Pol II pausing. By combining TSS data with polyA-selected RNA sequencing, we also identified thousands of potential new genes producing stable RNA as well as non-genic transcripts representing possible regulatory elements.
CONCLUSIONS: Our study has produced the first Start-seq dataset for the rat. Apart from profiling transcription initiation, our data reaffirm the prevalence of Pol II pausing across the rat genome and indicate conservation of pausing mechanisms across metazoan genomes. We suggest that pausing location, at least in mammals, is constrained by a distance from initiation of transcription, whether it occurs at or outside of a gene promoter. Abundant antisense transcription initiation around protein coding genes indicates that Pol II recruited to the vicinity of a promoter is distributed to available start sites of transcription at either DNA strand. Transcriptome profiling of neural progenitors presented here will facilitate further studies of other rat cell types as well as other organisms.

overall_design: Two independent biological replicate of untreated neural projenitors are analyzed, each analyzed with START-seq and with mRNA-seq. mRNA seq was done using two technical replicates for each biological replicate

first: Adam

last: Scheidegger

first: Carrisa

last: Dunn

first: Ann

last: Samarakkody

first: Nii

last: Koney-Kwaku Koney

first: Ramendra

middle: N

last: Saha

first: Sergei

last: Nechaev


title: CD137 promotes bone metastasis of breast cancer by enhancing the migration and osteoclast differentiation of monocytes/macrophages

city: Tianjin

last: Li

address: 94 Weijin Road

institute: Nankai University

summary:
Rationale: Bone is the most common metastatic site of breast cancer. CD137(4-1BB), a member of the tumor necrosis factor (TNF) receptor superfamily, is mainly expressed in activated leukocytes. Previous study demonstrates the effect of CD137-CD137L bidirectional signaling pathway on RANKL-mediated osteoclastogenesis. However, the role of CD137 in bone metastasis of breast cancer needs further study.

Methods: Stable monocyte/macrophage cell lines with Cd137 overexpression and silencing were established. Western blot, real-time PCR, transwell and tartrate-resistant acid phosphatase staining were used to detect the regulatory effect of CD137 on migration and osteoclastogenesis of monocytes/macrophages in vitro. Spontaneous bone metastasis mouse model was established, bioluminescent images, immunohistochemistry and histology assay were performed to detect the function of CD137 in bone metastasis in vivo.

Results: We found that CD137 promotes the migration of monocytes/macrophages to tumor microenvironment by upregulating the expression of Fra1. It also promoted the differentiation of monocytes/macrophages into osteoclasts at the same time, thus providing a favorable microenvironment for the colonization and growth of breast cancer cells in bone. Based on these findings, a novel F4/80-targeted liposomal nanoparticle encapsulating the anti-CD137 Ab blocking antibody (NP-aCD137 Ab-F4/80) was synthesized. This nanoparticle could inhibit both bone and lung metastases of 4T1 breast cancer cells with high efficacy in vivo. In addition, it increased the therapeutic efficacy of Fra1 inhibitor on tumor metastasis.

Conclusions: Taken together, these findings reveal the promotion effect of macrophage/monocyte CD137 on bone metastases and provide a promising therapeutic strategy for metastasis of breast cancer.

overall_design: Examination of mRNA profiles in RAW264.7 cells with Cd137 overexpression.

first: Wenjuan

last: Gao

first: Pengling

last: Jiang


title: Transcriptome analysis of gene expression of strains JNB5-1 and ZK66

city: Wuxi

first: Xuewei

last: Pan

address: 1800, Lihu Avenue

institute: Jiangnan University

summary: RNAseq analysis was performed to evaluate gene expression differences between strains JNB5-1 and ZK66. S. marcescens JNB5-1 and ZK66 cells were grown in LB medium for 12 h before harvesting. The collected cells were then treated with RNAprep pure Kit (TIANGEN) to extract total bacterial RNA and delivered to GENEWIZ in dry ice for transcriptome resequencing analysis. For annotation, the genome of S. marcescens WW4 (NC_020211.1) was used as reference. A total of 24048918 reads matched to the referenced genome in the sample of JNB5-1, and 24569696 reads in the sample of ZK66. The differentially expressed genes (DEGs) were determined between strains JNB5-1 and ZK66 with the standards of false discovery rate (FDR) ≤ 0.05, fold change |log2Ratio|≥1. Transcriptome data showed that expression of 641 genes were upregulated while 784 genes were down regulated by at least 2-fold when comparing the metR mutant strain ZK66 to its parent strain JNB5-1. Based on the annotation of KEGG_B_class, the up-regulated and down-regulated genes were classified into 30 and 27 major cellular processes, respectively. The transcriptome data indicated that MetR may regulate a variety of cellular processes in S. marcescens, including prodigiosin synthesis, and cell motility.

overall_design: Gene expression of strains JNB5-1 and ZK66 were generated by deep sequencing, in triplicate, using Illumina HiSeq X10.

first: Zhiming

last: Rao


title: Refinement of breast cancer molecular classification by miRNA expression profiles

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

institute: Lund University, Sweden

summary:
Background: Accurate classification of breast cancer using gene expression profiles has contributed to a better understanding of the biological mechanisms behind the disease and has paved the way for better prognostication and treatment prediction.

Results: We found that miRNA profiles largely recapitulate intrinsic subtypes. In the case of HER2-enriched tumors a small set of miRNAs including the HER2-encoded mir-4728 identifies the group with very high specificity. We also identified differential expression of the miR-99a/let-7c/miR-125b miRNA cluster as a marker for separation of the Luminal A and B subtypes. High expression of this miRNA cluster is linked to better overall survival among patients with Luminal A tumors. Correlation between the miRNA cluster and their precursor LINC00478 is highly significant suggesting that its expression could help improve the accuracy of present day’s signatures.

Conclusions: We show here that miRNA expression can be translated into mRNA profiles and that the inclusion of miRNA information facilitates the molecular diagnosis of specific subtypes, in particular the clinically relevant sub-classification of luminal tumors.

overall_design:
Illumina paired-end RNA-sequencing was performed on 1600 sequencing libraries (49 technical replicates, 1552 tumour samples) for fusion gene detection analysis. miRNA sequencing was performed on a subset of the fusion detection samples, 191 sequence libraries (5 technical replicates, 186 tumour samples), for miRNA transcript expression estimation.

This series is a re-analysis of GSE100769.
------------------------------------
The authors state "due to Swedish law, the patient consent, and the risk that the   sequencing data contains personally-identifiable information   andhereditary mutations, we cannot deposit the short sequencing read data in a repository".
--------------------------------------
This represents the miRNA sequencing component of 191 libraries only.

first: Helena

last: Persson

first: Carlos

last: Rovira

first: Jari

last: Häkkinen

first: Johan

last: Vallon-Christersson

first: Åke

last: Borg

first: Anna

middle: C

last: Pirona

first: Mattias

last: Höglund

first: Felix

last: Mitelman

first: Fredrik

last: Mertens

first: Anders

last: Kvist


title: The differentially expressed genes profile upon HNRPDL silencing in K562 cells

city: Suzhou

first: Xiuyan

last: Zhang

address: 199 Ren'ai Road

institute: Soochow University

summary: In our previous study, the roles of heterogeneous nuclear ribonucleoprotein D-like (HNRPDL) in CML cells were revealed. We found that overexpression of HNRPDL transformed murine BaF3 cells and induced lethal mice leukemia. Conversely, HNRPDL silencing inhibited colony-forming cell (CFC) production of CML CD34+ cells and attenuated BCR-ABL induced mice leukemia. In addition, HNRPDL modulated imatinib response of K562 cells and HNRPDL silencing sensitized CML CD34+ cells to imatinib treatment. To obtain molecular insights of how HNRPDL modulates the growth and imatinib response of human CML cells, we generated microarray data comparing HNRPDL silenced K562 cells with control (Scramble) cells.

