title: DNA replication-mediated error correction of ectopic CENP-A deposition maintains centromere identity

city: Santa Cruz

first: Karen

middle: Hayden

last: Miga

state: CA

address: 501 Engineering 2 Building, 1156 High Street,

department: Biomolecular Engineering Department

country: USA

institute: UC Santa Cruz

summary: Chromatin assembled with histone H3 variant CENP-A is the heritable epigenetic determinant of human centromere identity. Using genome-wide mapping and reference models for 23 human centromeres, CENP-A is shown in early G1 to be assembled into nucleosomes within megabase, repetitive a-satellite DNAs at each centromere and onto 11,390 sites on the chromosome arms. Centromere-bound CENP-A is found to be quantitatively maintained during DNA replication by coordinated action of the MCM2 helicase, CAF1, HJURP, and the CCAN network of constitutive centromere components. CCAN serves to tether CENP-A removed by MCM2, thereby enabling local reassembly onto both daughter centromeres with identical DNA sequence preferences and nucleosome phasing as the loading in G1 and independent of CENP-B. Conversely, without CCAN-mediated tethering, DNA replication removes CENP-A from sites on the chromosome arms. Our data identify an MCM2/CAF1/HJURP- and CCAN-dependent error correction mechanism that acts in S-phase to maintain CENP-A-dependent centromere identity.

overall_design: Centromere protein A ChIP-seq during different stages of the cell cycle and with reference to replication data

first: Yael

last: Nechemia-Arbely

middle: H

first: Moira

middle: A

last: McMahon

first: Ofef

last: Shoshani

first: Aaron

last: Aslanian

first: Ah

middle: Y

last: Lee

first: Daniele

last: Fachinetti

last: Yates III

first: Bing

last: Ren

first: Don

middle: W

last: Cleveland


title: Genome-wide maps of chromatin state and Gene Expression Profiling in HCT116 cells

status: Public on Mar 20 2019

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Small Sample-Big Data: Integrative Indexed Systems Biology Reveals Dramatic Molecular Ontogeny over the First Week of Human Life

first: Joann

middle: Diray

last: Arce

state: MA

address: 300 Longwood Ave

department: Infectious Disease

institute: Boston Childrens Hospital- Harvard Medical School

summary: Systems biology provides a powerful approach to unravel complex biological processes yet it has not been applied systematically to samples from newborns, a group highly vulnerable to a wide range of diseases. Published methods rely on blood volumes that are not feasible to obtain from newborns. We optimized methods to extract transcriptomic, proteomic, metabolomic, cytokine/chemokine, and single cell immune phenotyping data from <1ml of blood, a volume readily obtained from newborns. Furthermore, indexing to baseline and applying innovative integrative computational methods that address the challenge of few data points with many features enabled identification of robust findings within a readily achievable sample size. This approach uncovered dramatic changes along a stable developmental trajectory over the first week of life. The ability to extract information from ‘big data’ and draw key insights from such small sample volumes will enable and accelerate characterization of the molecular ontogeny driving this crucial developmental period.

overall_design:
This study examines the global transcriptomic profiles in peripheral blood of newborns at birth (D0) comparing with follow up at day 1 (D1), day 3 (D3), or day 7 (D7) post birth.

Contributor: Expanded Program on Immunization Consortium (EPIC)

