title: Crebl2 regulates cell metabolism in muscle and liver cells (Hepa RNA-seq)

status: Public on Dec 31 2019

city: Heidelberg

first: Marcel

last: Tiebe

state: Germany

address: Humboldtstr., 18

country: Germany

institute: DKFZ Heidelberg

type: Expression profiling by high throughput sequencing

summary: We report knockdown of Crebl2 in C2C12 and Hepa1-6 cells to explore its function in metabolism. To understand its role we perform RNS-Seq of control and Crebl2 RNAi cells in both cell lines.

overall_design: Hepa1-6 cells were treated with control (Renilla Luciferase) and Crebl2 siRNAs for three days, RNA was extracted and then sequenced.

first: Marilena

last: Lutz

first: Deniz

last: Senyilmaz Tiebe

first: Aurelio

middle: A

last: Teleman


title: Delineating the Role of MITF Isoforms in Pigmentation and Tissue Homeostasis

city: Irvine

first: Anand

last: Ganesan

state: CA

address: 836 Health Science Rd

department: Dermatology

country: USA

institute: University of California, Irvine

summary: MITF, a gene that is mutated in familial melanoma and Waardenburg syndrome,  encodes multiple isoforms expressed from alternative promoters that share common coding exons but have unique amino termini.  It is not completely understood how these isoforms influence pigmentation in different tissues and how expression of these independent isoforms of MITF are regulated.  Here, we show that melanocytes express two isoforms of MITF, MITF-A and MITF-M.   Expression of MITF-A is partially regulated by a newly identified retinoid enhancer element located upstream of the MITF-A promoter.  Mitf-A knockout mice have only subtle changes in melanin accumulation in the hair and reduced Tyr expression in the eye.  In contrast, Mitf-M null mice have enlarged kidneys, lack neural crest derived melanocytes in the skin, choroid, and iris stroma; yet maintain pigmentation within the retinal pigment epithelium and iris pigment epithelium of the eye.  Taken together, these studies identify a critical role for MITF-M in melanocytes, a minor role for MITF-A in regulating pigmentation in the hair and Tyr expression in the eye, and a novel role for MITF-M in size control of the kidney.

overall_design: Sorted EGFP+ melanocytes and tdTomato+ other skin cells were isolated from ROSA<mTmG>, Tyr:Cre<ERT2> mice.  Two mice were treated with UVB wavelength light and two mice were not exposed to UVB prior to collection. Standard RNA isolation protocols were used.

first: Jessica

middle: L

last: Flesher

first: Rolando

last: Ruiz

middle: K


title: In silico analysis of long noncoding RNAs in medulloblastoma and its subgroups

city: St. Petersburg

first: Piyush

last: Joshi

state: FL

address: 600 5th St S

department: Oncolog/JHACH

institute: Johns Hopkins University

summary: Medulloblastoma is the most common pediatric brain tumor exhibiting high malignancy and fatality rates. Recent large-scale patient studies utilizing genome wide technologies have put forth transcriptomic and epigenetic heterogenties among the medulloblastomas, classifying them into four major subgroups: WNT, SHH, group 3 and group 4.  However, the contribution of long non-coding RNAs in medulloblastoma remains unknown. Long non-coding RNAs represent a crucial part of the regulatory transcriptome that has shown to control gene expression levels and protein interactions. The relative lack of understanding of long non-coding RNA in medulloblastoma is partly due to dearth of putative functional candidate long non-coding RNAs. From RNA-seq data beloning to 175 medulloblastoma patientswe identified a diagnostic and prognostic signature. We validated the diagnostic model in the PDX dervied from t samples beloning to SHH, group 3 and group 4 patients.

overall_design: Total RNA was isolated from PDX samples belonging to different medulloblastoma subgroups for subsequent RNA-seq analysis.

first: Ranjan

last: Perera


title: Differential RNA expression profiling in response to TET inhbition

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Ten-to-Eleven Translocation (TET) family of proteins oxidize 5mC in to 5hmC on the genomic DNA and act as interesting class of epigenetic medulators. A novel small molecule inhbitor of TET enzymatic activity, C35 is developed.

overall_design: Mouse Embryonic Fibroblasts are treated with C35 for 7 days and total mRNA sequecning is performed.

first: Anup

last: Kumar Singh

first: Hanjun

last: Qin

first: Xiaochun

last: Yu


title: Interpheron-γ signaling is associated with BRCA-1 loss-of-function mutations in high grade serous ovarian cancer [ChIP-seq]

city: Indianapolis

first: Guanglong

last: Jiang

state: IN

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Purpose: Loss-of-function mutations of the breast cancer type 1 susceptibility protein (BRCA1) are associated with breast (BC) and ovarian cancer (OC).  We assessed responses to histone deacetylase inhibitors (HDACi) and performed genome-wide RNA and chromatin immunoprecipitation (ChIP)-sequencing in isogenic OC cells UWB1.289 (carrying a BRCA1 mutation) and UWB1.289 transduced with wild type BRCA1.   Experimental Design: Gene expression profiles of cells harboring mutated vs. functional BRCA1 and treated with the HDACi were integrated with chromatin mapping of histone H3 lysine 9 or 27 acetylation (H3K9ac, H3K27ac) at active promoters and enhancers.  Key pathways found deregulated in BRCA1 mutated cells were validated.   Results: Gene networks activated in BRCA1-mutated vs. BRCA1+ OC cells relate to Cellular Movement, Cellular Development, Cellular Growth and Proliferation and shared upstream regulators included TGFb1, TNF, and IFN-g.  The IFN-g pathway was significantly altered in response to HDACi in BRCA1+ vs. BRCA1-mutated cells and in BRCA1-mutated/or low vs. BRCA1-normal ovarian tumors profiled in the TCGA database. Key IFN-γ-induced genes upregulated at baseline in BRCA1-mutated vs. BRCA1+ OC and BC cells included CXCL10, CXCL11, and IFI16. Increased localization of STAT1 to the promoters of these genes was observed in BRCA1-mutated cells, resulting in diminished cellular responses to IFN-γ or to STAT1 knockdown. The IFN-g signature was associated with improved survival among tumors profiled by the TCGA.   Conclusions: Transcriptomic changes affecting IFN-γ response are associated with inactivating BRCA1 mutations in OC. These alterations could contribute to diminished anti-tumor immunity in BRCA1 mutated cells or tumors.

overall_design: H3K9ac and H3K27ac levels were compared between BRCA1-null UWB1.289  ovarian cancer cells and UWB1.289 cells with BRCA1 restored.

first: Horacio

last: Cardenas

middle: T

last: Pepin

first: J

middle: B

last: Parker

first: Salvatore

last: Condello

first: Batzaya

last: Davaadelger

middle: J

last: Kim

first: Harikrishna

last: Nakshatri

first: Kenneth

middle: P

last: Nephew

first: Debabrata

last: Chakravarti

first: Yunlong

last: Liu

first: Daniela

last: Matei


title: Transcriptome analysis of differential expressed genes in B cell lymphomas from myeloid-specific Beclin-1 (Becn1ΔM) KO mice compared to (wild type) WT cervical lymph node controls.

city: Houston

first: Peng

last: Tan

state: TX

address: 6670 Bertner Ave, R9-460

institute: Houston Methodist Research Institute

summary: We report that myeloid-deficient Becn1 (Becn1ΔM) mice develop spontaneous B cell lymphoma. To determine the gene expression profiling of the tumor, we extracted total RNA from cervical lymph node tumors for RNA-seq, and found an upregulation of genes coding for inflammatory and B cell-stimulating molecules and a downreglation of cell junction molecules related to leukocyte transendothelial migration.

overall_design: Transcriptome analysis of cervical lymph nodes (or cervical lymphomas) of  WT and Becn1 myeloid-deficient tumor-bearing mice using ion torrent.

first: Tan

last: Peng

first: Wang

last: Rong-Fu


title: RNA-seq comparative analysis of HOTAIRM1 knockdown in Caki-1 cells

city: La Jolla

first: Michael

last: Hamilton

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

overall_design: Transfection of control and HOTAIRM1 siRNAs in Caki-1 cells and evaluation of RNA expression 60 hrs after transfection

first: Ernest

last: Martinez


title: ECM mediated FGF-induced estrogen receptor activity and therapy response

city: Baltimore

first: Daniele

middle: Marie

last: Gilkes

state: MD

address: 1650 N Orleans St, CRB1 128, None

department: Oncology

institute: Johns Hopkins

summary: We wanted to investigate the effects of stromal signaling on ER+ breast cancer cells as recent work implicates the tumor microenvironment in the acquisition of resistance to endocrine therapy. We desired to examine the effects of both coculture with fibroblasts, and 2.5D monoculture of breast cancer cells on decellularized, fibroblast-derived extracellular matrix scaffolds. We cultured MCF7 cells alone (Unc_#_Mono) or in coculture (Co_#) with BJ fibroblasts to examine stromal signalling on ER+ breast cancer. Cocultured MCF7 were isolated by magnetically activated cell sorting. We also cultured MCF7 cells in decellularized ECM scaffolds generated by BJ fibroblasts (ECM1_#) or IMR90 fibroblasts (ECM2_#) or on an uncoated, plastic cell culture dish (Unc_#). Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment. After RNA purification, samples were confirmed to have a RIN value > 9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 14 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

overall_design: Replicate coculture sets were generated by culturing MCF7 cells alone or in coculture with BJ fibroblasts prior to magnetic separation. Replicate ECM sets were generated by culturing MCF7 cells on ECM generated by IMR90 or BJ fibroblasts or on uncoated surfaces.

middle: M


title: Developmental Origins of Transgenerational Sperm Histone Retention Following Ancestral Exposures

city: Pullman

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: This study was designed to investigate the developmental origins of the transgenerational differential histone retention sites (called DHRs) during gametogenesis of the sperm. Vinclozolin and DDT were independently used to promote the epigenetic transgenerational inheritance of these DHRs. Male control, DDT lineage and vinclozolin lineage F3 generation rats were used to isolate round spermatids, caput epididymal spermatozoa, and caudal sperm. The DHRs between the control versus DDT lineage or vinclozolin lineage were determined in these three developmental stages. DHRs and a reproducible core of histone H3 retention sites were observed using an H3 chromatin immunoprecipitation (ChIP-Seq) analysis in the germ cell populations. The chromosomal locations and genomic features of the DHRs were also analyzed. A cascade of epigenetic histone retention site alterations was found to be initiated in or prior to the round spermatids that is further altered during epididymal sperm maturation. Observations show that in addition to alterations in sperm DNA methylation previously identified, the induction of differential histone retention sites (DHRs) in the later stages of spermatogenesis also occurs.