overall_design: 3 biological replicates of Scramble and HNRPDL silenced K562 cells were harvested for microarray analysis using Agilent whole human genome oligo-chips (4×180K) in Shanghai Biotechnology Corporation. The differentially expressed transcripts were determined based on Student’s t-test (P<0.05) and fold change (>2).

first: Yun

last: Zhao

first: Dehuan

last: Ji


title: MSCs in co-culture with CLL cells acquire a CAF-like phenotype.

city: Heidelberg

first: Lena

last: Schulze-Edinghausen

address: Im Neuenheimer Feld 580

department: Molecular Genetics (B060)

country: Germany

institute: German Cancer Research Center (DKFZ) Heidelberg

summary:
Human primary mesenchymal stromal cells (MSCs) were either left untreated, treated with 3 µg/ml/day GRN, or co-cultured with CD19-sorted CLL cells of two different patients for 5 days.
Gene expression of the MSCs was quantified using an Illumina HumanHT-12 v4 Expression BeadChip.
Thereby, genes assigned to 454 Illumina probes were identified to be significantly altered by CLL co-culture compared to control MSCs cultured alone (analysed dataset provided).
MSCs in co-culture with CLL cells resembled a CAF-like phenotype.
There were no significant transcriptional changes detected in GRN treated compared to untreated MSCs.

overall_design:
The control group (n=4) comprised primary MSCs of four different donors (#1-4) cultured without additional treatment.
The GRN group (n=4) comprised MSC 1-4, which were treated with GRN.
The CLL group (n=4) comprised MSC1 and MSC2, which were each co-cultured with CLL cells derived from two different patients.

first: Axel

last: Benner

first: Patrick

last: Wuchter

first: Peter

last: Lichter

first: Martina

last: Seiffert


title: G protein accelerates epidermal cell migration via activation of PI3K/Akt-dependent mTORC1 signaling under hypoxia

city: Chongqing

first: Xin

last: Zhou

state: Chongqing

address: Xinqiao Road, Sha Ping Ba District

department: Department of Plastic and Cosmetic Surgery, Xinqiao Hospital

institute: Army Medical University

summary: When skin tissue is damaged, the wound microenvironment is hypoxic or anoxic due to the rupture of blood vessels and the high oxygen consumption of related cells; so far, it is not clear whether such hypoxic microenvironment will promote epidermal cell migration and the underlying molecular regulatory mechanisms of this effect remains unclear. Studies to date have shown that, immortal keratinocyte cell line HaCaT and primary human keratinocytes are maintained under conditions of hypoxia (1% oxygen) or normoxia. The researchers would adopt methods such as live cell imaging system, Western blotting, transwell assays and wound scratch assays etc. to study the changes of cell migration. Expression profile of mRNAs in HaCaT cells from 3 hypoxia and 3 normoxic conditions were analyzed by the Clariom D microarray assay. Gene Ontology (GO) and KEGG genomics analyses were performed to identify significant functions, pathways, and the associations of differentially expressed mRNAs. Moreover, the potential mechanism is discussed and studied. According to relevant results, the epidermal cell migration is promoted in the early hypoxia. Furthermore, experiment showed that 1456 mRNAs showed differential expression between the hypoxia and normoxic conditions, which included 537 upregulated and 919 downregulated mRNAs. These results also shown that all G proteins are upregulated. At the same time, GO analysis indicated that most upregulated mRNA are in connection with cell inflammation and migration. Pathway analysis indicated that 20 pathways corresponded to the upregulated mRNA and 6 pathways corresponded to the upregulated mRNA. These pathway analyses have indicated that genes involved in inflammation, migration and PI3K-Akt signaling are potentially regulated. Combine with microarray assay, we further shown that G protein accelerates epidermal cell migration via activation of PI3K/Akt-dependent mTORC1 signaling under the condition of hypoxia. Based on this evidence, researchers can further reveal the molecular and cellular mechanisms of local wound hypoxia, and for improving the wound healing.

overall_design: HaCaT cells were selected and divided into normoxia group and hypoxia group. The normoxic group was cultured in a normal culture incubator, and the hypoxic group was cultured in a 1% hypoxic incubator for 0.5 hours, 1 hour, 3 hours, and 24 hours, respectively. Thereafter, each group of RNA was extracted for gene chip detection.

last: ZHOU

first: Yiming

last: ZHANG


title: Activation of P-TEFb by cAMP-PKA signaling in autosomal dominant polycystic kidney disease (RNA-Seq)

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

summary: We showed that pharmacological inhibition of P-TEFb attenuated cyst development in ADPKD mouse models. Genome-wide analyses demonstrated that P-TEFb inhibition abrogated transcriptional pause release and suppressed a pathologic gene expression program during cystogenesis. This work revealed a mechanism by which aberrant activation of P-TEFb-mediated transcription elongation promotes cystogenesis in ADPKD.

overall_design: We performed gene expression analysis on mRNA from WT and ADPKD mouse kidneys treated with or without flavopiridol.

first: Yupeng

last: Chen


title: Genome-wide Profiling of H3K27ac binding in human MCF-7 cell lines

first: Yafang

last: Wang

state: Shanghai

address: 555 Zuchongzhi R.D

department: Division of Anti-Tumor Pharmacology

institute: Shanghai Institute of Materia Medica

summary: The histone methyltransferase EZH2 has been shown to function as a multifaceted molecule which can switch from a transcriptional repressor to an activator inducing a subset of genes that promote oncogenesis, including breast cancer. TfR-1, a key mediator in iron absorption, is highly expressed in a variety of tumors and associated with tumor grade, tumor stage and prognosis of patients. However, the known regulation mechanism of TfR-1 mainly remains on post-transcriptional level. To figure out whether TfR-1 expression is under epigenetic control, we examined the influence of EZH2 depletion and inhibition on TfR-1 expression in different subtypes of breast cancer cells. We discovered that EZH2 context-dependently modulates TfR-1 level and manipulates cellular iron uptake. Moreover, we identified TfR-1 as an NF-κB target gene which is positively regulated by EZH2 via constructing a complex with p65-p50 and transcription factor AP-1 in ER- cells. Inversely, TfR-1 is repressed by EZH2 and ER through histone methylation on its promoter in ER+ cells. These ﬁndings demonstrated an additional role of EZH2 in promoting breast cancer progression through iron homeostasis regulation and underscore the need for developing context-speciﬁc strategy for therapeutic targeting of epigenetic inhibition in breast cancer.

overall_design: Examination of H3K27ac modification in MCF-7 cancer cell lines

first: Yi

first: Jian

last: Ding


title: Activation of P-TEFb by cAMP-PKA signaling in autosomal dominant polycystic kidney disease (ChIP-Seq)

overall_design: We performed ChIP-Seq analysis of RNA Polymerase II in WT, ADPKD and ADPKD mice treated with flavopiridol.


title: Colistin heteroresistance in Enterobacter cloacae is regualted by PhoPQ-dependent 4-amino-4-deoxy-L arabinose addition to lipid A

city: Richardson

first: Joseph

middle: Michael

last: Boll

address: 800 W Campbell

department: Biological Sciences

institute: University of Texas at Dallas

summary: We report the transcriptional expression from wild type, ΔphoPQ, and ΔpmrAB to understand their contribution to colistin resistance.

sample_organism: Enterobacter cloacae subsp. cloacae ATCC 13047

overall_design: Examination of the global transcriptome.

middle: M


title: Expression data from A2780 cells treated with DMSO, Olaparib(Ola), Palbociclib(PD), and their combination (Ola/PD)

city: Dalian

first: Hailing

last: Cheng

address: 467 Zhongshan Road

institute: The Second Hospital of Dalian Medical University

summary: Drug treatment-induced transcriptional changes in A2780 cells.