first: Erin

middle: E

last: Gill

first: Casey

last: Shannon

first: Nelly

last: Amenyogbe

first: Rym

last: Ben-Othman

first: Tue

last: Bennike

last: Diray-Arce

first: Olubukola

last: Idoko

first: Amy

first: Simon

last: van Haren

first: Kim-Anh

last: Le Cao

first: Momoudou

last: Cox

first: Alansana

last: Darboe

first: Reza

last: Falsafi

first: Davide

last: Ferrari

first: Daniel

last: Haberson

last: He

first: Sam

middle: J

last: Hinshaw

first: Jorjoh

last: Ndure

first: Jainaba

last: Njie-Jobe

first: Matthew

last: Pettengill

first: Elishia

last: Roberts

first: Amrit

last: Singh

first: Kinga

middle: K

last: Smolen

first: Ryan

last: Brinkman

first: Al

last: Ozonoff

first: Hanno

last: Steen

first: Robert

last: Hancock

first: Scott

last: Tebbutt

first: Beate

last: Kampmann

first: Ofer

last: Levy

first: Tobias

last: Kollmann


title: Intestinal epithelial microvilli are abnormal in Crohn's disease

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

summary:
Biopsy samples (n=362) were collected from terminal ileum at baseline, 8 weeks after induction (Ustekinumab or placebo), and 44 weeks after maintenance (Ustekinumab 90 mg SC q12w, Ustekinumab 90 mg SC q8w, or placebo) therapies during endoscopy for RNA extraction and microarray analysis from patients with moderate-to-severe CD who participated in stelara CD phase 3 studies (UNITI-2 and IM-UNITI).  These patients failed conventional therapies previously and largely naive to anti-TNF therpy.  Ileum biopsies (n=26) collected from non-IBD subjects were also analyzed to serve as control.
Enrichment of a core microvilli gene set was found to be reduced in UNITI-2 CD samples relative to controls, correlated with microvilli length and endoscopy score, and associated with response to treatment.

overall_design: A gene expression profiling study was conducted in which ileum biopsy samples were collected for RNA extraction and hybridization to microarrays from patients (n=362) with moderate-to-severe Crohn's disease and from non-IBD subjects (n=26).

first: Kelli

middle: L

last: VanDussen

first: Aleksandar

last: Stojmirović

first: Katherine

first: Ta-Chiang

last: Liu

first: Patrick

last: Kimes

first: Brian

middle: D

last: Muegge

middle: F

last: Simpson

last: Ciorba

first: Jacqueline

middle: G

last: Perrigoue

first: Joshua

middle: R

last: Friedman

first: Jennifer

last: Towne

first: Richard

last: Head

first: Thaddeus

middle: S

last: Stappenbeck


title: RNA-sequencing and swarm intelligence-enhanced classification algorithm development for blood-based disease diagnostics using spliced blood platelet RNA

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

summary: We report RNA-sequencing data of 80 tumor-educated blood platelet (TEP) samples isolated from 39 patients with lower-grade glioma (LGG) and 41 healthy donors (HD). This dataset can be employed as input for the thromboSeq source code (available via GitHub: https://github.com/MyronBest/) to reproduce the thromboSeq drylab pipeline.

overall_design: Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the humane reference genome using STAR, and intron-spanning reads were summarized using HTSeq.

first: Thomas

last: Wurdinger


title: Transcription profiles of fate mapped IL17aiCre+flox/stop/flox-YFP+ TH17 cells, CD44intCD27+ TH17 cells and CD44hiCD27- TH17 cells from WT or Raptor-ko (flox/flox) mice after immunization with Myelin Oligodendrocyte Glycoprotein (MOG)

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
Mechanisms governing memory responses in IL-17 secreting CD4+ T cells (TH17), especially in autoimmune disorders, remain poorly understood. TH17 cells play pleiotropic roles in autoimmunity and tissue inflammation and are characterized by inherent plasticity, although how plasticity is regulated remains elusive. We investigated the transcriptional profiles of fate mapped (IL17aiCre-flox/stop/flox-YFP) TH17 cells and WT and Raptor-ko (flox/flox) TH17 cells (both IL17aiCre-flox/stop/flox-YFP) as well as sorted within CD27+ and CD27- subsets of WT in experimental autoimmune encephalomyelitis, a human model for human multiple sclerosis.
We used microarrays to compare the global transcription profiles of YFP+ (IL17aiCre-flox/stop/flox-YFP) fate mapped TH17 cells as well as CD27+ and CD27- subsets of CD44+ fate mapped TH17 cells from draining lymph nodes on day 9 after immunization with Myelin oligodendrocyte glycoprotein from WT and IL17aCre-Raptor-flox/flox mice.

overall_design: We analyzed a total of 18 samples from immunized mice: YFP+ fate mapped TH17 cells (6 total: 4 WT, 2 IL17aCre-Rptor-flox/flox; both flox/stop/flox-YFP), YFP+CD44intCD27+ fate mapped TH17 cells (6 total: IL17aiCre-flox/stop/flox-YFP), YFP+CD44hiCD27- fate mapped TH17 cells (6 total: IL17aiCre-flox/stop/flox-YFP)

first: Peer

last: Karmaus

first: Yogesh

last: Dhungana

first: Hongbo

last: Chi


title: Wood kraft pulp supplementation alters the rumen fermentation characteristics and epithelial transcriptomes in Holstein cattle during the high-grain diet challenge

status: Public on Mar 19 2019

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

summary: We investigated the effects of wood kraft pulp (WP) supplementation on ruminal pH, fermentation, and epithelial transcriptomic dynamics in Holstein cattle during the high-grain diet challenge.