overall_design: Three different germ cell stages from transgenerational great-grand offspring F3 generation control, DDT and vinclozolin lineage male rats were used in this experimental design for epigenetic analysis. The F0 generation gestating female rats at 90 days of age were transiently exposed to DDT, vinclozolin or a vehicle control during gestational days 8-14.  At 90 days of age, the F1 generation offspring were bred within the control, DDT and vinclozolin lineages to generate the F2 generation (grand offspring) which were then bred at 90 days of age to obtain the transgenerational F3 generation for each control, DDT and vinclozolin lineage. No cousin or sibling breeding was used to avoid any inbreeding artifacts. Only the F0 generation gestating females were exposed to DDT or vinclozolin, which also directly exposed the F1 generation fetus and the germline within the F1 generation fetus that will generate the F2 generation. Therefore, the F3 generation is the first transgenerational generation not directly exposed, so was used to study the developmental origins of the transgenerational histone retention. The F3 generation control, DDT and vinclozolin lineage male rats were aged to 120 days for isolation of round spermatid, caput spermatozoa, and cauda epididymal sperm. Three different pools each with different individual sets of animals from different litters were obtained with 3 adult males per pool. The H3 histones and methylation H3K27me3 histones were isolated from each purified round spermatid stage pool and from individual animals for epididymal caput spermatozoa and cauda sperm and then three pools generated for subsequent epigenetic analysis. The analysis of differential histone retention regions (DHRs) was performed with a chromatin immunoprecipitation (ChIP) procedure followed by next generation sequencing for a ChIP-Seq protocol.

first: Millissia

last: Maamar

first: Daniel

last: Beck

first: Eric

last: Nilsson

first: John

middle: R

last: McCarrey


title: Chronic voluntary ethanol drinking in cynomolgus macaques elicits gene expression changes in prefrontal cortical area 46

city: Portland

first: Nicole

last: Walter

state: OR

address: 3181 SW Sam Jackson Park Road

department: Behavioral Neuroscience

institute: Oregon Health & Science University

summary: The data presented here are the first to use a longitudinal biopsy strategy to examine how chronic ethanol consumption affects gene expression in the primate PFC.

overall_design: Longitudinal paired analyses in brain biopsies following chronic alcohol consumption

first: Robert

last: Hitzemann


title: Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

summary: Single strand breaks (SSBs) represent the major form of DNA damage, yet no technique exists to map these lesions genome-wide with nucleotide-level precision. Herein, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes in genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realm of cellular biology, not obtainable with current approaches.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Profiling of single-strand DNA breaks in response to anti-cancer drug treatments and in multiple cell types

first: Philipp

last: Kapranov


title: Non-invasive approach for evaluation of CTEPH using extracellular vesicle-associated small non-coding RNA

city: Frankfurt am Main

first: Ricardo

middle: Mamede

last: Figueiredo

address: Altenhöferallee 3

institute: GenXPro GmbH

type: Non-coding RNA profiling by high throughput sequencing

summary: The aim of this study was to determine whether extracellular vesicle (EV)-associated small non-coding RNAs (sncRNAs) have potential as biomarkers for chronic thromboembolic pulmonary hypertension (CTEPH). EVs were isolated using different methods from serum of 23 CTEPH patients and 23 controls. EV-associated RNAs were analysed by next-generation sequencing using the TrueQuant method for molecular barcoding, and differentially expressed sncRNAs were validated by qRT-PCR. We identified 18 miRNAs and 21 piRNAs or piRNA clusters that were differentially expressed in CTEPH patients compared with the control group. Bioinformatic analysis predicted a contribution of these piRNAs to the progression of cardiac and vascular remodelling. Furthermore, the expression levels of DQ593039 correlated with clinically meaningful parameters such as mean pulmonary arterial pressure, pulmonary vascular resistance, right ventricular systolic pressure, and levels of N-terminal pro-brain natriuretic peptide. In summary, EV-associated piRNA DQ593039 shows promise as biomarker and may be a potential therapeutic target for CTEPH.

overall_design: Small RNA profiles of CTEPH patients and age- and sex-matched healthy controls were generated by deep sequencing, in triplicate, using Illumina NextSeq 500.

first: Lipps

last: Christoph

first: Northe

last: Philipp

first: Figueiredo

last: Ricardo

first: Rohde

last: Manfred

first: Brahmer

last: Alexandra

first: Krämer-Albers

last: Eva-Maria

first: Liebetrau

first: Mayer

last: Eckhard

first: Kriechbaum

last: Steffen

first: Keller

last: Till

first: Dörr

last: Oliver

first: Nef

last: Holger

first: Hamm

middle: W

last: Christian

first: Troidl


title: DNMT3A Reads and Connects Histone H3K36me2 to DNA methylation [RNA-seq]

city: shanghai

first: Yujiang

middle: Geno

last: Shi

address: 131 Dong An Road

department: Institute of Biomedical Science

institute: Fudan university

summary: DNA methylation at the 5-position of cytosine (5mC) is a crucial epigenetic mark in regulating biological processes including gene silencing, gene imprinting, and X chromosome inactivation. It has long been questioned how de novo DNA 5mC patterns are established in different genomic regions and whether histone modifications crosstalk to the process. Here, we report a previously uncovered mechanism of histone mark H3K36me2 in recruiting and activating DNMT3A, primarily in the intergenic regions. Our biochemistry studies discovered that H3K36me2 could be specifically bound by DNMT3A PWWP domain and substantially stimulate DNMT3A activity, representing the first example of histone modification in activating DNMT3A activity. Using multiple myeloma model, KMS11, we further found that the genome-wide gain-of-H3K36me2 resulted in global increase of 5mC, primarily in the intergenic regions. Importantly, DNA inhibitor treatment specifically blocked KMS11 growth demonstrating the functional importance of this regulatory pathway.

overall_design: Examination of polyA RNA in 2 cell types.

first: Feizhen

last: Wu


title: Profiling of RNAs from human islet-derived exosomes in a model of type 1 diabetes

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

summary: Type 1 diabetes (T1D) is characterized by immune mediated destruction of insulin producing β cells. Biomarkers capable of identifying T1D risk and dissecting disease-related heterogeneity represent an unmet clinical need. Aims: Towards the goal of informing T1D biomarker strategies, we profiled different classes of RNAs in human islet-derived exosomes and identified RNAs that were differentially expressed under cytokine stress conditions. Human pancreatic islets were obtained from cadaveric donors and treated with/without IL-1β and IFN-γ to mimic the pro-inflammatory T1D milieu. Total RNA and small RNA sequencing were performed to identify long (mRNA and long non-coding RNAs) and different classes of small non-coding RNAs. RNAs with fold change ≥ 1.3 and p-value < 0.05 were considered as differentially expressed. mRNAs and miRNAs species represented the most abundant long and small RNA species, respectively. Expression patterns of each class of RNA were changed with cytokine treatment. Differentially expressed long RNAs and targets of small non-coding RNAs were predicted to be involved in insulin secretion, calcium signaling, necrosis and apoptosis. Our data provides the first comprehensive catalog of protein coding and non-coding RNAs in human islet-derived exosomes and identifies RNAs that are dysregulated under cytokine stress.

overall_design: Identification of differentially expressed mRNA and lncRNA from cytokine treated vs. untreated human pancreatic islets.

first: Raghavendra

middle: G

last: Mirmira

first: Farooq

last: Syed

first: Preethi

last: Krishnan

first: Nicole

last: Kang


title: Interpheron-γ signaling is associated with BRCA-1 loss-of-function mutations in high grade serous ovarian cancer

first: Guanglong

last: Jiang

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

overall_design: Refer to individual Series


title: Crebl2 regulates cell metabolism in muscle and liver cells (MEFs microarray)

first: Marcel

last: Tiebe

summary: Purpose of this experiment is to investigate whether Crebl2 is required for the transcriptional changes that happen upon rapamycin treatment in TSC2-/- p53-/- MEFs.

overall_design: TSC2 null MEFs were treated with siRNA for control Luciferase or Creb2 for 2.5 days. Then cell were treated with either Ethanol or 20nM rapamycin for 12 hours, then RNA was isolated.

first: Marilena

last: Lutz

first: Deniz

last: Senyilmaz Tiebe

first: Aurelio

last: Teleman


title: TALE- and NF-Y-dependent Genes in 12 hpf Zebrafish Embryos

city: Worcester

first: William

last: Stanney

state: MA

address: 364 Plantation Street, LRB-870D

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

summary: In this RNA-seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE (PBCAB) or NF-Y (NF-YA DN). We normalized each dominant negative condition to GFP. For PBCAB, we find 646 downregulated and 854 upregulated genes. For NF-YA DN, we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription, development, and homeodomain ontologies, while genes downregulated by NF-YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF-YA DN; these genes are enriched for transcription, development, and homeodomain ontologies.

overall_design: Zebrafish embryos were injected at the 1-cell stage with either a dominant negative Pbx (PBCAB), dominant negative NF-YA (NF-YA DN), or GFP (control). Three replicates of 50-100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ-500 platform.

first: Franck

last: Ladam

first: Ian

last: Donaldson

first: Nicoletta

last: Bobola

first: Charles

last: Sagerstrom


title: Effects of Overexpression of Dube3a in Drosophila Brain

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: Fly Dube3a was expressed using either the neuronal driver (elav-GAL4) or the glial driver (Repo-GAL4). RNAseq data was compared among groups (elav>Dube3a), (repo>Dube3a) and (Dube3a alone).  Expression was measured in whole dissected fly brain.

overall_design: Flies expressing Dube3a (Das45) were grown at 25deg and aged approximately 3 days prior to brain dissections. RNA was isolated from control (uas-Dube3a alone), glial Dube3a overexpression (repo>Dube3a), or neuronal overexpression of Dube3a (elav>Dube3a) flies by removing 15-25 fly heads per genotype and homogenizing in TRI Reagent (Applied Biosystems). Total RNA was extracted with Directzol RNA MiniPrep Plus (Zymo Research Corp) according to the manufacturer’s instructions which included a DNAse treatment step. Purity and concentration was verified using NanoDrop spectrophotometer (ThermoFisher Scientific), and integrity was confirmed using a Bioanalyzer (Agilent). Each genotype was run in triplicate. RNAseq was performed by PGM sequencing at the UTHSC Molecular Resource Center (MRC). Each RNA sample was converted to ion torrent sequencing libraries and run on 318v2 chips using an Ion Torrent Proton sequencer. All groups and replicates were run simultaneously to eliminate chip-to-chip variability.

first: Lawrence

last: Reiter

first: Kevin

last: Hope


title: Gene expression in normal and cancer associated oral fibrolasts

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

summary: To identify genes differentially expressed between normal oral fibroblasts and CAFs derived from genetically stable and unstable oral squamous cell carcinomas.

overall_design: Whole transcriptome analysis, 3 normal oral fibroblasts, 4 CAFs from genetically stable oral cancers and 4 CAFs from genetically unstable oral cancers

last: Paterson


title: STING, IRF1 and IRF3/7 dependent gene expression in response to c-di-GMP stimulation of bone marrow derived dendritic cells

city: Dallas

first: Hans-Christian

last: Reinecker

state: Texas

address: J5.136, 5959 Harry Hines Boulevard

department: Medicine

institute: University of Texas Southwestern Medical Center

summary: STING activation induced IRF 1 dependent transcriptional programs in dendritic cells (DCs) determine T cell fate during mucosal host defense activation.