overall_design: A2780 ovarian cancer cells were treated with DMSO, Olaparib, Palbociclib, and their combination (Ola/PD) for 24 hours, followed by RNA extraction and RNA sequencing analysis. Each has two biological repeats.

first: J

last: Yi

first: Z

last: Tao

first: P

first: H


title: Crosstalk between murine marginal zone B cells, macrophages and CD8alpha+ dendritic cells promotes Listeria monocytogenes infection

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

summary: Type 1 CD8α+ conventional dendritic cells (cDC1s) harbor and transport Listeria monocytogenes (LM) within the spleen and thereby promote infection; cDC1s are also required for CD8+ T cell priming. To test the role of the second lineage of splenic cDC in regulating infection or adaptive immunity to LM we used Dock8-deficient mice, which have impaired 33D1+ type 2 cDC (cDC2) function. We found reduced CD8+ T cell activation in Dock8-deficient mice, but this was not due to impaired cDC2 function but rather resistance to LM infection.  Bacterial resistance was due to loss of marginal zone B (MZB) cells. We showed that IL-10 production by MZB cells did not alter antigen handling pathways in dendritic cells (DCs), including ones relevant for cross-priming or Listeria survival. Instead, IL-10 increased intracellular LM in macrophages in the marginal zone, which transfer bacteria to cDC1s. Bacteria-harboring cDC1s then traffic into the splenic white pulp where protection from sterilizing phagocytes promotes LM expansion. This work uncovers a unique crosstalk between the innate immune cells in the marginal zone, facilitated by IL-10, that promotes both infection but also CD8+ T cell activation.

overall_design: RNA-seq of murine splenic CD8a+ DCs incubated for 4 hours with or without IL10

first: Dong

first: Xiangyun

last: Yina

first: Sam

last: Olyha

first: Manuela

last: Sales L. Nascimento

first: Pei

first: Theresa

last: White

first: Uthaman

last: Gowthaman

first: Biyan

last: Zhang

first: Lan

last: Xu

first: Lesley

last: Devine

first: Adam

last: Williams

first: Stephanie

last: Eisenbarth


title: Gene expression of human colon cancer HCT116 cells [HOXA5_si]

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

institute: Tokushima University Graduate school

summary: Abberant expression of HOXA5 is implicated in cancer development. We identified a novel long non-coding RNA (HOXA5 short RNA) transcribed from HOXA6-HOX5 locus using a next generation-based target RNA capture system. In this study, HCT116 cells were treated with siRNAs targeting the novel non-coding RNA. Gene expression levels of these cells were measured by microarray analysis.

overall_design: HCT116 cells were treated with siRNAs targeting HOXA5 short RNA for 48 h. Total RNA was extracted from these cells, and gene expression was measured by human whole-genome microarray (Agilent Technology).


title: Gene expression of human colon cancer HCT116 cells [HOXA5_OE]

summary: Abberant expression of HOXA5 is implicated in cancer development. We identified a novel long non-coding RNA (HOXA5 short RNA) transcribed from HOXA6-HOX5 locus using a next generation-based target RNA capture system. In this study, HCT116 cells were overexpressed with a vector containing HOXA5 short RNA. Gene expression levels of these cells were measured by microarray analysis.

overall_design: HCT116 cells were transfected with a pEB vector containg a novel long non-coding RNA (HOXA5 short RNA), and then, the cells were cultured in selection medium (blastcidin) for 2 weeks. Total RNA was extracted from these cells, and gene expression profiles were measured by human whole-genome microarray (Agilent Technology).


title: Gene expression of human colon cancer HCT116 cells

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

overall_design: Refer to individual Series


title: Whsc1 controls mesendodermal transcription factor expression

city: Barcelona

first: Maria

last: Vila-Casadesús

state: Barcelona

address: Carrer del Dr. Aiguader, 88

institute: CRG

summary: We report here chromatin related factor Whsc1 links pluripotency exit and mesendodermal differentiation. We performed RNA-seqs to compare Whsc1+/+ and Whsc1-/- embryonic stem cells (ESCs)  to compare the transcriptomes. UMI-4C experiments have been performed to identify regions having contacts with promoter regions of downstream Whsc1 targets: the mesendoderm transcritpion factors

overall_design: RNA-seq in Whsc1+/+ and Whsc1-/-  ESCs. UMI-4C in Whsc1+/+ and Whsc1-/- ESCs compared to D6 Whsc1+/+ and Whsc1-/- embryoid bodies (Ebs).


title: RNA-seq analysis of MPCs treated with FGF1 variants

city: Wenzhou

first: Dezhong

last: Wang

address: Chashan town

department: ILS

institute: Wenzhou Univsersity

summary: RNA-seq is a powerful tool to analyze differential expression of cellular pathways under different conditions. The goal of this study is to analyze the potential pathways involved in cellular defense against high glucose challenge with or without FGF1 intervention.

overall_design: MPC cells were starved for 12 hours in serum-free RPMI-1640 medium and pretreated with FGF1 wild type or FGF1 variant (100 ng/mL) for 1 hour. Then, the cells were challenged with high glucose (25 mM) (with D-mannitol as an osmotic control) for 12 hours. After that, cells were harvested for RNA-seq analysis.

first: Zhifeng

last: Huang


title: Recurrent Group A Streptococcus Tonsillitis

city: San Diego

first: Jennifer

last: Dan

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute of Immunology

summary:
To determine differences in GC Tfh cells isolated from the tonsils of children who have undergone tonsillectomy for either recurrent Group A Streptococcus (GAS) tonsillitis (RT) or non-RT (sleep apnea).

Grants:
Thrasher Research Fund for an Early Career Award 12969 - Jennifer Dan
UM1 AI100663 - Shane Crotty
Clinical Research Fellowship Grant UK Charity No. 1089464 - David Layfield, Ramsey Cuttress, Christian Ottensmeier

overall_design: Tonsillar cells were isolated from 5 RT and 5 non-RT children. Cells were left unstimulated or stimulated with GAS or recombinant streptococcal pyrogenic exotoxin A (SpeA), a critical GAS virulence factor. Cells cultured for 18 hours. Cells were sorted for GC Tfh cells (CXCR5hiPD-1hiof CD45RA-CD4+T cells) using the Activation Induced Marker (AIM) assay. For unstimulated cells, CD25-OX40-GC Tfh cells were sorted. For GAS-specific or SpeA-responsive GC Tfh cells, CD25+OX40+GC Tfh cells were sorted. All cells were sorted into RNA lysis buffer. All data are derived from GC Tfh cells.

first: Shane

last: Crotty


title: Gene expression data of  iPS clones before melanocyte differentiation

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

summary: We found distinct and self-renewal cell linages that could differentiate into melanocytes, named melanocyte precursor cells(MPCs) in which MPCs revealed drastically differntiation to authentic melanocytes by a small amount of GSK3β inhibitor in about seven days.  Comparing MPCs ,iPSCs and melanocytes, we showed wnt sigal systems in differentiation to melanocytes.

overall_design: We extracted total RNAs from two iPSCs (21F1 and 201B7) and performed microarray for pluritest.

first: Chieko

last: Hosaka

first: Mariko

last: Taniguchi-Ikeda

first: Chikako

last: Nishigori


title: Immune microenvironments differ in immune characteristics and outcome of glioblastoma multiforme

city: Beijing

first: tao

middle: bo

last: zhang

address: No. 17 South Panjiayuan, Chaoyang District

institute: Cancer Hospital

summary: Understanding the interactions between tumors and the host immune system holds great promise to uncover biomarkers for targeted therapies, predict the prognosis of patients and guide clinical treatment. However, the immune signatures of glioblastoma multiforme (GBM) remain largely unstudied in terms of systematic analyses. We aimed to classify GBM samples according to immune-related genes and complement the existing immunotherapy system knowledge. In this study, we designed a strategy to identify 3 immune subtypes representing 3 different immune microenvironments (M1-M3) and associated with prognosis. The three subtypes were significantly different in terms of specific immune characteristics (immune cell subpopulations, immune responses, immune cells and checkpoint gene interactions). In additional, somatic alterations and methylation changes were identified that correlated with genes related to a worse prognosis subtype in the microenvironment. More importantly, in M3 (worst prognosis subtype) and M2 (best prognosis subtype), the interaction between immune cells and checkpoint genes was different, and this had an important effect on the prognosis. Finally, we used risk scores of immune cells and checkpoint genes to evaluate the prognosis of GBM patients and validated the results with 3 independent datasets. Disordered interactions between immune cells and checkpoint genes result in a change in the immune microenvironment and affects the prognosis of patients. We propose that a better understanding of the immune microenvironment of advanced cancers may provide new insights into immunotherapy.

overall_design:
There are 89 samples. Gene expression profiling analysis of these samples was performed using Agilent 4x44K human whole genome gene expression microarray.