overall_design: Five rumen-fistulated Holstein bulls (215.2 ± 20.4 kg of body weight; 7.4 ± 0.3 months of age) were used in a cross-over design without a wash-out period. Cattle were fed a high-grain diet containing corn flakes (control diet) or the WP as a half replacement of corn flakes in the control diet (WP diet) during the first 14 days, and then, the diets were switched for last 14 days.

first: Yo-Han

last: Kim


title: Comprehensive analysis of exosomal miRNA in type 1 autoimmune pancreatitis

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: We comprehensively analyzed the miRNA expression derived from serum exosomes using microarrays in patients with type 1 AIP (n = 10) in comparison to that in healthy adults (n = 10) and in patient with chronic pancreatitis. The high or low expression of miRNAs in microarray analysis  were considered candidate biomarkers or related to the pathogenesis of disease.

overall_design: Serum exosome-derived miRNA expression was analyzed using microarrays in type 1 AIP patients (n = 10), healthy adults (n = 10) and chronic pancreatits (n=10).

first: Koh

last: Nakamaru

first: Takashi

last: Tomiyama


title: Expression data of lung tissues of rats exposed to chronic hypoxia

city: Tianjin

first: Wei

last: Cai

address: No. 92 Weijin Road, Nankai District

country: China

institute: School of disaster medical research，Tianjin University

summary:
Under hypoxic exposure in rats, activation of VEGF/Notch pathway may lead to pulmonary angiogenesis, and the expression of related proteins may be associated with down-regulation of miRNAs.
We used microarrays to screen out miRNAs related to VEGF/Notch pathway in hypoxic exposure, and in this process, we found genes with a downregulation trend with prolonged exposure time.

overall_design: Lung tissues of male SD rats were selected for RNA extraction and hybridization on Affymetrix microarrays. In order to further screen out hypoxia genes related to VEGF/Notch pathway and explore their tendency and downregulation with the increase of hypoxia exposure time. To this end, rats were divided into the normoxic control group (C)h and the rat exposure time of 24 hours (H_24), 48 hours (H_48) and 72 hours (H_72) groups.

first: Hui

last: Ding

first: Haojun

last: Fan


title: Differences in expression profiling between tumoral colorectal carcinomas subsets and normal tissue and polyps [miRNA]

city: Murcia

first: Angel

last: Esteban-Gil

state: Murcia

address: Campus de Ciencias de la Salud Carretera Buenavista s/n

department: Biomedical Informatics and Bioinformatics Platform

country: Spain

institute: Institute for Biomedical Research of Murcia (IMIB)

summary: Colorectal cancer (CRC) is the third leading cause of cancer mortality worldwide. Different pathological pathways and molecular drivers have been described and some of the associated markers are used to select effective anti-neoplastic therapy. This dataset is part of ColPortal, a platform that integrates transcriptomic, microtranscriptomic, methylomic and microbiota data of patients with colorectal cancer. ColPortal also includes detailed information of histological features and digital histological slides from the study cases, since histology is a morphological manifestation of a complex molecular change.

overall_design: In this study, we used miRNA expression arrays to investigate differences between tumoral and normal colorectal tissues and polyps

first: Fernando

last: Pérez-Sanz

first: José

last: García-Solano

first: Begoña

last: Alburquerque-González

first: María

last: Parreño-González

last: del Carmen Legaz-García

first: Jesualdo

middle: T

last: Fernández-Breis

first: Edith

last: Rodriguez-Braun

first: Paola

last: Pimentel

first: Anne

last: Tuomisto

first: Markus

last: Mäkinen

first: Ondrej

last: Slaby

first: Pablo

last: Conesa-Zamora


title: Differences in expression profiling between tumoral colorectal carcinomas subsets and normal tissue and polyps [mRNA]

overall_design: In this study, we used gene expression arrays to investigate differences between tumoral and normal colorectal tissues and polyps


title: Differences in expression profiling between tumoral colorectal carcinomas subsets and normal tissue and polyps

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


title: Hypoxia-Induced Gene Expression Profiling of Gastric Cancer-Associated Myofibroblasts

city: Liverpool

first: Hanna

last: Najgebauer

address: Crown Street

department: Cellular and Molecular Physiology

country: United Kingdom

institute: University of Liverpool

summary: The Illumina HumanHT-12v4 Expression BeadChip arrays were performed on a collection of primary gastric cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM) as well as unrelated normal tissue myofibroblasts (NTM). CAM and ATM samples were obtained from patients undergoing gastric cancer surgery; whereas NTM samples were generated from deceased transplant donors with normal morphology.