overall_design: Analysis of BMDCs from Tmem173-/-, Irf1-/-, IRF3/7-/- and C57BL/6 mice after 18 hours stimulation with c-di GMP


title: Trasncriptome analysis of intemediate cells of the stria vascularis in neonatal mice

city: Cleveland

first: Martin

last: Basch

state: Ohio

address: 10900 Euclid Ave

department: Otolaryngology

institute: Case Western Reserve University

summary: We performed RNAseq on FACS-sorted cells of the lateral wall of the cochlea from neonatal mice. The goal was to identify singaling pathways acting during the differentiation of neural crest progenitors into intermediate cells of the stria.

overall_design: Using Wnt1-CRE mice crossed to a YFP reporters,  we generted mRNA profiles of neonatal intermediate cells of the stria vascularis and comopared them to mRNA profiles of YFP negative cells from the cochlea lateral wall


title: Systematic identification of long non-coding RNAs under allelopathic interference of PHBA in S. lycopersicum

city: Shouguang

first: Liang

last: Guoting

state: Shandong

address: No.1299, Jinguang street

institute: Weifang University of Science and Technology

summary: In this study, we identifyed the LncRNAs expressed in S. lycopersicum leaves under different para-hydroxybenzoic acid concentration treatments.

overall_design: The expression profiles of mRNAs and non-coding RNAs of leaves after 2 days of  PHBA treatments and normal leaves

first: Guoting

last: Liang


title: Crebl2 regulates cell metabolism in muscle and liver cells (C2C12 RNA-seq)

city: Heidelberg

first: Marcel

last: Tiebe

address: Humboldtstr., 18

institute: DKFZ Heidelberg

summary: We report knockdown of Crebl2 in C2C12 and Hepa1-6 cells to explore its function in metabolism. To understand its role we perform RNS-Seq of control and Crebl2 RNAi cells in both cell lines.

overall_design: C2C12 cells were treated with control (Renilla Luciferase) and Crebl2 siRNAs for three days, RNA was extracted and then sequenced. In parallel some samples for treated with either EtOH or rapamycin for 12 hours to assess Crebl2 role in rapamycin induced transcriptional changes.

last: Lutz


title: Interpheron-γ signaling is associated with BRCA-1 loss-of-function mutations in high grade serous ovarian cancer [RNA-seq]

first: Guanglong

last: Jiang

summary: Purpose: Loss-of-function mutations of the breast cancer type 1 susceptibility protein (BRCA1) are associated with breast (BC) and ovarian cancer (OC).  We assessed responses to histone deacetylase inhibitors (HDACi) and performed genome-wide RNA and chromatin immunoprecipitation (ChIP)-sequencing in isogenic OC cells UWB1.289 (carrying a BRCA1 mutation) and UWB1.289 transduced with wild type BRCA1.   Experimental Design: Gene expression profiles of cells harboring mutated vs. functional BRCA1 and treated with the HDACi were integrated with chromatin mapping of histone H3 lysine 9 or 27 acetylation (H3K9ac, H3K27ac) at active promoters and enhancers.  Key pathways found deregulated in BRCA1 mutated cells were validated.   Results: Gene networks activated in BRCA1-mutated vs. BRCA1+ OC cells relate to Cellular Movement, Cellular Development, Cellular Growth and Proliferation and shared upstream regulators included TGFb1, TNF, and IFN-g.  The IFN-g pathway was significantly altered in response to HDACi in BRCA1+ vs. BRCA1-mutated cells and in BRCA1-mutated/or low vs. BRCA1-normal ovarian tumors profiled in the TCGA database. Key IFN-γ-induced genes upregulated at baseline in BRCA1-mutated vs. BRCA1+ OC and BC cells included CXCL10, CXCL11, and IFI16. Increased localization of STAT1 to the promoters of these genes was observed in BRCA1-mutated cells, resulting in diminished cellular responses to IFN-γ or to STAT1 knockdown. The IFN-g signature was associated with improved survival among tumors profiled by the TCGA.   Conclusions: Transcriptomic changes affecting IFN-γ response are associated with inactivating BRCA1 mutations in OC. These alterations could contribute to diminished anti-tumor immunity in BRCA1 mutated cells or tumors.

overall_design: Transcriptome of BRCA1-null UWB1.289 ovarian cancer cells treated or not treated with entinostat were compared with UWB1.289 cells with BRCA1 restored treated or not treated with entinostat (n=2 replicates per group).

first: Horacio

last: Cardenas

first: Jessica

last: Pepin

first: J

last: Parker

first: Salvatore

last: Condello

first: Batzaya

last: Davaadelger

last: Kim

first: Harikrishna

last: Nakshatri

first: Kenneth

last: Nephew

first: Debabrata

last: Chakravarti

first: Yunlong

last: Liu

first: Daniela

last: Matei


title: Co-incidence of RCC-susceptibility polymorphisms with HIF cis-acting sequences supports a pathway tuning model of cancer

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford


title: RNAseq of NTCU-induced mouse lung squamous cell carcinoma

city: Seattle

first: Laura

last: Riolobos

address: 850 Republican St

institute: University of Washington

summary: Topical treatment with N-nitrosotris-(2-chloroethyl)urea (NTCU) induces lung squamous cell carcinoma in mouse. The aim of this study is to analyze the expression profile of the mouse NTCU-induced SCC compared to normal lung to identify gene expression changes in the SCC cells.  NIH Swiss mice presenting lung SCC and control healthy mice were used for laser capture microdissection (LCM).  LCM was performed in a LMD7000 microscope (Leica Microsystems GmbH, Wetzlar, Germany).  RNA was extracted using the RNeasy FFPE kit (Qiagen, Hilden, Germany) and libraries were prepared from using the SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian (Clontech Laboratories, Inc., Mountain View, CA, USA).  Sequencing was performed using an Illumina HiSeq 2500 generating 50 base pair paired end reads. Reads of low quality were filtered, and adapters trimmed using Cutadapt v1.9.1. Alignment to the reference genome (UCSC mm10) was performed using TopHat v2.0.1, and RNA counts were generated for each gene using the Python package HTSeq v0.6.1, employing the “intersection-strict” overlap mode. DESeq2 was used to normalize and transform the data, examine the relationship between samples (by plotting the first two principal components) and to test for differential expression

overall_design: RNAseq of mouse normal lung and lung SCC induced by NTCU

first: Ekram

last: Gad

first: Piper

last: Treuting

first: Andrew

middle: E

last: Timms

first: Elliot

last: Hershberg

first: Lauren

last: Corulli

first: Erin

last: Rodmaker

first: Mary

last: Disis


title: Multi-step Epigenetic Programming of Monocytes during Infection

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Monocytes play a major role in the defense against pathogens. They are rapidly mobilized to inflamed sites where they exert both proinflammatory and regulatory effector functions. It is still poorly understood how this dynamic and exceptionally plastic system is controlled at the molecular level. Herein, we evaluated the differentiation process that occurs in Ly6Chi monocytes during oral infection by T. gondii. Flow cytometry and single-cell analysis revealed distinct activation status and gene expression profiles in the bone marrow, the spleen and the lamina propria of infected mice. We provide further evidence that this stepwise acquisition of effector functions, such as the capacity to produce interleukin-27, is accompanied by distinct waves of epigenetic programming, highlighting a role for STAT1/IRF1 in the bone marrow and AP-1/NF-kB in the periphery. This work broadens our understanding of the molecular events that occur in vivo during monocyte differentiation in response to inflammatory cues.

overall_design: Study of chromatin accessibility in monocytes isolated from Bone Marrow, Spleen and Lamina Propria, in steady state or during oral Toxoplasma gondii infection.

first: Aurélie

last: Detavernier

first: Abdulkader

last: Azouz

first: Hussein

last: Shehade

first: Marion

last: Splittgerber

first: Laurye

last: Van Maele

first: Muriel

last: Nguyen

first: Séverine

last: Thomas

first: Younes

last: Achouri

last: Svec

first: Emilie

last: Calonne

first: François

last: Fuks

first: Guillaume

last: Oldenhove


title: Transcriptome analysis of mir-1-deficient and ins-1-deficient Caenorhabditis elegans

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

summary: We examined the transcriptome of mir-1(gk276) and ins-1(nj32) mutant animals compared to wild-type of L4 larvae. This was performed to identify genes that are regulated by mir-1 and ins-1 signaling.

overall_design: Triplicate samples for each genetopye were analysed

first: Camilla

last: Nehammer

first: Patrick

last: Ejlerskov

first: Sandeep

last: Gopal

first: Ava

last: Handley

first: Leelee

last: Ng

first: Pedro

last: Moreira

first: David

middle: C

last: Rubinsztein

first: Roger

last: Pocock


title: Glucocorticoids paradoxically facilitate steroid resistance in subsets of T-cell acute lymphoblastic leukemias and normal thymocytes (CCRF-CEM)

city: San Francisco

first: Benjamin

last: Huang

address: 1450 3rd Street

institute: University of California San Francisco

summary: Glucocorticoids (GCs) are a central component of therapy for patients with T-cell acute lymphoblastic leukemia (T-ALL) and while resistance to GCs is a strong negative prognostic indicator in T-ALL, mechanisms of GC resistance remain poorly understood. Using diagnostic samples from patients enrolled on the frontline Children’s Oncology Group (COG) T-ALL clinical trial AALL1231, we demonstrate that one-third of primary T-ALLs are resistant to GCs when cultured in the presence of interleukin-7 (IL7), a cytokine that is critical for normal T-cell function and that plays a well-established role in leukemogenesis. We demonstrate that in these T-ALLs and in distinct populations of normal developing thymocytes, GCs paradoxically induce their own resistance by promoting upregulation of IL7 receptor (IL7R) expression. In the presence of IL7, this augments downstream signal transduction resulting in increased STAT5 transcriptional output, which leads to upregulation of the pro-survival protein BCL-2. Taken together, these data demonstrate that IL7 mediates an intrinsic and physiologic mechanism of GC resistance in normal thymocyte development that is retained during leukemogenesis in a subset of T-ALLs and is reversible with targeted inhibition of the IL7R/JAK/STAT5/BCL-2 axis.