These 89 samples are a subset of samples from GSE109857.

first: Botao

first: Lin

last: Feng

first: Shujun

last: Cheng


title: Gene expression in the rcb (regulator for chloroplast biogenesis) mutant in red light conditions

city: Riverside

first: MENG

last: Chen

state: CALIFORNIA

address: 900 University Ave, 2150 Batchelor Hall

department: Botany and Plant Sciences

institute: UC Riverside

summary: The regulator for chloroplast biogenesis (rcb) mutant was identified as a mutant defective in phytochrome-mediated chloroplast biogenesis. The rcb mutant has long hypocotyl and albino phenotypes. RCB initiates chloroplast biogenesis in the nucleus by promoting the degradation of the master repressors for chloroplast biogenesis, the PIFs (Phytochrome Interacting Factors). To understand how RCB regulates the expression of PIF-regulated genes, we performed genome-wide expression analysis of RCB-dependent genes using a rcb-10 null allele.

overall_design: Wild-type (Col-0) and rcb-10 mutant seeds were surface-sterilized and plated on half-strength Murashige and Skoog (MS) growth medium without sucrose. After 4 days of stratification in the dark at 4ºC, seedlings were grown in 10 μmol m-2 s-1 R light.

first: Chan

middle: Y

last: Yoo

first: Meng


title: Gene expression profiling of the yeast cells treated with phytosphingosine

city: Kyoto

first: Hiromu

last: Takematsu

state: Kyoto

address: Shogoin-Kawahara 53

department: Human Health Science

institute: Kyoto Univ. Sch. of Medicine

summary:
Saccharomyces cerevisiae, SEY6210a/KMY1006a cells were treated with a sphingolipid species, phytosphingosine and time course change was monitored to understand mediator function of phytosphingosine. Gene expression differences were monitored with DNA microarray.
Transcriptomic analyses showed that systemic reduction of ribosome-related genes, leading to the new insight in the transcriptional regulation downstream of phytosphingosine.

overall_design: Time course change upon phytosphingosine treatment was monitored at 30, 60, 120 and 180 min. To rule out the effect of auxotroph amino acid in the transcriptome, YEp351 (LEU2 marker) was introduced in some sample.

first: Reiko

last: Fujinawa


title: HOXC10 Overexpression Promotes Cell Proliferation and Migration through Regulation of CST1 Expression in Gastric Cancer

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: This study propose HOXC10 overexpression by reduced DNA methylation promotes gastric cancer progression through regulation of CST1 and S100P.

overall_design: control cells, HOXC10 overexpressed cells

first: Jina

first: Jong

middle: H

last: kim

first: Seon


title: piRNA-guided co-transcriptional silencing coopts nuclear export factors

city: Cambridge

first: Martin

middle: Heinrich

last: Fabry

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: Cancer Research UK, Cambridge Institute

institute: University of Cambridge

summary: The PIWI-interacting RNA (piRNA) pathway is a small RNA-based immune system that controls the expression of transposons and maintains genome integrity in animal germlines1,2. In Drosophila, piRNA-guided silencing is achieved, in part, via co-transcriptional repression of transposons by Piwi. This depends on Panoramix (Panx)3,4; however, precisely how an RNA binding event silences transcription remains to be determined. Here we show that Nuclear Export Factor 2 (Nxf2) and its co-factor, Nxt1, form a complex with Panx, and are required for co-transcriptional silencing of transposons in somatic and germline cells of the ovary. Tethering of Nxf2 to either RNA or DNA results in silencing of target loci and the concomitant accumulation of repressive chromatin marks. Nxf2 and Panx proteins are mutually required for proper localization and stability. We mapped the protein domains crucial for the Nxf2/Panx complex formation and show that the amino-terminal portion of Panx is sufficient to induce transcriptional silencing. Loss of Nxf2 or Panx results in nuclear accumulation of transposon transcripts, which is for some transposons Piwi-dependent. We propose a model whereby Piwi binding to nascent transposon RNAs can provide a fail-safe mechanism, by promoting their nuclear retention, for those few transcripts that might be generated during the process of recognition and co-transcriptional repression.

overall_design: ChIP-seq, RNA-seq, smallRNA-seq and RIP-seq experiments from Drosophila melanogaster ovaries and cell lines (OSCs) performed to study a newly discovered transcriptional gene silencing factor called Nxf2 and its interacting partner called Panoramix.

first: Filippo

last: Ciabrelli

first: Marzia

last: Munafò

first: Evelyn

middle: L

last: Eastwood

first: Emma

last: Kneuss

first: Ilaria

last: Falciatori

first: Federica

last: Falconio

first: Gregory

last: Hannon

first: Benjamin

last: Czech


title: Loss of PRC1 activity in different stem cell compartments activates a common transcriptional program with cell-type dependent outcome

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

summary: Polycomb Repressive Complexes (PRCs) are evolutionary-conserved multiprotein complexes that maintain transcriptional repression during development and differentiation to establish and preserve cell identity. Through the enzymatic activity of the subunits Ring1A and Ring1B, PRC1 monoubiquitinates histone H2A on lysine 119, promoting nucleosome compaction. We recently described a fundamental role of PRC1 in preserving intestinal stem cells identity through the inhibition of non-lineage specific transcription factors. To gain more insight into the role of PRC1 in adult stem cell maintenance, we have now investigated its role in LGR5+ hair follicle stem cells during physiological regeneration. We show that PRC1 depletion in LGR5+ cells severely affects hair regeneration. Differently from what we described for ISCs, the release of target transcriptional repression upon loss of PRC1 activity induces the ectopic activation of an epidermal-specific program. Our data support a general role of PRC1 in preserving cell identity that is shared between different stem cell compartments. However, we propose that the final outcome of the ectopic activation of non-lineage specific transcription factors observed upon loss of PRC1 in stem cells is largely context-dependent and likely related to the transcription factors repertoire and the specific epigenetic landscape of the different cellular compartments.

overall_design: HFSC-RingKO and HFSC-WT RNA-seq; HFSC-Ring1b_ChIPseq; ISC-Ring1b_ChIPseq

first: Silvia

last: Pivetti

first: Daniel

last: Fernandez-Perez

first: Caterina

last: Barbieri

first: Alessandra

last: Rossi

first: L

last: Bernabei

first: Fulvio

last: Chiacchiera


title: Potent anti-tumor efficacy of palbociclib in H3K27M-mutant diffuse intrinsic pontine glioma

first: Yu

last: Sun

state: China

address: No.6,tiantan xili,Dongcheng District

institute: Beijing Tiantan Hospital, Capital Medical University

summary: Diffuse intrinsic pontine glioma (DIPG) is a rare and fatal pediatric brain cancer without cure. DIPG has high percentage histone mutation at K27M on histone H3 locus, which is believed to be one of the drivers of the tumorigenesis. Dysregulation of G1/S cell cycle checkpoint is more enriched in the H3.3K27M mutant subgroup. In this study, we reported that palbociclib (PD0332991), a specific and cytostatic inhibitor of CDK4/6, effectively suppresses the growth of DIPG cells in vitro and in vivo. We established patient derived cell lines from treatment-naïve specimens, which all have H3.3K27M mutation. And our DIPG cell lines with H3.3K27M mutation have high CDK4/6 expression. Then, we showed that depletion of CDK4 or CDK6 inhibits DIPG cells growth and blocks G1/S transition. Furthermore, palbociclib effectively repressed all 8 cell lines self-renewal, proliferation and cell cycle progression from G1 to S phase in vitro. Transcriptome analysis showed that palbociclib not only blocks G1/S transition, it also blocks other oncogenic targets such as Myc. Finally, palbociclib activity was assayed in vivo against DIPG orthotropic xenografts to demonstrate the high efficiency of blocking tumor growth. Our findings revealed that palbociclib could be the therapy strategy for DIPG.