overall_design: Total RNA obtained from gastric stromal myofibroblasts was hybridised to the Illumina HumanHT-12v4 Expression BeadChip

first: Chris

last: Sanderson


title: Genetic lineages of colorectal adenocarcinomas with and without adenoma components

city: Otsu

first: Hiroyuki

last: Sugihara

state: Shiga

address: Seta, Tsukinowa-cho

department: Pathology

institute: Shiga University of Medical Science

type: Genome variation profiling by genome tiling array

summary: We tried to examine whether the de novo colorectal carcinomas (CRCs) without an adenoma component can be discriminated from those deriving from adenoma by DNA copy-number alteration profile. The unsupervised clustering of DNA copy-number profiles of 112 colorectal cancer samples, using large-sized (≥ 9 probes) genes, disclosed 4 clusters: Clusters 1, 3, and 4 correspond to carcinoma with an adenoma component. Cluster 2 and some samples in cluster 3 correspond to carcinoma without adenoma component. Our approach suggested that Cluster 2 may represent de novo CRCs since penetrance plots were very different between cluster 2 and the other clusters. Adenocarcinoma in cluster 3 have higher potential for lymph node metastasis than those in cluster 1 and 4 and can derive from clusters 1/4 tumors.

overall_design: We used formalin-fixed paraffin embedded tissues from 48 colorectal cancers. Genomic DNAs extracted from 112 samples that were taken from adenoma, mucosal, invasive and lymph node parts of tumors were used for array CGH analysis and subsequent hierarchical clustering analysis and penetrance plots

first: Tu

last: Duong


title: PKHD1-deficient human induced pluripotent stem (iPS) cell-derived cholangiocyte-like cells (PKHD1-KO CCs) vs heterozygously mutated PKHD1 human iPS cell-derived cholangiocyte-like cells (PKHD1-Hetero CCs)

first: Satoshi

last: Kondo

summary: Transcriptional profiling of PKHD1-KO and PKHD1-Hetero CCs. PKHD1-deficient (PKHD1-KO) and heterozygously mutated PKHD1 iPS clones were established by RNA-guided genome editing using CRISPR/Cas9 system. The iPS clones were differentiated into cholangiocyte-like cells in cysts (cholangiocytic cysts, CCs) in a 3D-culture system.

overall_design: Two-condition experiment, PKHD1-KO and PKHD1-Hetero CCs. PKHD1-deficient (PKHD1-KO) and heterozygously mutated PKHD1 (PKHD1-Hetero) iPS clones were established by RNA-guided genome editing using CRISPR/Cas9 system. PKHD1-Hetero iPS clones obtained using same gRNA as PKHD1-KO iPS clones were used as control cell lines in this study to exclude the possibility that an off-target mutation by the genome editing method affected the phenotype of such clones. Targeted homologous recombination of the gene cassette into TkDA3-4 iPS cells (established from dermal fibroblasts of a normal healthy human) was performed by electroporation. The genotype of the clones was determined by PCR. Clones carrying the mutant fragment were selected and the DNA sequences of the wild type fragment were determined by direct sequencing. Clones with a premature stop codon in PKHD1 exon 2 were selected as the PKHD1-KO cell line and the loss of PKHD1 protein in the KO lines was confirmed by immunostaining. The iPS clones were differentiated into cholangiocyte-like cells in cysts (cholangiocytic cysts, CCs) in a 3D-culture system for 10 days, and the cells were harvested.

first: Tomoyuki

last: Tsunoda

first: Sei

last: Kakinuma


title: SFPQ is a FTO binding protein that assists specific m6A demethylation

city: Los Angeles

first: Ye

last: Wang

state: California

address: 611 Charles E Young Dr E

department: Bioinformatics

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: We identified the major RNA binding protein-SFPQ as a direct interaction partner of FTO. Our study showed that FTO and SFPQ were located in close proximity throughout the transcriptome and overexpression of SFPQ led to the demethylation of adjacent N6-methyladenosine on RNA

overall_design: Examination for alternation of RNA methylation states in overexpression SFPQ and overexpression vector cells.

first: Haiping

last: Song


title: Functional conservation of jasmonate-related MYC transcription factors in Marchantia polymorpha