overall_design: STAT5A and STAT5B knockout CCRF-CEM cell lines exposed to dexamethasone and IL-7

first: Lauren

last: Meyer

first: Kevin

last: Shannon

last: Teachey

first: Michelle

last: Hermiston


title: Transcriptome data used for Sus scrofa gene annotation

city: Chengdu

first: Song

last: Yang

address: No.211, Huimin Road, Wenjiang District, Chengdu City, Sichuan Province, P.R.China

institute: Sichuan Agricultural University College of Animal Science and Technology

summary: To optimize the genome annotation, nine tissue and one pool RNA libraries (i.e. heart, liver, spleen, lung, kidney, muscle, fat, ovary, pool.) were constructed using the Illumina mRNA-spleeneq Prep Kit

overall_design: We sequenced nine tissues and one pooled sample using illumina Hiseq 2500 platform

first: Yan

last: Li

first: Yang

last: Song

first: Mingzhou


title: Evalutation of global gene expression changes in NGLY1 deficient mouse embryonic fibroblasts (MEF)

city: Philadelphia

first: Zhe

last: Zhang

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

summary: the gene expression profiles of 3 cultured MEFs from NGLY1 knockout mice was compared to 3 cultured MEF from the wild type control mice.

first: Falk

last: Marni

first: Zhang

last: Zhe

first: Miao

last: He


title: Comparing the m6A transcriptoms of Mettl14fl/fl and oligodendrocyre precursor cell (OPCs) and mature oligodendrocytes(OL) using m6A-SMART-seq

city: Chicago

first: Huan

last: Xu

state: Illinois

address: 5841 S. Maryland Ave MC2030, Ab514

department: Neurology

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

summary:
The goal of the experiment is to determine the m6A  tagged transcripts after the Mettl14 gene inactivation in OPCs and mature oligodendrocytes using Z score > 0 .
Methods: mRNA from total RNA of  Mettl14fl/fl OPCs and mature oligodendrocytes was purified with Dynabeads Oligo (dT)25 (ThermoFisher; 61006). The equivalent amount of input and m6A-imunoprecipitated RNA were prepared for library generation using the SMART-seq protocol as described (Picelli et al., 2014). Three biological replicates of control OPCs and  three biological replicates of control oligodendrocytes were sequenced using Illumina NextSeq 500. Adapters were trimmed from original reads using Trimmomatic and low-quality reads were removed. The remaining reads were then mapped to the mouse genome (mm10) using STAR aligner (Dobin et al., 2013). To measure the relative m6A level per gene, the ratio of m6A IP/ Input was first calculated. The Z scores were then obtained by comparing the ratios (m6A IP/ Input) to the mean of the group to reflect the relative m6A level per gene on a transcriptome-wide scale.
Results: The m6A-seq analyses detected 3554 m6A marked transcripts in OPCs and 2606 m6A marked transcripts in oligodendrocytes.There are 2806 transcripts with the m6A mark in OPCs that were present but not marked in oligodendrocytes , and 1626 transcripts that possessed the m6A mark in oligodendrocytes but not in OPCs . Only 23 of the shared transcripts , showed the m6A mark in both OPCs and oligodendrocytes.
Conclusions: The dynamic nature of the m6A mark in oligodendrocyte lineage cells suggests that it may play an important role in oligodendrocyte differentiation and CNS myelination.

overall_design: mRNA from total RNA of  Mettl14fl/fl OPCs and mature oligodendrocytes was purified , immunoprecipitaed with m6A antibody, and then sequenced using the SMART-seq protocol.

first: Yilan

last: Weng


title: Comparing the transcriptoms of Mettl14fl/fl and oligodendrocyre precursor cell (OPCs) and mature oligodendrocytes(OL)

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


title: Developmentally controlled expression of Cxcr4 by hematopoietic progenitors allows tracing of monocyte function in stroke

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Monocyte-derived and tissue-resident macrophages, such as microglia, belong to independent lineages with distinct functions in steady state. During inflammation, however, changes in phenotypes and transcriptional profiles make it difficult to assess their respective roles in pathology. Here, we report that developmentally controlled expression of Cxcr4 by hematopoietic progenitors allows highly specific inducible lineage tracing of hematopoietic stem cell-derived monocytes during inflammation. In two stroke models, we found that monocytes recruited to the brain were confined to the lesion and its surrounding during the acute phase. However, monocytes did not engraft in peri-lesional tissue, but were enclosed in scar tissue by microglia and astrocytes after completed repair. Transcriptional profiles of brain monocytes and microglia reflect major differences in signaling pathways, paracrine mediators, and proliferative behavior. Initial recruitment and subsequent enclosure of monocytes required Cxcr4. Our data show that CXCR4 signaling regulates a specific monocyte-mediated contribution to injury and repair in stroke.

overall_design: Cxcr4-GFP mice 2 populations (monocytes and microglia) 3d post permanent photothrombosis (n=4) & Cxcr4 conditional KO (Cxcr4CreER KO) and wt mice (Cxcr4CreER contol) 2 populations each (monocytes and microglia) 3d post permanent photothrombosis (n=3)

first: Yves

last: Werner

first: Elvira

last: Mass


title: Expression data from MCP-1-treated human kidney cancer CRL-1932 cell line

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary:
Microarray analysis revealed MCP-1 treatment altered protein folding processes in RCC CRL1932 cells. In response to MCP-1 treatment, CRL1932 cells and xenograft tumors expressed MCP-1-induced protein (MCPIP) which was reported to cause endoplasmic reticulum (ER) stress-induced apoptosis in human cardiomyocytes. In line with MCPIP induction, the expression of ER stress mediators, such as GRP78, PERK, IRE1α, and PDI, as well as molecules involved in ER stress-induced apoptosis, CHOP, calnexin, and Ero1α, presented in MCP-1 treated RCC cell line and xenograft tumors whereas absent or downregulated in untreated controls. TUNEL assay confirmed apoptosis of MCP-1 treated CRL1932 cells. MCPIP ectopically expressed in HEK293 cell resulted in apoptosis. Meta-analysis showed low level of MCP-1 associated with lower one year-survival rate after nephrectomy in RCC.
In this dataset, we include the expression array data from human kidney cancer CRL-1932 cell line with or without the treatment of MCP-1. These data were used to obtain genes upregulated in MCP-1-treated CRL-1932 cells.

overall_design: In total, 4 samples were analyzed. We generated the following pairwise comparisons using Affymetrix Expression Console™ Software (version 1.4): CRL 1932 compared with MCP-1-CRL1932. Genes with a P value < 0.05 and a fold-change ≥1.5 were selected. To identify the potential epigenetic targets of MCP-1, we performed Venn diagram analysis with genes showing either up-regulated by MCP-1 treatment.

first: Chia-Huei

first: Chiao-Yin

last: Sun


title: Transcriptome of clec-4 for the nematode Caenorhabditis elegans

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

summary: C-type lectin-like domain (CTLD) encoding genes are highly diverse in C. elegans, comprising a clec gene family of 283 members. Since vertebrate CTLD proteins have characterized functions in defense responses against pathogens and since expression of C. elegans clec genes is pathogen-dependent, it is generally assumed that clec genes function in C. elegans immune defenses. In this study we challenged this assumption and focused on the C. elegans clec gene clec-4, whose expression is highly upregulated upon infection with various pathogens. We tested the involvement of clec-4 in the defense response to infection with Pseudomonas aeruginosa PA14, Bacillus thuringiensis BT18247, and the natural pathogen Serratia rubidaea MYb237. Contrary to our expectation clec-4(ok2050) mutant worms were not more susceptible to pathogen infection than wildtype worms. To explore potential redundant function between different C. elegans clec genes, we investigated expression of several clec-4 paralogs, finding that clec-4, clec-41, and clec-42 expression shows similar infection-dependent changes and co-localizes to the intestine. We found that only clec-42 is required for the C. elegans defense response to BT18247 infection and that clec-4 genetically interacts with clec-41 and clec-42. The exact role of clec-4 in pathogen defense responses however remains enigmatic. Our results further indicate that a complex interplay between different clec genes regulates C. elegans defense responses.

overall_design: mRNA profiles of wild type (WT) and clec-4 (ok2050) C.elegans exposed to either Bacillus thuringiensis B-18247, B-18679 and B18407 or standard lab food E. coli OP50 at 6h or 12h were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Barbara

last: Pees

first: Katja

last: Dierking


title: Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection.

city: Warszawa

first: Aneta

last: Więsyk

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

summary: We employed microarray analysis to observe dynamic changes of gene expression profiles in response to mild and severe potato spindle tuber (PSTVd) infection in the roots of tomato cv ‘Rutgers’.

overall_design: Solanum lycopersicum cv 'Rutgers' was infected with mild (M) and severe (S23) PSTVd isolates. Root samples were collected at three phases of disease: i) early stage of symptoms -17 dpi; ii) full spectrum of symptoms – 24 dpi; iii) recovery - 49 dpi. Three independent biological replicates of PSTVd-M, PSTVd-S23 and pUC9 (control) were analised at every time point but two replicates of PSTVd-S23 at 17dpi. Totally 26 samples of RNA were analysed.

first: Anna

last: Góra-Sochacka

last: Fogtman


title: Disrupting ß-catenin dependent Wnt signaling activates an invasive gene program predictive of colon cancer progression

city: Irvine

first: Marian

middle: L.

last: Waterman

state: CA

address: Rm B251 Medical Sciences I, School of Medicine

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: The recent classification of colon cancer into molecular subtypes revealed that patients with the poorest prognosis harbor tumors with the lowest levels of Wnt signaling. This is contrary to the long-standing understanding that overactive Wnt signaling promotes tumor progression from early initiation stages through to the later stages including invasion and metastasis. Here, we lower the levels of Wnt signaling in SW480 and SW620 colon cancer cell lines via interference with two different steps in Wnt signaling that lie upstream or downstream of the effector protein ß-catenin. We find that these Wnt-reduced lines exhibit a more aggressive disease phenotype, including increased mobility in vitro and localized invasion in an orthotopic mouse model. RNA sequencing reveals that interference with Wnt signaling leads to an upregulation of gene programs that favor cell migration and invasion. We identify a set of upregulated genes common among the Wnt perturbations, and find that elevated expression of these genes is strongly predictive of poor patient outcomes in early-invasive colon cancer. These genes may have clinical applications as either patient biomarkers or new drug targets to be used in concert with existing therapies.

overall_design: Gene expression profiles of colorectal adenocarcinoma cell lines SW480 (dominant negative LEF1 and mock), SW620 (dominant negative LEF1, mock, LRP6 knock-out using CRISPR/Cas9, and Cas9 mock), and mock (PBS injection) xenografts in mouse host. All experiments were done in biological triplicates.

middle: L

first: Ali

last: Mortazavi

first: Robert

middle: A

last: Edwards

first: George

middle: T

last: Chen

first: Rabi

last: Murad

first: Delia

last: Tifrea

first: Yung

last: Lyou


title: Platelet gene expression profiling of acute myocardial infarction

city: Parma

first: Guidantonio

last: Malagoli Tagliazucchi

address: Via Gramsci 14

department: Division of Research and Innovation

country: Italy

institute: Hospital of Parma

summary: Acute myocardial infarction (AMI) is primarily due to coronary atherosclerotic plaque rupture and subsequent thrombus formation. Platelets play a key role in the genesis and progression of both atherosclerosis and thrombosis. Since platelets are anuclear cells that inherit their mRNA from megakaryocyte precursors and maintain it unchanged during their life span, gene expression (GE) profiling at the time of an AMI provides information concerning the platelet GE  preceding the coronary  event. In ST-segment elevation myocardial infarction (STEMI), a gene-by-gene analysis of the platelet GE identified five differentially expressed genes (DEGs): FKBP5, S100P, SAMSN1, CLEC4E and S100A12. The logistic regression model used to combine the GE in a STEMI vs healthy donors score showed an AUC of 0.95. The same five DEGs were externally validated using platelet GE data from patients with coronary atherosclerosis but without thrombosis. Early signals of an imminent AMI are likely to be found by platelet GE profiling before the infarction occurs.