overall_design: mRNA profiles of palbociclib or vehicle treated DIPG cells were generated by deep sequencing, in duplicate, using Illumina HiSeq X Ten.

first: Ye

first: Kun

last: Yan


title: P-body mediated translational control in photomorphogenesis

city: Taipei

first: Geng-Jen

last: Jang

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia Sinica

summary: Light, an important environmental factor regulates most of plant physiology and development. In the photomorphogenic stage, light globally enhances translation status in de-etiolating Arabidopsis seedlings. More than 1500 genes showed increased translation but not transcription in this developmental process. This implies these mRNAs are translationally repressed in dark-grown seedlings. Through transcriptome and translatome comparisons, we revealed that p-bodies attenuate the translation of mRNAs in the etiolated seedlings. We found hundreds of mRNAs accumulated and also increased translation for thousands of genes in dark-grown dcp5-1, including genes known to regulate the transition from skotomorphogenesis to photomorphogenesis. Our data reports p-bodies regulate both RNA stability and attenuation of translation for specific mRNAs in the dark.

overall_design: Three biological replicates for control and dcp5-1 4-d-old etiolated seedlings with or without 4 h of white-light treatment.

first: Shu-Hsing

last: Wu


title: Identifying Intestine Specific Homeobox gene ISX as a biomarker and therapeutic target for metastatic pancreatic cancer: developing spontaneous progression models displaying stage-specific genomic changes

city: Minneapolis

first: Mohammad

last: Saleem

state: Mn

address: 2231 6th St SE

department: Urology

institute: University of Minnesota

summary:
Purpose: Majority of pancreatic cancer (PDAC) patient deaths are associated to the metastatic progression of disease. To identify novel targeted-therapies, a complete understanding of transformation in genetic landscape in tumors during disease progression is needed. Widely in use, the artificially immortalized PDAC cell lines do not rightly represent the progression because of multiple donors and disparate genetic characteristics. To identify key genes underlying the progression of PDAC from localized disease to a metastatic form, we performed whole transcriptome RNA-Sequencing analysis of cell models representing localised to metaststic stage through paired-end deep sequencing
Method:  Mouse expressing a Cre-activated KrasG12D allele inserted into the endogenous Kras locus, and these mice were crossed with mice expressing Cre recombinase in pancreatic tissue by virtue of a PDX-1 promoter-driven transgene. Next a cross between K-rasG12D Pdx-Cre and p16-/- mice, transgenic K-rasG12D Pdx-Cre p16-/- mice were generated harboring tissue specific mutant Kras and p16 deletion resulting in an earlier appearance of PanIN lesions followed by rapid progression into highly invasive and metastatic pancreatic cancers.
Results:  Transgenic K-rasG12D Pdx-Cre p16-/- mice developed spontaneous- localized, invasive and metastatic pancreatic tumors  and transcriptome of these cell models representing localized, invasive and metastatic pancreatic tumors were sequenced.
Conclusions:  Based on genetic analysis of a same-lineage genetic background cell models, this study identifies a novel molecular pathway underlying the progression of pancreatic cancer disease. This study shows that Intestine Specific Homeobox (ISX) gene is a novel biomarker unique to pancreatic cancer progression.

overall_design: By using tumors from K-rasG12D/p16-/- transgenic mice, we generated a spectrum of spontaneous (without immortalization) murine cell models representing localized (HI-Panc-L), invaise  (HI-Panc-I) and metastatic (HI-Panc-M) stages.  HI-Panc progression model is a valuable tool  and by studying  gene expression  during progression of pancaretic cancer from localised to metaststic stage in a genetically same  linaege wll be beneificail for pancartic cancer reaserch.

first: Arsheed

middle: A

last: Ganaie

first: Aijaz

last: Parray


title: Transcriptomics changes in liver metastatic biopsies of colorectal carcinoma between pre-treated and acquired resistance to Cetuximab

first: Zongcheng

last: Li

address: No. 8 East Street, Fengtai District

institute: Fifth Medical Center of Chinese PLA General Hospital


title: Genetic control of cellular morphogenesis in Müller glia

first: Mark

last: Charlton-Perkins

address: Tennis court rd

summary: How the various cell-types of the body achieve their specific shapes is fundamentally unknown.  Here, we explore this issue by identifying genes involved in the elaboration of the complex, yet conserved, cellular morphology of Müller glial (MG) cells in the retina.  Using genomic  based strategies in zebrafish, we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter-related genes that have roles in generating the particular anatomical features of these cells, suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system.

overall_design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage


title: Effects of high sugar diet on gene expression in the Drosophila labellum

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

summary: Driven by findings that exposure to a high sugar diet reduced taste sensation in Drosophila, we performed RNA-seq on isolated proboscis tissue from animals that had either received a sugar diet or a control diet. Subsequently, we also profiled expression of animals expressing an RNAi construct to knock down OGT transcript levels in Gr5a+ neurons.

overall_design: There are two subexperiments given here. The first concerns the difference in gene expression in the proboscises of flies fed a sugar diet for seven days (SD) vs. age-matched flies on a control diet (CD). Two biological replicates are included for each sample type. The second subexperiment concerns the expression profile in the proboscis for flies that are Gr5a-Gal4→OGT-RNAi (RNAi) vs Gal4/+ genetic controls (Gal), both after seven days of exposure to high sugar diet. Four to five biological replicates are included for each condition in the second subexperiment.

first: Christina

last: May

first: Anoumid

last: Vaziri

first: Olga

last: Grushko

first: Morteza

last: Khabiri

first: Peter

first: Monica

last: Dus


title: Expression data from panicle in heat tolerant and heat susceptible rice under high temperature stress

city: Changsha

first: Xianwen

last: Zhang

state: Hunan

address: 1 Nongda Road Furong district

institute: Hunan Agricultural University

summary:
To better understand the mechanisms that regulate the heat stress response in rice, we conducted a comparative analysis of transcriptome profile in panicles from two rice lines, heat-tolerant line 252 (HTL252) and heat-susceptible line 082 (HSL082) using rice Affymetrix GeneChip.
In HTL252 panicles, 1538 differentially expressed genes (DEGs) genes with at least four-fold expression changes compared with the control under heat treatment were considered heat-responsive (HR). Of these DEGs, 522 genes were up-regulated while 1016 genes were repressed. Among DEGs in HSL082, 496 genes were induced and 1707 genes were repressed. Out of the 370 common DEGs found between HTL252 and HSL082, 129 genes were induced and 241 genes were repressed.

overall_design: After continuous high temperature treatment for 5d from both lines and each treatment type, panicles were collected for RNA extraction and hybridization on Affymetrix microarrays,For each sample ,three biological  replicates.

first: Zhang

last: Guilian

first: Chen

last: Liyun


title: Regulation of resource partitioning coordinates lateral root and nodule development in the legume Medicago truncatula

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

institute: University of Warwick

summary: Using a systems biology approach we asked to what extent lateral root development and nodulation share regulatory mechanisms to balance their formation. To do this we integrated phenotypic and transcriptomic data from wild-type (A17) and the hypernodulating mutant sunn-1 on deplete or replete nitrogen treatments.