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

summary: The lipid-derived phytohormone jasmonoyl-isoleucine (JA-Ile) regulates plant immunity, growth and development in vascular plants by activating genome-wide transcriptional reprogramming. In Arabidopsis, this is largely orchestrated by the master regulator MYC2 and related transcription factors (TFs). However, the TFs activating this pathway in basal plant lineages are currently unknown. We report the functional conservation of MYC-related TFs between the eudicot Arabidopsis thaliana and the liverwort Marchantia polymorpha, a plant belonging to one of the most basal land-plants lineages. Phylogenetic analysis suggests that MYC function first appeared in charophycean algae, and therefore predates the evolutionary appearance of any other jasmonate pathway component. Marchantia possesses two functionally interchangeable MYC genes, one in females and one in males. Similar to AtMYC2, MpMYCs showed nuclear localization, interaction with JAZ-repressors, and regulation by light. Phenotypic and molecular characterization of loss- or gain-of-function mutants demonstrated that MpMYCs are necessary and sufficient for the activation of the pathway in Marchantia, but unlike their Arabidopsis orthologs, do not regulate fertility. Our results show that despite 450 million years of independent evolution, MYCs are functionally conserved between bryophytes and eudicots. Genetic conservation in one of the most basal lineages suggests that MYC function existed in the common ancestor of land plants and evolved from a pre-existing MYC function in charophycean algae.

overall_design: Transcriptomic analysis of Mpmycy vs (Experiment) vs Tak-1 (Control) in response to OPDA treatment for 3 hours (3 replicates);  Mpmycx vs (Experiment) vs Tak-2 (Control) in response to OPDA (3 replicates) treatment for 3 hours;  Mpmycy vs (Experiment) vs Tak-1 (Control) 2 hours after wounding  (2 replicates)

first: María

last: Peñuelas

first: Isabel

last: Monte

first: Fabian

last: Schweizer

first: Armelle

last: Vallat

first: Philippe

last: Reymond

first: Gloria

last: García-Casado

first: José

middle: M

last: Franco‑Zorrilla

first: Roberto

last: Solano


title: Distinct peripheral blood mononuclear cells transcriptional modules in the response to human respiratory syncytial virus or human rhinovirus in hospitalized infants with bronchiolitis

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: Human respiratory syncytial virus (HRSV) is the main cause of bronchiolitis during the first year of life, but other viruses such as rhinovirus also occur and are clinically indistinguishable. In hospitalized infants with bronchiolitis, the analysis of the peripheral blood mononuclear cells (PBMC)  gene expression might be useful for identification the etiologies caused by HRSV and human rhinovirus (HRV) and to the development of future tests, as well as to elucidate the pathogenic mechanisms triggered by different viral agents and new therapeutic possibilities. In this study, we conducted a comparative global gene expression analysis of infants with acute viral bronchiolitis infected by HRSV (HRSV group) or HRV (HRV group).

overall_design: The transcriptomic profiles of peripheral blood mononuclear cells from patients with HRSV or HRV were obtained. We employed a weighted gene co-expression network analysis which allows the identification of transcriptional modules and their correlations with HRSV or HRV groups.

first: Sandra

last: Vieira

first: Silvia

last: Bando

first: Milena

last: de Paulis

first: Danielle

middle: B

last: Oliveira

first: Luciano

last: Thomazelli

first: Edison

last: Durigon

first: Marina

last: Martinez


title: Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 2

city: Frederick

first: Kalyan

middle: C

last: Vinnakota

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute

summary:
Purpose: The purpose of this study is to measure the changes in liver transcriptome in response to short-term fasting between 5 and 10 h where the rats were dosed with 2 ml/kg of corn oil vehicle at 0 h
Methods: Total RNA was isolated from the liver, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA Mini Prep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA). At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 150-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000, San Diego, CA).
Results:
Conclusions: There were 100 genes that could be mapped to the rat metabolic network iRno, with significant changes in expression between 5 and 10 h of fasting in the top 10% by effect size parameter b (b > 0.6).

overall_design: Liver mRNA profiles of 5- and 10-h fasted Sprague-Dawley rats were generated by RNA-seq.

first: Venkat

last: Pannala

first: Martha

last: Wall

first: Mohsin

last: Rahim

first: Shanea

last: Estes

first: Irina

last: Trenary

first: Tracy

middle: P

last: O'Brien

first: Richard

last: Printz

first: Jaques

last: Reifman

first: Masakazu

last: Shiota

first: Jamey

last: Young

first: Anders

last: Wallqvist


title: Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 1

summary:
Purpose: The purpose of this study is to measure the changes in liver transcriptome in response to short-term fasting between 5 and 10 h where the rats were dosed with 6 ml/kg of polyethylene glycol vehicle at 0 h
Methods: Total RNA was isolated from the liver, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA Mini Prep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA). At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp single-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000, San Diego, CA).
Results: No genes were were found to be differentially expressed with a false discovery rate less than 0.1
Conclusions: There were no significant changes in liver gene expression between 5 and 10 h of fasting