overall_design: Platelet gene expression profiling in ST-acute myocardial infarction (STEMI) patients, Healthy Donor (HD), coronary artery diseases (SCAD) patients

first: Giuliana

last: Gobbi

first: Cecilia

last: Carubbi

first: Elena

last: Masselli

first: Prisco

last: Mirandola

first: Filippo

last: Pigazzani

first: Antonio

last: Crocamo

first: Maria Francesca

last: Notarangelo

first: Sergio

last: Suma

first: Elvezia

last: Paraboschi

first: Giuseppe

last: Maglietta

first: Srikanth

last: Nagalla

first: Daniela

last: Galli

first: Paolo

last: Fortina

first: Sankar

last: Addya

first: Adam

last: Ertel

first: Paul

last: Bray

first: Stefano

last: Duga

first: Carlo

last: Berzuini

first: Marco

last: Vitale

first: Diego

last: Ardissino


title: Comparing the transcriptoms of Mettl14fl/fl and Mettl14 fl/fl; Olig2-Cre oligodendrocyre precursor cell (OPCs) and mature oligodendrocytes using Next Generation Sequencing

first: Huan

last: Xu

summary:
The goal of the experiment is to determine the transcriptome alternation of Mettl14 gene inactivation in different oligodendrocyte lineage cells(OPCs and mature oligodendrocytes), by comparing the Mettl14 fl/fl; Olig2-Cre(mutant) and Mettl14fl/fl(control) OPC and mature oligodendrocyte transcriptoms.
Method:  RNA collected from Mettl14fl/fl control and Mettl14fl/fl;Olig2-Cre OPC and oligodendrocytes was collected by standard protocols, sequenced using next generation high throughput sequencing technology, and processed in triplicate to produce a transcriptome profile deliminating the variable gene expression in the mutant cells.
Results: We identified 11809 transcripts present in the OPC transcriptome, 586 were significantly upregulated and 177 were significantly downregulated in the mutant cells; Among 12,542 transcripts present in mature oligodendrocytes, 1388 transcripts were upregulated and 1247 were downregulated in the mutant cells(significance: q-value<0.001; fold changes (FC) that exceed 2.0 fold (log2 |FC|>1) in expression and an expression level that exceeds two counted transcripts per million (log2 |CPM| >1))
Conclusions: Mettl14 ablation differentially alters the OPC and oligodendrocyte transcriptomes

overall_design:
mRNA profiles of cultured  Mettl14fl/fl (control) and Mettl14 fl/fl; Olig2-Cre (mutant) oligodendrocyre precursor cell (OPCs) and mature oligodendrocytes were generated by sequencing, in triplicate, using Illumina HiSeq 4800.
contributor: Genomic facility at the University of Chicago, Bioinformatics core at the University of Illinois of Chicago, Joshua S Johns


title: YAP activation mediates acquired resistance to ALK inhibitor in ALK rearranged non–small cell lung cancer

city: Seoul

first: Mi Ran

last: Yun

address: 50-1 Yonsei-Ro Seodaemun-Gu

department: Yonsei Cancer Research Institute

country: South Korea

institute: JE-UK Laboratory of Molecular Cancer Therapeutics

summary: To investigate a possible candidate for overcoming the acquired resistance to ALK-TKI, we established an in vitro model of acquired resistance to crizotinib (H3122-CR) by exposing EML4-ALK–positive H3122 lung cancer cells to increasing doses of crizotinib.

overall_design: We extracted RNA using QIAGEN Rneasy mini kit from three normal H3122 cell lines, three Crizotinib resistant cells and hybridized to the Affymetrix GeneChip Array.

first: Mi

first: Hun

last: Choi

first: You

last: Lee

first: Hyeong

middle: S

last: Joo

first: Chae

last: Park

first: Jae

first: Hyo

last: Shim

first: Ross

last: Soo

first: James

last: Yang

first: Sung

first: Hyun

last: Chang

first: Min

middle: H

last: Kim

last: Hong

first: Hye

first: Byoung

last: Cho


title: The transcriptome of Penicillium expansum and apple interaction during early infection

city: Zhenjiang

first: Kaili

last: Wang

state: Jiangsu

address: Xuefu Road 301

department: School of food and biological engineering

institute: Jiangsu University

summary: This study aims to better understand the transcriptome changes of P. expansum and apple during early infection process.

sample_organism:
Penicillium expansum
Malus pumila

platform_organism:
Penicillium expansum
Malus pumila

overall_design: Examination of 4 different time points modifications in pathogen and host.

first: Xiangfeng

last: Zheng


title: Gene expression profiling of control and Carmil3-deficient 4T1 cells

city: Shanghai

first: Xiaojing

last: Ma

address: Dongchuan Rd. 800

institute: Shanghai Jiao Tong University

summary: To systemically study the molecular function of CARMIL3 in cancer cells, we used mammary tumor cells, 4T1, as a model and genetically depleted Carmil3 via CRISPR/Cas9 strategy, followed by genome-wide transcriptional analysis by RNA-seq. We find that loss of Carmil3 leads to down regulation of genes that are involved in cell adhesion, including Cdh1 which encodes E-cadherin, a marker of epithelial cells. Thus, our study suggests that CARMIL3 is implicated in regulating epithelial to mesenchymal transition and cancer metastasis.

overall_design: The mRNA expression profiles between control and Carmil3 KO 4T1 cells were compared with RNA-seq in triplicate.

first: Huan


title: RNA illumina sequencing of Panax notoginseng under CK and Cd stress treatment

city: Kunming

first: Peiran

last: Liao

address: No.727 South Jingming Rd., Chenggong District, Kunming 650500, China

institute: Kunming University of Science and Technology

summary: The total RNA were extracted from tissues of roots from several plants of Panax notoginseng under CK and Cd stress treatment by using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The purified PCR product was sequenced using Illumina Genome Analyzer II. The qualified reads were used to study of Panax notoginseng transcriptome under CK and Cd stress treatment.

overall_design: Identification of Panax notoginseng transcriptome under CK and Cd stress treatment

first: Ye


title: Truncated BRPF1 cooperates with Smoothened to induce adult Shh medulloblastoma

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

institute: University of Trento

summary: We performed ATAC-seq analysis, in order to understand the role of SmoM2 and truncated BRPF1 on the epigenetic landscape during medulloblastoma disruption

overall_design: We performed ATAC-seq analysis on frozen cerebella from Gabra6-cre;LSL-SmoM2 and control Gabra6-cre mice and on hSynI-creER+LSL-tdTomato, hSynI-creER+LSL-BRPF1 TR, hSynI-creER+LSL-SmoM2 and hSynI-creER+LSL-SmoM2+LSL-BRPF1 TR nucleofected AF22 neuroephitilial-like stem cells

first: Luca

last: Fagnocchi

first: Alessio


title: Genome-wide RNA-seq from c-MYC-depleted and rescued MDA-MB-231BrM cells

city: DaeJeon

first: Mi Young

address: Biological science

institute: KAIST

summary:
Purpose: To identify downstream signaling pathways that mediate functions of c-MYC
Methods: RNAs isolated from MDA231-BrM cells expressing shCntr or shc-MYC,  pCDH-puro control vector or c-MYC expression vector were analyzed by using an Illumina Nextseq500
Conclusions: Our study represents the first transcriptome profile of c-MYC-depleted and rescured MDA231-BrM

overall_design: mRNAs prepared from c-MYC knockdown or c-MYC rescued  MDA-MB-231 BrM cells were analyzed in duplicaters by Illumina Nextseq500. RNA-Seq reads were aligned to the human reference genome (NCBI 38) using the spliced read aligner STAR software (ver2.5)

first: Ho

middle: Y

first: Mi

first: Seon

middle: K


title: RNA-seq based identification of potential RARgamma target genes in Xenopus laevis

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary: The development of massively parallel sequencing technologies has revolutionized transcriptome analysis. Sequencing of total cDNA (RNA-Seq) can determine the expression levels of known and novel transcripts with high sensitivity from various developmental stages or conditions. Here we report a robust method for RNA-Seq in Xenopus laevis and apply it to understanding how modulation of retinoic acid signaling alters the transcriptome in early Xenopus laevis development. Three biological conditions were tested: early blastula stage embryos were treated with 1. a retinoic acid receptor (RAR) agonist NRX204647 (4647) at a concentration that stimulated all 3 RAR subtypes (alpha, beta, and gamma); 2. The same agonist at an RAR[gamma] selective dose, and 3. vehicle control. Five single-clutch replicates were obtained for each chemical treatment group, and harvested at neurula stage. We found that single-clutch replicates reflect the stochastic variation of the general outbred population and contribute more statistical power to RNA-Seq experiments due to their feasibility of replication. Our RNA-Seq dataset identified 1590 up-regulated and 685 down-regulated unique genes differentially regulated by all RAR subtypes, and 160 up-regulated and 60 down-regulated genes likely to be regulated specifically by RAR[gamma]. Differential expression detected by RNA-Seq was validated for selected genes by QPCR, which demonstrated nearly 100% quantitative agreement with the deep sequencing data. We further validated RAR-responsive genes by comparison with two previous, published microarray datasets and found substantial agreement. Gene ontology analysis identified RAR targets which may underlie such developmental processes as axial elongation, neurogenesis/synaptogenesis, dorsoventral regulation of the retina, homeotic fate specification, and central nervous system development. We investigated RAR[gamma]-selective targets identified by RNA-Seq and inferred that transcriptional repression by unliganded RARs is of substantial importance to embryonic patterning events. Overall, this paper demonstrates the utility of RNA-Seq in Xenopus laevis, obviating the perceived requirement to use X. tropicalis for genomic analyses.

overall_design: Xenopus laevis early blastula stage embyos were exposed to (1) 0.1% EtOH as vehicle, (2) an RARgamma-selective dose (10 nM) NRX204647, and (3) a high dose (1 microM) of NRX204647, which activates all three RAR subtypes (RARalpha, beta, gamma). Each exposure group cosisted of five single-clutch replicates.

first: Amanda

last: Janesick

first: Weiyi

last: Tang

first: Bruce

last: Blumberg

first: Toshi


title: A gene expression signature for NOTCH receptor activation

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

summary: In many solid cancers and leukemia’s deregulation of the NOTCH signalling pathway is frequently observed, which led to the initiation of clinical trials. However, results from clinical trials using small molecule inhibitors of NOTCH so far are disappointing due to low efficacy and a high toxicity. One shortcoming in these patient studies is the lack of prognostic, predictive and pharmacological biomarkers that could accompany trial design and treatment adaptation. The purpose of this study was to develop an mRNA based NOTCH isoform-specific gene expression signature, which allows for robust identification of NOTCH activity in human tumours.