overall_design: There were two sets of experiments. One experiment sampled wild-type Medicago truncatula A17 or the hypernodulating mutant SUPERNUMERARY NODULES (Medtr4g070970, sunn-1) after 6hr of replete nitrogen (5mM NH4NO3) treatment or no treatment (control) after plants had been grown for 14 days after beig either Sinorhizobium meliloti 1021 (rhizobia)-inoculated or mock-inoculated. This experiment was carried out in triplicate with 24 microarrays in total (8 experiments). Th second experiment sampled the wild-type Medicago truncatula A17 ecotype at 0hr, 2hr and 6hr of replete nitrogen (5mM NH4NO3) treatment after plants had been grown for 14 days on deplete nitrogen (0.1mM NH4NO3) after being either Sinorhizobium meliloti 1021 (rhizobia)-inoculated or mock-inoculated. This experiment was carried out in triplicate with 18 microarrays in total (6 experiments). Gene expression for all was analysed using NimbleGen 12 x 135K microarrays, designed for the Medicago truncatula A17 genome. After normalisation one replicate from the second experimental set was removed since it had a low QC values (Rhizobia-6hr-Rep2).

first: Beatriz

last: Lagunas

first: Mingkee

last: Achom

first: Roxanna

last: Bonaydi-Pour

first: Alonso

last: Pardal


title: Maternal Plag1 deficiency delays two-cell stage embryo development and embryonic genome activation [Embryos]

city: Stockholm

first: Pauliina

last: Damdimopoulou

address: Karolinska University Hospital OBGY K57

institute: Karolinska Institute

summary: Pleomorphic adenoma gene 1 (PLAG1) encodes a transcription factor involved in cancer and growth. We study the role of PLAG1 in preimplantation embryos using STRT RNA-seq of single embryos from wild type and knockout mothers (both mated with wild type studs). The lack of maternal Plag1 led to delayed mouse 2-cell stage embryo development, compensatory expression of Plag1 from the paternal allele, and dysregulation of 1,089 genes. Half of these genes displayed a pattern of delayed activation and play roles in ribosome biogenesis and protein synthesis. These mouse genes further showed a significant overlap with human EGA genes with similar ontology, and an enrichment of the PLAG1 de novo motif. We conclude that Plag1 affects EGA through retrotransposons influencing ribosomes and protein synthesis, a mechanism that might also explain its roles in cancer and growth

overall_design: Single wild type and maternal Plag1 knockout embryos at MII, 2-cell and 8-cell stage development in 14-16 biologicla replicas per developmental stage and genotype.

first: Anastasios

last: Damdimopoulos

first: Shintaro

last: Katayama

first: Juha

last: Kere


title: Maternal Plag1 deficiency delays two-cell stage embryo development and embryonic genome activation [Uterus]

summary: Pleomorphic adenoma gene 1 (PLAG1) encodes a transcription factor involved in cancer and growth. We study the role of PLAG1 in female reproductive tract and preimplantation embryos using STRT RNA-seq of single embryos from wild type and knockout mothers (both mated with wild type studs). We did not find significant effects in ovaries or uterus. The lack of maternal Plag1 led to delayed mouse 2-cell stage embryo development, compensatory expression of Plag1 from the paternal allele, and dysregulation of 1,089 genes. Half of these genes displayed a pattern of delayed activation and play roles in ribosome biogenesis and protein synthesis. These mouse genes further showed a significant overlap with human EGA genes with similar ontology, and an enrichment of the PLAG1 de novo motif. We conclude that Plag1 affects EGA through retrotransposons influencing ribosomes and protein synthesis, a mechanism that might also explain its roles in cancer and growth

overall_design: Uterus was dissected from 8 WT and 8 Plag1KO mice that were used in superovulation experiments and used for RNA-seq. One uterine horn was split longitudinally and mucosa exposed. The endometrial cells were scraped with a scalpel. Endometrial cells (ENDO), remaining myometrium (MYO), and a piece of intact uterine horn were transferred to RNA later.


title: TOX Transcriptionally and Epigenetically Programs CD8 T cell Exhaustion [CT vs TOX ATAC-Seq CD8]

status: Public on Jun 19 2019

city: Philadelphia

first: Omar

last: Khan

state: PA

address: 421 Curie Blvd. BRB II/III

institute: University of Pennsylvania

summary: Transcriptional and epigenetic features were detected in WT versus TOX-/- P14 T cells following 8 days of Cl-13 infection and in in vitro differentiated CD8 T cells or NIH3T3 fibroblasts following retroviral transduction with control or TOX

overall_design: Epigenetic features of CD8 T cells following transduction with control or TOX-encoding retrovirus

first: E

last: Wherry

first: Sasikanth

last: Manne


title: TOX Transcriptionally and Epigenetically Programs CD8 T cell Exhaustion [WT vs TOX-KO RNA-Seq]

overall_design: Transcriptional features of WT and TOX-/- P14 T cells following adoptive co-transfer into hosts and subsequent infection with LCMV Cl-13 for 8 days


title: TOX Transcriptionally and Epigenetically Programs CD8 T cell Exhaustion [CT vs TOX RNA-Seq CD8]

overall_design: Transcriptional features of CD8 T cells following transduction with control or TOX-encoding retrovirus


title: TOX Transcriptionally and Epigenetically Programs CD8 T cell Exhaustion [CT vs TOX RNA-Seq NIH3T3]

overall_design: Transcriptional features of NIH3T3 fibroblasts following transduction with control or TOX-encoding retrovirus


title: Transcriptomics changes in liver metastatic biopsies of colorectal carcinoma between pre-treated and acquired resistance to Cetuximab [mRNA]

first: Zongcheng

last: Li

summary: Two patients who were newly diagnosed and pathologically confirmed metastatic colorectal cancer were screened for eligibility between August 2011 and December 2013 in Affiliated Hospital, Academy of Military Medical Sciences. They were treated with Cetuximab in combination with FOLFOX regimen and obtained continuous partial responses in more than six months. CT scans of liver lesions were performed every two to eight weeks. The four biopsies were evaluated by two pathologists and were confirmed that the tumor purities were greater than 50%. Each biopsy was subjected to high-throughput RNA and small RNA sequencing to obtain expression profiles of genes and miRNAs.

overall_design: The mRNA profiling of 4 liver metastatic biopsies of colorectal carcinoma from 2 patients with matched-pairs design of pre-treated and acquired resistance to Cetuximab.

first: Xiaomin

last: Ying

first: Jianmin

last: Xu

first: Yan

last: Wang


title: Transcriptomics changes in liver metastatic biopsies of colorectal carcinoma between pre-treated and acquired resistance to Cetuximab [miRNA]

overall_design: The small RNA profiling of 4 liver metastatic biopsies of colorectal carcinoma from 2 patients with matched-pairs design of pre-treated and acquired resistance to Cetuximab.


title: Maternal Plag1 deficiency delays two-cell stage embryo development and embryonic genome activation