title: Trans-generational inheritance of a phenotypically neutral epimutation enables descendants to reinstate an ancestral silencing episode

status: Public on Mar 22 2019

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Non-coding RNA profiling by high throughput sequencing

summary: Phenotypic differences caused by epimutations rather than changes in DNA sequence have been described in various organisms. Epimutations are potentially adaptive if inherited across generations and might even respond to environmental challenges. Yet experimental evidence is scarce1.  Examples of heritable phenotypic changes are paramutation in plants and RNA-induced epigenetic silencing (RNAe) in nematodes, in which small RNAs trigger the formation of silent epialleles that are stable across generations2-7. Consequently, RNA-directed epimutagenesis has been associated with persistent gene repression. Here, using the fission yeast Schizosaccharomyces pombe, we demonstrate that RNA-induced epimutations are stably transmitted to subsequent generations also after reactivation of the silenced gene. This enables descendants to remember and reinstate preceding silencing episodes that had occurred in their ancestors. We show that temporary expression of hairpin-derived small interfering RNAs (siRNAs) triggers RNAe that is stably propagated for at least 18 generations upon inactivation of the polymerase-associated factor 1 complex (Paf1C). In the presence of Paf1C, the silent state is lost, but resumes if Paf1C is again impaired, even in the absence of the original trigger and in later generations. Thus, in yeast RNAe installs a molecular imprint that can be inherited through meiosis with no discernible phenotypic consequences. We show that trimethylated histone H3 lysine 9 (H3K9me3) is a major constituent of this imprint, and that stable propagation thereof is coupled to RNA interference (RNAi). Our findings reveal a distinct form of epigenetic memory in which fission yeast cells acquire heritable, transcriptionally active epialleles that confer gene silencing and manifest a phenotype only in particular, recurring situations. This demonstrates that epigenetic inheritance is adaptive and could potentially constitute a strategy to cope with adverse environmental conditions. If conserved in other eukaryotes, this phenomenon will impact our comprehension of natural variation and epigenetics in evolution.

overall_design: To characterize the phenotypically neutral mark, F10 h- paf1-Q264Stop ade6si3 OFF cells were crossed with h+ paf1+ ade6+ ON cells, that were otherwise wild-type or mutantX (ago1D, dcr1D, rdp1D, clr4D, clrF499Y). 3 - 4 biological replicates of F11 h- paf1+ wild-type/mutantX colonies were sequenced for small RNAs (28 samples). Furthermore, ChIP-seq of H3K9me2, H3K9me3, H3K36me3, H3 total and PolII was performed in triplicates on strains with and without ade6 si3-mark (35 samples). We also performed small RNA sequencing of 61 samples to examine the de novo formation and inheritance of endogenous siRNA peaks.

first: Lea

last: Duempelmann

first: Yukiko

last: Shimada

first: Daniele

last: Oberti

first: Silke

last: Lochs

first: Marc

last: Bühler


title: Molecular profiling of resident and infiltrating mononuclear phagocytes during rapid adult retinal degeneration using single-cell RNA sequencing

city: Davis

first: Marie

last: Burns

address: 1 Shields Ave

institute: University of California Davis

summary: Neuroinflammation commonly accompanies neurodegeneration, but the specific roles of resident and infiltrating immune cells during degeneration remains controversial. Much of the difficulty in assessing myeloid cell-specific functions during disease progression arises from the inability to clearly distinguish between activated microglia and bon e marrow-derived monocytes and macrophages in various stages of differentiation and activation within the central nervous system. Using an inducible model of photoreceptor cell death, we investigated the prevalence of infiltrating monocytes and macrophage subpopulations after the initiation of degeneration in the mouse retina. In vivo retinal imaging revealed infiltration of CCR2+ leukocytes across retinal vessels and into the parenchyma within 48 hours of photoreceptor degeneration. Immunohistochemistry and flow cytometry confirmed and characterized these leukocytes as CD11b+CD45+ cells. Single-cell mRNA sequencing of the entire CD11b+CD45+ population revealed the presence of resting microglia, activated microglia, monocytes, and macrophages as well as 12 distinct subpopulations within these four major cell classes. Our results demonstrate a previously immeasurable degree of molecular heterogeneity in the innate immune response to cell-autonomous degeneration within the central nervous system and highlight the necessity of unbiased high-throughput and high-dimensional molecular techniques like scRNAseq to understand the complex and changing landscape of immune responders during disease progression.