overall_design: Here we generated gene expression profile of 15 cell lines using RNA-Sequening. In total, we have 5 groups. We have control group (EV) and 4 gorups each expressing different NOTCH receptor. So, NOTCH 1-4 groups. In total, we have 15 RNA-Seq datasets (5 groups and 3 replicate per group= 15 samples)

first: Marc

last: Vooijs

first: Zita

last: Soons

first: Roger

last: Habets

first: Lydie

last: Barbeau

first: Arjan

last: Groot


title: Gene Expression Profiling of Gemcitabine, Genistein and Combinatorial Effects on Pancreatic Cancer Cell Lines

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

country: Sweden

institute: KTH Royal Institute of Technology

summary: We reported the transcriptional effects of gemcitabine, genistein and the combined gemcitaibe/gensitein treatments on two pancreatic cancer cell lines MiaPaCa2 and PANC1. The overall purpose of the study to understand the underlying mechanism of genistein chemoenhancing function.

overall_design: Two pancreatic cancer cell lines were treated either with 40nM of gemcitabine (Gem2), 50uM of genistein (Gen) or in combination for 24 hours. RNA was isolated and purified by using Qiagen RNAasy kit. The quality and concentraion of RNA were detected by using bioanalyzer.

first: Sebastian

last: DiLorenzo

first: Fahmi

last: Mesmar


title: Genome-wide expression analysis of mesenchymal stem cells isolated from clinical donors in response to FGF2 binding heparan sulfate

status: Public on Dec 30 2019

city: Singapore

first: Padmapriya

last: Sathiyanathan

address: 8A Biomedical Grove

department: Glycotherapeutics Group

country: Singapore

institute: Institute of Medical Biology

summary: Effect of FGF2 binding heparan sulfate on mesenchymal stem cells was studied and found to influence potency. Gene expression profiling was then performed to undertand its response at the transcriptome level.

overall_design: Total RNA obtained from mesencymal stem cells treated with heparan sulfate for two weeks.

first: Ling

last: Ling


title: Differential Gene Expression of Mucosal-Associated Invariant T Cells of HCC patients and Healthy Controls

first: Yun

last: Liu

address: 130 Dong An Road

institute: Fudan University

summary: The goal is to investigate whether the transcription profile of MAIT cells are changed in HCC tumors compared to normal livers.

overall_design: MAIT cells were sorted out from primary tumors or tumor peripherals of HCC patients or healthy liver donors. These sorted cells were subjected to NGS to identify differentially expressed genes.


title: RNA sequencing for tumor-initiating stem-like cells (TICs) treated with all-trans retinoic acid (ATRA) and suberoylanilide hydroxamic acid (SAHA)

city: Los Angeles

first: Keigo

last: Machida

address: 2011 Zonal Ave., HMR503C

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary:
TIC population plays a vital role for tumor recurrence and therapy resistnace. In this study, we identified the drug combination of ATRA and SAHA can specifically target TICs in vitro and in vivo.
By conducting RNA sequencing and genome-wide transcriptome analysis, we comprehesively illustrate that the combination treatment epigenetically regulates TICs.

overall_design: The TICs were treated with 5ug/ml of ATRA, 0.5ug/ml of SAHA or both for RNA sequencing by using Illumina HiSeq2500 system.

first: Chia-Lin

last: Chen


title: OX40 mediates crosstalk between innate and adaptive immunity and promotes nonalcoholic steatohepatitis development

city: Beijing

first: Guangyong

last: Sun

address: Yongan Street 95, Xicheng District

institute: Beijing Friendship Hospital

summary:
Methods: To better understand the role of OX40 in the regulation of monocyte activation and polarization, OX40/Fc- or control IgG-treated liver monocytes were compared in a transcriptome sequencing study. Total RNA was isolated from FACS-separated hepatic monocytes. Transcriptome sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Sequences were aligned to the reference genome with TopHat and processed with Cufflinks, which quantifies each transcript in each sample using reference annotations produced bythe University of California Santa Cruz UCSC. Differentially expressed genes with a fold change of >=2.0 and padj < 0.05 between OX40 treated and control monocytes were submitted to GO and KEGG enrichment analysis, which uses unbiased methods to assess pathway enrichment.
Results: Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that upregulated genes from OX40-stimulated monocytes are involved in inflammatory response; cytokine production regulation; lipid, cytokine and bacteria responses; innate immune response; enhanced cellular response to cytokines and the cytokine-cytokine receptor interaction; and the phagosome and chemokine signaling pathway, among others. Compared to control monocytes, OX40/Fc-treated monocytes exhibited upregulated levels of cytokines (Tnf, Il1a, Il1b, Il6 and Il12a), cytokine receptors (Il1rl1, Il2r, Il18r and Il23r), chemokines (Ccl3, Ccl4, Ccl22, Cxcl1, Cxcl2, Cxcl10 and Cx3cl1), chemokine receptors ( Ccrl2, Cxcr5 and Cxcr6) and antigen processing and presentation molecules (Cd40, Cd80, Cd86, Tlr1, Tlr2, and Ox40l). The coordinated action of various inflammatory modulators, signaling molecules, and transcription factors, including Nlrp3, Tank, Jak2, Stat5a, Hif1a, Nos2, Socs3, Mir155hg and Pparg, was determined to be involved in the OX40 regulation of monocyte M1 polarization. MyD88, Irf3, Irf5, Stat1, Nod1 and Nod2 may not be involved in OX40-triggered monocyte M1 polarization.

overall_design: The hepatic monocytes mRNA profiles of IgG control and OX40 Fc stimulated were generated by deep sequencing in duplicate, using Illumina HiSeq.

first: Dong

last: Zhang


title: Gene expression profile in Caco-2 cells infected with Japanese encephalitis virus

city: Tirupati

first: Guruprasad

middle: Ramarao

last: Medigeshi

state: Andhra Pradesh

address: Panguru (G.P.), Yerpedu Mandal

department: Biology

country: India

institute: Indian Institute of Science Education and Research Tirupati

summary: Caco-2 cells grown on transwells were infected with Japanese encephalitis virus (JEV) and total RNA was isolated from cells at the time when trans-epithelial electrical resistance was reduced by about 50% of uninfected cells

overall_design: Cells grown on 12-well transwell filters. Three replicates of uninfected and infected samples

middle: R

first: Ashish

last: Trivedi


title: Gene expression profiles of differentiating BMSCs from WT and Irx5 knockout mice during osteoblastogenesis (day 4 post differentiation)

first: Li

last: Jinsong

address: Yueyang Road

institute: SIBCB, CAS

summary: Functional mutagenic screening has been used to identify key factors required for a wide range of developmental processes. However, such screens can only be successfully applied in lower organisms. Here, through combined application of androgenetic haploid embryonic stem cells (haESCs) and CRISPR-Cas9-based genome editing, we quickly identify pivotal factors involved in early bone development from a medium-scale gene library. Injection of haESCs carrying constitutively expressed Cas9 and an sgRNA library containing 216 sgRNAs targeting 72 preselected candidate genes into oocytes produced biallelic mutant mice with high efficiency. Through skeletal phenotype analysis by Alcian blue and Alizarin Red staining at birth, we identified transcriptional factor Irx5 as a positive regulator of bone development. Irx5 KO mice generated by regular method exhibited obvious decreased bone mass and increased adipogenesis in the bone marrow. Moreover, the deletion of Irx5 from bone marrow cells prohibited osteoblast differentiation and enhanced adipocyte differentiation ability in vitro. Mechanistically, IRX5 promotes osteoblastogenesis and inhibits adipogenesis by suppressing PPARγ expression. We conclude that haESC-mediated SC technology, in combination with a targeted sgRNA library, can be used as a powerful reverse genetic screening strategy to identify pivotal factors involved in mouse development.

overall_design: Gene expression examination of BMSCs from WT and Irx5 knockout mice after 4 days osteoblast differentiation.Each sample has 3 repeats.

first: Jinsong

last: Li

first: Weiguo

last: Zou


title: Regulatory Macrophages

city: Regensburg

first: James

middle: Alexander

last: Hutchinson

state: Bavaria

department: General Surgery

institute: University Hospital Regensburg

summary: The phenotypic proximity of the human regulatory macrophage (M reg) to a panel of comparator macrophages in defined polarisation states was assessed by whole-genome transcriptional profiling.

overall_design: Human M regs and comparator macrophages were generated from positively-isolated CD14(+) peripheral blood monocytes from three normal, healthy individuals.

first: Michael

last: Rehli


title: Genomic Signatures for Pesticide Exposure in Latino Farmworkers

city: Durham

first: Lisa

last: Satterwhite

state: North Carolina

address: 101 Science Drive

department: Department of Civil and Environmental Engineering

institute: Duke University

summary: We tested the hypothesis that differential  gene expression in whole blood will reveal candidate blood biomarkers for exposure to agricultural pesticides and herbicides.  Blood gene expression in male Latino farmworkers, where chronic pesticide exposure is occupational, was compared to blood gene expression in age and gender matched Latino manual workers. We identified an expression signature for farmwork, differential expression in genes that correlated with levels of urinary pesticide metabolites, alterations in axonal guidance pathways and statistical models that link farmworker differential expression to Parkinson's disease.

overall_design: Case control, 20 male Latino farmworkers compared to 20 age matched male Latino manual workers.

first: Joseph

last: Lucas

first: Martyn

last: Darby


title: Expression data from livers of 15-weeks garlic-fed mice

city: Urla

first: Bunyamin

last: Akgul

state: izmir

address: Gulbahcekoyu

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

summary:
Garlic is a popular flavor enhancer in modern cuisines. Although anti-atherosclerotic, anti-proliferative, hypolipidemic and chemopreventative effects of garlic are known for a long time, the mechanisms of garlic as a dietary supplement ramain largely unknown.
We used microarrays to analyze the global programme of gene expression in the liver tissues of control (cellulose) and garlic-fed C57BL/6J mice maintained at an SPF (Specific Pathogen Free) facility.

overall_design: 8-week old male C57BL/6J mice were divided into two diet groups and maintained at a barrier facility (SPF). Mice were fed (ad libitum) a special diet (Yeh and Yeh, 1994) with 4% cellulose (Control group, 3 mice) or 4% lyophilized raw garlic powder (Treatment group, 3 mice). At the end of the 15-week treatment, liver organs were used for RNA isolation and arraying.

first: Bünyamin

last: Akgül

first: Chen-Pei

middle: D

last: Tu


title: A novel lineage of adipose tissue regulatory T cells controls obesity and insulin resistance