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

overall_design: Refer to individual Series


title: Lentiviral CRISPR Epigenome Editing of Inflammatory Receptors as a Gene Therapy Strategy for Disc Degeneration

city: Salt Lake City

first: Robert

middle: Sean

last: Bowles

state: UT

department: Biomedical Engineering

institute: University of Utah

summary:
Background: Degenerative disc disease (DDD) is a primary contributor to low back pain, a leading cause of disability. Progression of DDD is aided by inflammatory cytokines in the intervertebral disc (IVD), particularly TNF-α and IL-1β, but current treatments fail to effectively target this mechanism. The objective of this study was to explore the feasibility of CRISPR epigenome editing based therapy for DDD, by modulation of TNFR1/IL1R1 signaling in pathological human IVD cells.
Methods: Human IVD cells from the nucleus pulposus of patients receiving surgery for back pain were obtained and the regulation of TNFR1/IL1R1 signaling by a lentiviral CRISPR epigenome editing system was tested. These cells were tested for successful lentiviral transduction/expression of dCas9-KRAB system and regulation of TNFR1/IL1R1 expression. TNFR1/IL1R1 signaling disruption was investigated via measurement of NF-κB activity, apoptosis, and anabolic/catabolic changes in gene expression post inflammatory challenge.
Results: CRISPR epigenome editing systems were effectively introduced into pathological human IVD cells and significantly downregulated TNFR1 and IL1R1. This downregulation significantly attenuated deleterious TNFR1 signaling but not IL1R1 signaling. This is attributed to less robust IL1R1 expression downregulation, and IL-1β driven reversal of IL1R1 expression downregulation in a portion of patient IVD cells. Additionally, RNAseq data indicated a novel transcription factor targets, IRF1 and TFAP2C, as being a primary regulators of inflammatory signaling in IVD cells.
Discussion: These results demonstrate the feasibility of CRISPR epigenome editing of inflammatory receptors in pathological IVD cells, but highlight a limitation in epigenome targeting of IL1R1. This method has potential application as a novel gene therapy for DDD, to attenuate the deleterious effect of inflammatory cytokines present in the degenerative IVD.

overall_design: Patient nucleus pulposus cells (TNFR1kd and nontargeting control) were analyzed by RNA-seq with and without TNF-α treatment.

first: Niloofar

last: Farhang


title: The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

institute: Centro de Biotecnología y Genómica de Plantas

summary: We have analyzed the poly(A) usage between Arabidopsis control and fip1-2 mutant seedlings grown in normal medium. FIP1 is a subunit of the polyadenalation machinary and loss of function of FIP1 affects plant development and response to salt, ABA and cadmium.

overall_design: Random sequencing of Poly(A) tag (PAT-seq) from Arabidopsis thaliana wild type and fip1-2 plants. Demultiplex trimmed reads.


title: TOX Transcriptionally and Epigenetically Programs CD8 T cell Exhaustion [WT vs TOX-KO ATAC-Seq]

overall_design: Epigenetic features of WT and TOX-/- P14 T cells following adoptive co-transfer into hosts and subsequent infection with LCMV Cl-13 for 8 days


title: Effects on gene expression of ibrutinib treatment in human stem cells-derived atrial- and ventricular-like cardiomyocytes

city: Vancouver

first: Liam

last: Brunham

state: British Columbia

address: 1081 Burrard Street

department: Department of Medicine

country: Canada

institute: University of British Columbia

summary: To gain further insight into the mechanisms underlying the different response of atrial- and ventricular-like cardiomyocytes to ibrutinib, we performed RNA-seq in ibrutinib- or vehicle-treated atrial and ventricular cardiomyocytes and investigate the differential expression genes as well as enriched molecular pathways.

overall_design: hESC-derived atrial- and ventricular-like cardiomyocytes were treated with 1uM ibrutinib in experiment group and vehicle (DMSO) in control group in 12-well plates for 24 hours with 3 replicates in each condition.

first: Haojun

last: Huang


title: Promyelocytic Leukemia Protein Deficiency Leads to Spontaneous Formation of Liver Tumors in HCV Transgenic Mice

city: Essen

first: Martin

last: Trippler

address: Hufelandstr. 55

department: Gastroenterology and Hepatology

institute: University Duisburg-Essen, Essen University Hospital

summary: Persistent infection with hepatitis C virus (HCV) is a known risk factor for the development of hepatocellular carcinoma (HCC). The lack of the tumor suppressor promyelocytic leukemia protein (PML) in combination with HCV fosters hepatocarcinogenesis via induction of HCC using diethylnitrosamine (DEN) in a rodent model. However, the spontaneous development of malignant lesions in PML-deficient mice with an HCV-transgene (HCVtg) has not been investigated thus far.   We crossed PML-deficient mice with HCV transgene expressing mice and observed the animals for a period of 12 months. Livers were examined macroscopically and histologically. Gene expression analysis was performed on these samples, and compared with expression of selected genes in human samples of patients undergoing liver transplantation for HCC. In vitro studies were performed in order to analyze the selected pathways.  Genetic depletion of PML in combination with HCVtg coincided with an increased hepatocyte proliferation, resulting in development of HCCs in 40% of the PML-deficient livers. No tumor development was observed in mice with either the PML-knockout (PML-/-) or HCVtg alone. Gene expression profiling uncovered pathways involved in cell proliferation, such as NLRP12 and RASFF6. These findings were verified in samples from human livers of patients undergoing liver transplantation for HCC. Further in vitro studies confirmed that lack of PML, NLRP12 and RASFF6 leads to increased cell proliferation.   The lack of PML in combination with HCV leads to increased cell proliferation, fostering tumor development in the liver. Our data demonstrate that PML acts as an important tumor suppressor in HCV-dependent liver pathology.

overall_design: Gene expression within liver tissue of PML-deficient, HCV-transgenic mice was compared with gene expression of mice that were either PML-deficient, or HCV-transgenic, or wildtype

first: K

last: Straub

first: P

last: Kocabayoglu

first: H

last: Baba

first: M

last: Wedemeyer

last: Herzer


title: Pleiotropic Regulation of Virulence Genes in Streptococcus mutans by the Conserved Small Protein SprV

city: Kansas City

first: Indranil

last: Biswas

state: KS

address: 3901 Rainbow Blvd

department: Microbiology

institute: University of Kansas Medical Center

summary: Streptococcus mutans, an oral pathogen associated with dental caries, colonizes tooth surfaces as polymicrobial biofilms known as dental plaque. S. mutans expresses several virulence factors that allow the organism to tolerate environmental fluctuations and compete with other microorganisms. We recently identified a small hypothetical protein (90 amino acids) essential for the normal growth of the bacterium. Inactivation of the gene, SMU.2137, encoding this protein caused a significant growth defect and loss of various virulence-associated functions. An S. mutans strain lacking this gene was more sensitive to acid, temperature, osmotic, oxidative, and DNA damage-inducing stresses. In addition, we observed an altered protein profile and defects in biofilm formation, bacteriocin production, and natural competence development, possibly due to the fitness defect associated with SMU.2137 deletion. Transcriptome sequencing revealed that nearly 20% of the S. mutans genes were differentially expressed upon SMU.2137 deletion, thereby suggesting a pleiotropic effect. Therefore, we have renamed this hitherto uncharacterized gene as sprV (streptococcal pleiotropic regulator of virulence). The transcript levels of several relevant genes in the sprV mutant corroborated the phenotypes observed upon sprV deletion. Owing to its highly conserved nature, inactivation of the sprV ortholog in Streptococcus gordonii also resulted in poor growth and defective UV tolerance and competence development as in the case of S. mutans Our experiments suggest that SprV is functionally distinct from its homologs identified by structure and sequence homology. Nonetheless, our current work is aimed at understanding the importance of SprV in the S. mutans biology.

overall_design: Transcriptional profiling was performed using RNA extracted from cultures of S. mutans parent strain UA159 and the ∆sprV derivative grown in Todd-Hewitt medium supplemented with yeast extract.