overall_design: All CD11b+ CD45+ cells were collected from mouse retinas using fluorescence-activated cell sorting before and during photorecetor degeneration (Arr1-/- mice, degenerating sample collected after 48 hours of light exposure of approximately 200 lux). Single-cell mRNA sequencing was performed using the 10x Genomics platform (Chromium). Six littermates (3 dark-reared controls, 3 degenerating) were used for single-cell sequencing.

first: Kaitryn

last: Ronning

first: Sarah

last: Karlen

first: Eric

last: Miler


title: Engulfment gene ELMO1 in neutrophils as a promoter of inflammatory arthritis

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

summary: Rheumatoid arthritis is an inflammatory disease of the synovial joints that affects ~1% of the human population, with severe distress due to progressive joint inflammation and deformation. When addressing the links between specific components of the apoptotic cell clearance machinery and human disease, we noted a correlation between single nucleotide polymorphisms (SNPs) in ELMO1, DOCK2, and RAC1 genes and rheumatoid arthritis. ELMO1 is a cytoplasmic adapter protein that associates with DOCK2 and RAC1 to promote cytoskeletal reorganization needed for apoptotic cell uptake by phagocytes. We initially hypothesized that, since ELMO1 is linked to apoptotic cell clearance, loss of ELMO1 would lead to increased inflammation in arthritis. Contrary to the accumulation of apoptotic cells and greater disease severity that we predicted, we observed significantly reduced joint inflammation in two models of arthritis in mice lacking ELMO1. Using genetic and cell biological approaches in vivo and ex vivo, we determined that ELMO1 deficiency significantly reduces neutrophil recruitment to inflamed joints, but does not result in general inhibition of inflammatory responses. Through proteomic analyses, we find that ELMO1 protein associates with cellular receptors that contribute to neutrophil function in arthritis, and regulates C5a and LTB4 receptor-mediated activation and early neutrophil recruitment to the joints. Neutrophil-specific transcriptomics show that ELMO1 modulates neutrophil-specific gene expression that includes genes with known linkages to human arthritis. Finally, neutrophils from the peripheral blood of human donors that carry the SNP in ELMO1 associated with arthritis display increased migratory capacity, whereas ELMO1 knockdown reduces human neutrophil migration to LTB4. These data identify key ‘non-canonical’ roles for engulfment machinery components in arthritis, and ELMO1 as an important regulator of specific neutrophil receptors and signaling linked to arthritis.

overall_design: The experiment consisted of two conditions: purified Ly6G+ bone marrow cells or peritoneal macrophages cultured overnight. Each condition consisted of four biological replicates.

first: Sanja

last: Arandjelovic

first: Christopher

last: Lucas

first: Kristen

last: Penberthy

first: Tae-Hyoun

last: Kim

first: Ming

last: Zhou

first: Dorian

middle: A

last: Rosen

first: Tzu-Ying

last: Chuang

first: Alexandra

last: Bettina

first: Laura

last: Shankman

first: Amanda

middle: H

last: Cohen

first: Alban

last: Gaultier

first: Thomas

last: Conrads

first: Minsoo

first: Michael

last: Elliot

first: Kodi

last: Ravichandran


title: Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 3

first: Kalyan

last: Vinnakota

summary:
Purpose: The purpose of this study is to measure the changes in liver transcriptome in response to short-term fasting between 7 and 13 h where the rats were dosed with 2 ml/kg of saline vehicle at 0 h
Methods: Total RNA was isolated from the liver, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA Mini Prep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA). At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000, San Diego, CA).
Results: No genes were were found to be differentially expressed with a false discovery rate less than 0.1
Conclusions: There were no significant changes in liver gene expression between 7 and 13 h of fasting

overall_design: Liver mRNA profiles of 7- and 13-h fasted Sprague-Dawley rats were generated by RNA-seq.

first: Venkat

last: Pannala

first: Martha

last: Wall

first: Mohsin

last: Rahim

first: Shanea

last: Estes

first: Irina

last: Trenary

first: Tracy

last: O'Brien

first: Richard

last: Printz

first: Jaques

last: Reifman

first: Masakazu

last: Shiota

first: Jamey

last: Young

first: Anders

last: Wallqvist


title: Gene expression profiling of adult murine RPE

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

institute: University of Miami Miller School of Medicine

summary: To characterize RPE isolated from adult mice, we studied gene expression in these cells using MEEBO microarrays.