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

institute: UCL Cancer Institute

summary: The epidemic of obesity and its associated systemic metabolic complications continues to increase. Adipose tissue (AT)-associated T cells have been proposed to play an important role in the regulation of bodyweight and insulin sensitivity with a link to Th1 or Th2 lineage specification. A specific subset of regulatory T cells (TREGS) plays a critical and non-redundant role in controlling systemic autoreactive immune responses. However, the lineage and functional role of TREGS found in AT (AT-TREGS) is undefined. Here we show that AT- TREGS comprise a distinct functional lineage. Remarkably, despite expressing a robust Th2 gene signature, AT-TREGS are predominantly derived from a precursor cell that had previously expressed the Th1 cell master regulator T-bet (Tbx21). This lineage relationship has profound functional consequences, as TREG- specific deletion of T-bet rendered mice completely resistant to diet induced obesity and insulin resistance. Mechanistically, T-bet directly suppresses ST2 (IL-33 receptor) expression, which renders Tregs less responsive to IL33-driven expression of amphiregulin in a cell-intrinsic manner. Our results identify a novel AT-selective TREG population with an unexpected lineage origin that determines the pathological response to a high fat intake. Understanding the upstream signals that regulate the survival and function of this cell-type may have profound relevance to the treatment of obesity and its associated disease, such as type II diabetes, cardiovascular disease, renal failure and stroke.

overall_design: ChIP-seq to identify T-bet binding sites in murine Treg cells

first: Emilie

last: Stolarczyk

first: Charlotte

last: Bailey

first: Natividad

last: Garrido-Mesa

first: Paul

last: Lavender

first: Graham

last: Lord

first: Jane

last: Howard


title: Comparative study on stage-specific transcriptomics reveals key characters in Chaetomium globosum sexual development

status: Public on Dec 29 2019

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Chaetomium globosum  is a model of conditional pathogens abundant on a wide variety of substrates in soil, water, and atmosphere environments. Homothallic C. globosum produces hairy perithecia bearing meiotic ascospores that are resistant to harsh conditions for dispersal, and asexual reproduction of conidia has never been observed. RNAs were samples from nine distinct morphological stages during the nearly synchronic perithecial development for C. globosum. Unlike the heterothallic Neurospora crassa, the mating type gene mat a-1 showed comparatively lower expression changes but highly coordinate with expression regulation of mat A-1 in C. globosum. Key regulators, including orthologs of N. crassa sub-1,  sub-1 dependent gene NCU00309, and asl-1, in the initiation of sexual development in response to light stimuli, showed similar regulation dynamics between C. globosum and N. crassa. Knockout phenotyping directed by the comparative analysis of transcriptomics between C. globosum and its’ closely related Neurospora crassa also suggested some genes that are critical for perithecial development. Among 24 secondary metabolism clusters composed more than 3 genes in C. globosum, 11 showed highly coordinated expression across the perithecial development, and dramatically up-regulation was recorded for all 12 genes in the cochliodones biosynthesis cluster. Up-regulation of chaetoglocin and aureonitol biosynthesis clusters was found to be associated with disturbance in early sexual development and with ascospore maturation. Similar to pathogenic Fusarium graminearum, C. globosum showed coordinately up-regulated expression of homologs of histidine kinases in hyperosmotic response pathways, consist with their ecology adapting to high humidity.

overall_design: mRNA were sampled from 9 stages of Chaetomium globosum sexual development, from protoperithecia (0hr), distrubance (2hr), then the other 7 timepoints with a 24hr interval for the perithecial development.

first: Zheng

last: Wang

last: Lopez-Giraldez

first: Junrui

first: Frances

last: Trail

first: Jeffrey

middle: P

last: Townsend


title: Gene expression profiles of mouse colonic epithelial monolayer cultured in air-liquid interface

city: Cleveland

first: Thaddeus

last: Stappnbeck

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Cleveland Clinic, Lerner Research Institute

summary: The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excessive inflammation. Our understanding of how this process occurs is limited by a lack of in vitro models that recapitulate key aspects of in vivo responses. We established a long-term, self-organizing 2D epithelial monolayer system to model the cyclic nature of epithelial alterations during injury-repair. Through RNA-seq analysis, we seek to evaluate the transcriptomic profiles of the cultured epithelial cells under select phases of “homeostasis-injury-repair” in vitro.

overall_design: We performed RNA-seq on three separate sets of cultured mouse colonic monolayer samples collected at various time points after swittching to air-liquid interface (ALI) or re-submersion (Re-Sub): (1) monolayer RNA samples collected at ALId0, ALId4, ALId7, ALId14 and ALId21; (2) monolayer RNA samples collected at ALId0, ALId1, ALId2 after switching to air-liquid interface; (3) monolayer RNA samples collected at Re-Sub 0h (=ALId21), Re-Sub 8h, Re-Sub 24h and Re-Sub d7.

first: Yi

first: Brian

last: Muegge

last: Stappenbeck


title: Epigenomic and transcriptomic dynamics of Arabidopsis senescent leaves

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

institute: SLU

summary: Senescence occurs in a programmed manner to dismantle the vegetative tissues and redirect the nutrients towards metabolic pathways supporting reproductive success. External factors can trigger the senescence program as an adaptive strategy, indicating that this terminal program is controlled at different levels. Using bisulphite conversion followed by sequencing, we interrogated changes in the methylome of senescent Arabidopsis leaves induced by darkness, and their impact on gene and transposable element (TE) expression with transcriptome sequencing. Two biological replicates were sequenced for each condition: S as senescent and NS as non senescent.

overall_design: The leaves No. 5-6th from 42 days old plants was individually covered with a black mitten for 5 days to induce senescence by darkness. Tissue was collected on the 48th day. Non-senescent tissue corresponds to a mix of uncovered leaves from the same plants. Bisulphite and RNA sequencing was perform in two biological replicates. Differentially methylated regions induced by senescence were called in the merged mapping files of the biological replicates.

last: Trejo-Arellano

first: Saher

last: Mehdi

first: Jennifer

last: de Jonge

first: Eva

last: Dvorák Tomastíková

first: Claudia

last: Köhler

first: Hennig

last: Lars


title: Transcriptome of heat-stressed lactating mice in hypothalamus, pituitary and mammary gland

city: Hangzhou

first: Jialiang

last: Han

address: yuhantang street 866

institute: zhejiang university

summary: Purpose: Using RNA-seq, this study explored the possible cross-talk between the hypothalamic-pituitary axis and mammary system under heat stress and to understand the biological process using a mice model, which may contribute to the understanding of the molecular mechanisms of poor lactation performance under exposure to high ambient temperatures.

overall_design: Animals: timed-pregnancy ICR mice, control group (25 °C, 55% ±5% RH) and heat stress group (36 °C, 55% ±5% RH). Temperature: controlled by an artificial climate incubator to expose the cages housing the mice to the experimental temperature (36 °C) and relative humidity (RH: 55% ±5%). Animals were sacrificed immediately after treatment on day 13 for the purpose to study the peak lactation responses to heat stress. The hypothalamus, pituitary and left inguinal (#4) mammary gland of all dams were collected.

first: Hongyun

last: Liu


title: Development and application of a Ligation-based Library vs Library high- throughput Yeast Two-Hybrid (LLL-Y2H) screening system

city: Wuhan

first: Yingying

last: Lei

state: China

address: NO. 1 shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: We developed a Ligation-based Library vs Library high-throughput Yeast Two-Hybrid (LLL-Y2H) screening system to explore protein interactions.

sample_organism:
Mycobacterium tuberculosis
Mus musculus

platform_organism:
Mycobacterium tuberculosis
Mus musculus

overall_design: full library,screening 1 and screening 2

first: Fang

last: Yang

first: Gang

last: Cao

first: Yichao

first: Meiling

last: Zhou

first: Xiang

last: Wu

first: Weize

last: Xu


title: Transcriptional correlates of pathological phenotype in a Huntington’s disease mouse model

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

summary: Huntington disease (HD) is a fatal neurodegenerative disorder without cure, caused by an aberrant expansion of CAG repeats in the exon 1 of the Huntingtin (HTT) gene. Although the negative correlation between the number of CAG repeats and the age of disease onset is well established, additional factors may contribute to the high heterogeneity in the complex manifestation of the symptoms among patients. This variability is also observed in the phenotype of mouse models, even under controlled genetic and environmental conditions. To better understand this phenomenon, we analyzed the R6/1 strain in search of potential correlates between pathological motor/cognitive phenotypical traits and transcriptional alterations. HD-related genes (e.g., Penk, Plk5, Itpka), despite being downregulated across the examined brain areas (prefrontal cortex, striatum, hippocampus and cerebellum), exhibited a tissue-specific correlative association with particular phenotypical traits, attributable to the contribution of the brain region to regulate the trait (e.g., striatum and rotarod performance, cerebellum and feet clasping). Focusing on the striatum, we determined that the transcriptional dysregulation associated with HD was partially exacerbated in those mice showing poor phenotypical scores, affecting genes extensively described in this disease (e.g. Pde10a, Drd1, Drd2, Ppp1r1b). However, we also observed transcripts associated with relative better outcome, such as CCAAT-binding transcription factor NF-Y and others related with neuronal development, apoptosis and differentiation. In this study we demonstrate that altered brain transcription is capable of tracking the variations in the manifestation of HD-like symptoms in mouse models that may be extrapolated to the highly heterogeneous population of HD patients.

overall_design: Comparison of R6/1 and wild-type littermates, with either good or poor performances in behavioural battery tests.


title: Differentially expressed cellular and exosomal miRNAs during inflammation or high fat diet-induced obesity in mouse

city: Kingston

first: Xinzhi

last: Li

state: Ontario

address: 18 Stuart Street

department: Biomedical and Molecular Sciences

country: Canada

institute: Queen's University

summary: The aim of the current study was to characterize the differential cellular and exosomal miRNAs during inflammation or high fat diet-induced obesity in mice. Mesenteric adipose tissue (MAT) and abdominal aorta (AA) from mice fed a normal chow diet (NCD) or a high fat diet (HFD) were harvested for miRNA profiling. MAT-derived adipocytes (MAT-Ad) challenged with either lipopolysaccharide (LPS, 1 µg/ml) or PBS were harvested for miRNA profiling. Meanwhile, miRNAs encapsulated in MAT-Ad-derived exosomes (MAT-Ad-EX) were also analyzed. Hierarchical clustering analysis performed on most significantly regulated miRNAs (HFD vs NCD in tissues; LPS challenge vs PBS in the cells) showed a set of miRNAs that are differentially expressed in obese versus lean MAT or AA tissues, and in LPS-challenged versus PBS-treated MAT-Ads. The dysregulated of miRNAs in MAT-Ad-EX was also generated and hierarchically clustered, induced by prolonged exposure to microbial product.

overall_design:
Mouse tissues: C57BL6 mice were fed a normal chow diet (NCD) or a high fat diet (HFD, 60% fat) ad libitum from 4 weeks of age to 20 weeks of age. Mouse mesenteric adipose tissue (MAT, annotated as MAT-NCD or MAT-HFD) and abdominal aorta (AA, annotated as AA-NCD or AA-HFD) were snap-frozen by liquid nitrogen and saved for future RNA assays.