first: Shankar

last: Manoharan


title: Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [RNA-Seq]

city: Nanjing

first: Zheng

middle: dong

last: yang

address: weigang NO.1

department: college of agronomy

institute: NJAU

summary: To elucidate the epigenetic regulation of salt-responsive genes helps to understand the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms function in regulating the salt-responsive genes in rice and other crops at a global level. In this study, we mainly focused on dynamic changes in transcriptome and histone marks between rice leaf and root tissues during salt treatment by using RNA-seq and ChIP-seq approaches. We demonstrated that the majority of salt-related differentially expressed genes (DEGs) display tissue-dependent changes. Similarly, tissue-dependent chromatin changes have been detected between leaf and root tissues during salt treatment. Most importantly, our study indicates that chromatin states with a combination of marks, rather than an individual mark, most likely play crucial roles in regulating differential expression of salt-responsive genes between leaf and root tissues. Especially, a special CS containing bivalent marks, H3K4me3 and H3K27me3 with a functional exclusion with each other, displays distinct functions in regulating expression of DEGs between leaf and root tissues, H3K27me3-related repressive mark mainly regulates expression of DEGs in root, but H3K4me3-releated active mark dominantly functions in regulation of down-regulated genes and possibly antagonize the repressive role of H3K27me3 in up-regulated genes in leaf. Thus, our findings indicate salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice, which provides new insights in the understanding of chromatin-based epigenetic mechanisms that confer salt tolerance in plants.

overall_design: mRNA profiles of two-week old leaf and root of rice  were generated by deep sequencing, in duplicate, using Illumina Hiseq2500 platform

first: Dongyang

last: Zheng

first: Lei

first: Xiucai

last: Pan

first: wenli

last: Zhang


title: Neocortical Slices of Human Tissue

city: Freiburg

first: Dieter

middle: Henrik

last: Heiland

address: Breisacherstr. 64

department: Department of Neurosurgery

institute: Medical Center Freiburg

summary: RNA-Seq data of human neocortical slices acute and after 7 and 14 days

overall_design: RNA-seq of neocortical slices

first: D


title: Circadian time-course microarray analysis of adult skeletal muscle from the Tamaxofin inducible muscle-specific Bmal1 knockout mice

city: MILL VALLEY

first: Brian

last: Hodge

address: 338 EDGEWOOD AVE, A

institute: Buck Institute

summary:
We generated a tamoxifen-inducible skeletal muscle-specific Bmal1 knockout mouse model and performed a time-course microarray experiment to identify gene expression changes downstream of the molecular clock.
We report the transcrpt expression profiles in adult gastrocnemius skeletal muscle harvested from iMS-Bmal1-/- and at 4 hour intervals for a full circadian time-course (6 time-points).

overall_design: Total RNA from gastrocnemius muscle tissue from 4 male mice were pooled every 4 h for 24 h (6 time-points) for both iMS-Bmal1-/- and iMS-Bmal1+/+. 1 microarray (Affymetrix Mouse Gene 1.0 ST) were performed per time-point per sample

first: Karyn

last: Esser

first: Yuan

last: Wen

first: Lance

last: Riley

first: Xiping

first: Jonathan

last: England

first: Brianna

last: Harfmann

first: Elizabeth

last: Schroder


title: Single cell RNA-seq of adult mouse heart endothelial transcriptomes following myocardial infarction

status: Public on Jun 18 2019

city: Edinburgh

first: Mairi

last: Brittan

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: University of Edinburgh

summary: A better understanding of the pathways that regulate regeneration of the coronary vasculature is of fundamental importance for the advancement of strategies to treat patients with heart disease. By analyzing single cell transcriptome of resident cardiac endothelial cells (ECs) in adult mouse hearts under both healthy and myocardial infarction (MI) settings, we provide molecular definitions of murine cardiac endothelial heterogeneity and characterizations of pro-angiogenic resident ECs.

overall_design: An EC-specific multispectral lineage-tracing mouse (Pdgfb-iCreERT2-R26R-Brainbow2.1) was used to demonstrate that structural integrity of adult cardiac endothelium following MI was maintained through clonal proliferation by resident ECs in the infarct border region, without significant contributions from bone marrow cells or endothelial-to-mesenchymal transition. Single cell RNA-seq was performed on FACS-sorted CD31+Confetti+Podoplanin- cell populations isolated from four healthy and four 7-day post-MI adult mouse hearts. Ten transcriptionally discrete heterogeneous EC states, as well as the pathways through which each endothelial state is likely to enhance neovasculogenesis and tissue regeneration following ischaemic injury were defined.

first: Ziwen

last: Li

first: Marco

last: Meloni

first: Richard

middle: S

last: Taylor

first: Ross

last: Dobie

first: Beth

last: Henderson


title: Protein amounts of the MYC transcription factor determine germinal center B cell division capacity

city: NEW YORK

first: Thiago

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: High affinity B cell selection in the germinal center (GC) is governed by signals delivered by follicular helper T cells (Tfh) to B cells. Selected B cells undergo clonal expansion and affinity maturation in the GC dark zone in direct proportion to the amount of antigen they capture and present to Tfh cells in the light zone. Here we examined the mechanisms whereby Tfh cells program the number of GC B cell divisions. Gene expression analysis revealed that Tfh induce MYC expression in light zone B cells in direct proportion to antigen capture. Conditional Myc haplo-insufficiency or over-expression combined with cell division tracking showed that MYC expression produces a metabolic reservoir in selected light zone B cells that is proportional to the number of cell divisions in the dark zone. Thus, MYC constitutes the germinal center B cell division timer that when deregulated leads to emergence of B cell lymphoma.

overall_design: Light zone germinal center B18hi B cells isolated from draining lymph nodes 6 days after NP-OVA boost and 10 hours following DEC-OVA/CS targeting were sorted and their mRNA profiles were generated by deep sequencing, in duplicates or triplicates, using Illumina NextSeq 500 sequencer.

first: Shlomo

last: Finkin

first: Harald

last: Hartweger

first: Ervin

middle: E

last: Kara


title: Metabolism of biosynthetic oligosaccharides by human-derived Bifidobacterium breve UCC2003 and Bifidobacterium longum NCIMB 88099

city: Madrid

first: Laura

last: Ruiz-Aceituno

address: Nicolas Cabrera, 9

department: CIAL

institute: CSIC

summary: This work aimed to investigate the ability of two human-derived bifidobacterial strains, i.e. Bifidobacterium breve UCC2003 and Bifidobacterium longum NCIMB 8809, to utilize various oligosaccharides (i.e., 4-galactosyl-kojibiose, lactulosucrose, lactosyl-oligofructosides, raffinosyl-oligofructosides and lactulose-derived galacto-oligosaccharides) synthesized by means of microbial glycoside hydrolases. With the exception of raffinosyl-oligofructosides, these biosynthetic oligosaccharides were shown to support growth of at least one of the two studied strains. Short-chain fatty acid (SCFA) analysis by HPLC corroborated the suitability of most of the studied novel oligosaccharides as growth substrates for the two bifidobacterial strains, showing that acetate is the main metabolic end product followed by lactic and formic acids. Transcriptomic and functional genomic approaches carried out for B. breve UCC2003 allowed the identification of key genes encoding glycoside hydrolases and protein transport systems involved in the metabolism of 4-galactosyl-kojibiose and lactulosucrose. In particular, the role of β-galactosidases in the hydrolysis of these particular trisaccharides was demonstrated, highlighting their importance in oligosaccharide metabolism by human bifidobacterial strains.

overall_design:
UCC2003 grown on 4-Galactosyl kojibiose vs Ribose, UCC2003 grown on Kojibiose vs Ribose, UCC2003 grown on  Lactulose vs Ribose, and UCC2003 grown on Lactulosucrose vs Ribose.
DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009)(van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, 2005). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Maria

last: Esteban-Torres

first: Kieran

last: James

first: FJ

middle: J

last: Moreno

first: Douwe

last: van Sinderen


title: Overexpression of eukaryotic translation initiation factor, eIF4E confers tamoxifen resistance in breast cancer via the ERα/FOXM1 axis

city: Hong Kong

first: Ui-soon

last: Khoo

address: Queen Mary hospital

department: Pathology

country: Hong Kong

institute: University of Hong Kong

summary: We report the application of RNA sequencing technology for high-throughput profiling of mRNA expression in breast cancer cell line

overall_design: Examination of the effect of eIF4E overexpression on the alteration of mRNA expression profile in breast cancer cell lines MCF-7 and ZR-75