Primary cell culture and exosome isolation: Mesenteric pre-adipocytes derived from stromal vascular cells were obtained by collagenase digestion and differentiated to primary adipocytes, designated MAT-Ad. Cells were challenged with PBS or lipopolysaccharide (LPS 1 µg/ml) for 24 h. The culture supernatants were used for exosome isolation and exosomal RNA purification (annotated as MAT-Ad-EX-LPS/PBS), and cells were pelleted for RNA isolation (annotated as MAT-Ad-LPS/PBS).

first: Colin

last: Funk


title: SAM68-specific splicing is required for proper selection of alternative 3'UTR isoforms in the nervous system

city: Isehara

first: Takatoshi

last: Iijima

state: Kanagawa

address: 143 Shimokasuya

department: School of Medicine

country: Japan

institute: Tokai University

summary: Neuronal alternative splicing is dynamically regulated in a spatiotemporal fashion. We previously found that STAR family proteins (SAM68, SLM1, SLM2) regulate spatiotemporal alternative splicing in the nervous system. However, the whole aspect of alternative splicing programs governed by STARs remains unclear. We deciphered the alternative splicing programs of SAM68 and SLM1 proteins using transcriptomics. We reveal that SAM68 and SLM1 encode distinct alternative splicing programs; SAM68 preferentially controls alternative last exon (ALE) splicing. Interleukin 1-receptor accessory protein (Il1rap) is a novel target for SAM68. The usage of Il1rap ALEs results in mainly two variants encoding two functionally different isoforms, a membrane-bound (mIL1RAcP) and a soluble (sIL1RAcP) type. The brain exclusively expresses mIL1RAcP. SAM68 knockout results in remarkable conversion into sIL1RAcP in the brain, which significantly disturbs IL1RAcP neuronal function. Thus, we uncover the critical role of proper neuronal isoform selection through ALE choice by the SAM68-specific splicing program.

overall_design: To decipher alternative splicing programs controlled by neural RNA binding proteins SAM68 and SLM1, candidate RNA substrates were screened using the midbrain of three wild-type, three SLM1 single knockout (Slm1 KO) and three SAM68/SLM1 double-knockout (Sam68/Slm1 DKO) mice.


title: IFNg treatment of monocytes

status: Public on Dec 28 2019

city: Columbus

first: Jonathan

last: Butchar

address: 400 W. 12th Avenue

department: Internal Medicine

country: USA

institute: The Ohio State University

summary: Human peripheral blood monocytes were treated with control or with 25 ng/ml IFNg for 24 hours. RNA was collected, processed and hybridized to Affymetrix HGU133Plus2 chips.

overall_design: Untreated (UT) versus Interferon-gamma (IFNg), 4 total donors.


title: Comparing transcriptomic analysis using QuantSeq and RNA-Seq with Salmon quantification and Tophat2 mapping

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

institute: UNSW

summary: We have compared a relatively new method for RNA 3’ prime sequencing, QuantSeq with traditional RNA-Seq which captures reads from the entire RNA-transcript.  In addition, we have compared read quantification using traditional base-to-base mapping (Tophat2) with the new pseudoalignment method Salmon.  We have performed this experiment on peripheral blood mononuclear cells (PBMC) stimulated with Poly (I:C), a viral mimic that induces innate antiviral responses.

overall_design: RNA was extracted from six samples of peripheral blood mononuclear cells (PBMC) three of which had been treated with the viral mimic Poly(I:C).  Libraries were prepared from the six samples using both the Illumina TruSeq mRNA kit and the QuantSeq 3' sequencing kit. All libraries were sequenced on the Illumina Nextseq 500. The sequenced reads were mapped using Tophat2 or  Salmon. Differential expression between the Controls and Poly(I:C) treated samples was assessed using the voom function and the limma package from Bioconductor. Downstream processing was also performed on a subset of the entire reads.

first: Niamh

last: Troy

first: Anthony

last: Bosco

first: Marc

last: Wilkins


title: Differentiation of lncRNAs expression  during the polarization macrophages

city: Shanghai

first: Xiao

last: Han

state: Select state...

address: 399 Wanyuan Rd, Minhang, Shanghai, China

country: China

institute: Children’s Hospital of Fudan University

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

summary: To determine lncRNAs transcribed during the polarization of macrophages, we have employed whole genome microarray expression profiling as a discovery platform to identify lncRNAs expression in mouse primary bone marrow derived macrophages (BMDMs) treated with M1 (lipopolysaccharide, LPS) and M2 (IL-4) stimulators.

overall_design: The changed lncRNA expression in mouse BMDMs untreated (M/Ctrl) , or treated with LPS  6hours, IL-4 24 hours, respectively. Three  independent experiments were performed at each treat (M, LPS, IL-4).

first: Yufeng


title: mRNA Transcriptase’s Analyses That Cotton fruit branch Development Status after silenced GhBRC1 gene byVIGS

city: Chongqing

first: quan

last: sun

address: Chongwen road 2#

department: College of Bioinformation

institute: Chongqing University of Posts and Telecommunications

summary:
Purpose: found out the regulated genes of nulliplex-branch and its forming molecular mechanism
Methods: the GhBRC1 genes of nulliplex branch and short branch cotton are silenced by VIGS, and then the shoot apical mRNA of controls and treated were sequenced, in four repeats, using Illumina  HiSeq 2000.
Results: we found 3519 and 17 differnent expressed genes in nulliplex-branch and short branch cotton, respectively.
Conclusions: Our study represents the genes control development of lateral branch.

overall_design: The GhBRC1 genes of nulliplex branch and short branch cotton are silenced by VIGS, and then the shoot apical mRNA of controls and silenced were sequenced, in four repeats, using Illumina  HiSeq 2000.

first: Quan

last: Sun

first: Yingfan

last: Cai


title: Identification and characterization of miRNAs in temperature-dependent sex determination (TSD) of Chinese pond turtles (Mauremys reevesii)

city: Zhengzhou

first: Jing

last: Wang

address: Huayuan Road No.116

institute: Institute of Animal Husbandry and Veterinary Science

summary: In the present study, the eggs of Chinese pond turtles (Mauremys reevesii) were incubated at three temperatures (26℃, 29℃ and 32℃). During the thermosensitive period (TSP) of incubation, the adrenal-kidney-gonad (AKG) complexes were sampled, and a comprehensive investigation for miRNAs was performed using next-generation small RNA sequencing.

overall_design: Global miRNA expression kinetics during sex determination in a TSD species have been extensively profiled.

first: Liushuai

last: Hua

first: Wenxiu

last: Ru


title: Expression data of miRNAs from splenic leukocytes of dogs infected with L. infantum

city: Araçatuba

first: Larissa

middle: Martins

last: Melo

address: Clovis Pestana st, 793

country: Brazil

institute: UNESP

summary: The disease visceral leishmaniasis (VL), caused by Leishmania (L.) infantum, its a serious public health problem in Brazil. Studies with miRNAs showed their regulation in the immune response, due to cell immune suppression to be determinant at disease progression, identify them is important for the mechanism of change in immune response. We suggest then, that miRNAs regulation at immune response of dogs with VL.

overall_design: Fourteen dogs were used to form two groups for the study: 5 healthy dogs in Control group and 9 dogs naturally infected with L. infantum in Infected group.

first: Jaqueline

last: Bragato

first: Gabriela

last: Venturin

last: Rebech

first: Erivelto

middle: C

last: de Araújo Júnior

first: Leandro

middle: E

last: Garcia

first: Flavia

last: Eugênio

first: Paulo

last: dos Santos

last: Lopes

first: Valéria

last: Lima


title: Targeting transcriptional control activity of long mononucleotide A-T repeats in lung cancer stem cells

status: Public on Dec 27 2019

city: Bangkok

first: Piyapat

last: Pin-on

address: ChalongKrung

country: Thailand

institute: KMITL

summary: To explore gene expression profiles in spheroid lung cancer cell line after transfection PNA-A (15) that shown potential reduce cell proliferation and cell growth.

overall_design: Gene expression profiles of spheroid H292 and A549 were explored at 48 hours after transfection 5 μM of PNA-A(15). Two groups of spheroid H292 and A549 transfected PNA-A(15) and scramble consisting of 2 samples in each group were studied.

first: Pin-on

last: Piyapat

first: Mutirangura

last: Apiwat


title: Next-generation sequencing of wild type and 5XFAD transcriptomes for Alzheimer's disease study

city: Yuseing-gu

first: JaeWoong

last: Min

state: Daejeon

address: 17 Techno 4-ro

institute: Biorchestra

summary: We found some novel miRNA that targets SIRT1 may contribute to the pathogenesis in AD mouse model. We first identified that SIRT1 is significantly reduced in Alzheimer patient`s precentral gyrus and 5XFAD mice. To determine whether the strategy of inhibiting some miRNA affects AD pathology, we synthesized antisense oligonucleotides of miRNA (miRNA ASO) and studied this sequence in the brain of 5XFAD through direct intracerebral ventricular injection using stereotaxic instrument. We identified miRNA ASO significantly reduced amyloid beta plaque and amyloid production enzyme. Importantly, the attenuation of amyloid beta plaques through miRNA ASO was caused by a phagocytic activity of glial cells, by which it can directly target CD36. miRNA ASO also decreases inflammatory responses. These results inhibit neuronal loss caused by amyloid beta and leading to improvement of cognitive impairment. These insights of miRNA ASO suggests as therapeutic scope against AD pathology.

overall_design: Frontal cortex mRNA profiles of 6- and 11-month-old wild type (WT) and 5XFAD mice were generated by next-generation sequencing, using Illumina NovaSeq 6000 system.

first: Han

last: Koh

first: Jin

last: Ryu

first: Hyun

middle: J

last: Cho

first: Jae

middle: W


title: A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

summary: These experiments were designed to quantify depletion of rRNA sequencing reads from bacterial RNA-seq libraries and verify that mRNA sequencing reads were not altered. Specifically, we tested an rRNA depletion method using custom-designed biotinylated oligonucleotides and compared these results to undepleted (total RNA) libraries and libraries made with the previously-available Ribo-Zero kit (Illumina).

sample_organism:
Escherichia coli
Bacillus subtilis
Caulobacter vibrioides

overall_design: This study consists of two sets of experiments. First, pairs of rRNA depleted libraries and total RNA libraries were prepared from the same RNA extractions to quantify depletion of rRNA by our custom biotinylated oligos. These experiments included RNA from three bacterial species. The second experiment compared the quantification of change in gene expression following treatment of E. coli with rifampicin and chloramphenicol using libraries prepared using Ribo-Zero (Illumina) or our custom biotinylated oligos. The same RNA extractions were split and treated with Ribo-Zero or our custom kit.

first: Chantal

last: Guegler

first: Michael

middle: T

last: Laub