overall_design: To perform the experiment, RNA extracted from the RPE of adult (2.5-3 month-old) mice was used for microarray analysis. A total of three independent biological replicates were obtained for profiling.


title: Characterization of the DNA methylome in retinal pigment epithelium (RPE) of adult mice

summary: We investigated the epigenetic plasticity of adult murine RPE using whole-genome bisulfite sequencing (WGBS)

overall_design: To study DNA methylation, two WGBS libraries were prepared using DNA from two independent RPE samples containing 150,000–200,000 cells. The WGBS libraries were sequenced and bisulfite sequence reads were aligned using the Bismark software package. Global methylation level in adult mouse RPE was measured and percentages of methylation of CpG, CHG, and CHH contexts (where H is A, C or T) were identified.


title: Genome-wide maps of chromatin state in retinal pigment epithelium (RPE) of adult mice

summary: We investigated the epigenetic plasticity of adult murine RPE using ChIP-seq analysis.

overall_design: To study genome-wide histone modifications in adult RPE, we chose four histone marks: H3K4me3, H3K4me1, H3K27me3 and H3K9me3.


title: AP-1cFos/JunB/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration

city: Woods hole

first: Karen

last: Echeverri

address: 7 MBL ST

department: Eugene Bell Center for Regeneration Biology and Tissue Engineering

institute: MARINE BIOLOGICAL LAB

summary: Salamanders have the remarkable ability to functionally regenerate after spinal cord transection. In response to injury, GFAP+ glial cells in the axolotl spinal cord proliferate and migrate to replace the missing neural tube and create a permissive environment for axon regeneration. Molecular pathways that regulate the pro-regenerative axolotl glial cell response are poorly understood. Here we show axolotl glial cells up-regulate AP-1cFos/JunB after injury, which promotes a pro-regenerative glial cell response. Axolotl glial cells directly repress c-Jun expression via up-regulation of miR-200a. Inhibition of miR-200a during regeneration causes defects in axonal regrowth and transcriptomic analysis revealed that miR-200a inhibition leads to differential regulation of genes involved with reactive gliosis, the glial scar, ECM remodeling and axon guidance. This work identifies a novel role for miR-200a in inhibiting reactive gliosis in glial cell in axolotl during spinal cord regeneration

overall_design: All axolotls used in these experiments were bred in the axolotl facility at the University of Minnesota or at the MBL under the IACUC protocols #1710-35242A, #18-49. Axolotls of 2–3 cm were used for all in vivo experiments, and animals were kept in separate containers and fed daily with artemia; water was changed daily. Animals were anesthetized in 0.01% p-amino benzocaine (Sigma) before microinjection was performed.

first: Keith

last: Sabin

first: Peng

last: Jiang

first: Micah

last: Gearhart

first: Ron

last: Stewart


title: Connectivity mapping of angiotensin-PPAR interactions involved in the amelioration of non-alcoholic steatohepatitis by Telmisartan

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

country: South Korea

institute: Seoul National University

summary:
Nonalcoholic fatty liver disease (NAFLD) is a rapidly increasing global health problem that is associated with metabolic disorders covering a broad spectrum of pathological abnormalities, including simple steatosis, nonalcoholic steatohepatitis (NASH), advanced fibrosis and cirrhosis, and hepatocellular carcinoma (HCC). Telmisartan is a potential treatment for NAFLD due to its ability to improve insulin sensitivity and decrease hepatic fat accumulation via modulation of peroxisome proliferator-activated receptor gamma (PPARγ), and to suppress hepatic fibrosis by blocking angiotensin II receptors. However, the underlying molecular mechanisms of action of telmisartan, and the interaction between the renin-angiotensin system (RAS) and PPAR, have yet to be fully elucidated. Thus, in the present study, NASH-HCC STAM mice received daily administrations of telmisartan for 6 weeks to assess the prevention of fibrosis and lipid accumulation in the liver, and to evaluate improvements in NASH.
Hepatic transcriptome analyses revealed that the amelioration of NASH likely occurred through the regulation of inflammatory- and fibrosis-related gene responses. An integrated protein-protein interaction network analysis including transcriptional and non-transcriptional genes regulated by telmisartan showed that the NAFLD pathway is located at the center of the network and has interconnections with the RAS and PPAR signaling pathways. Additionally, the downstream targets of the transcription factors in the network, PPARα, PPARδ, and RELA, significantly overlapped with telmisartan-induced differentially expressed genes (DEGs). This alternative approach to assessing the transcriptome provided the opportunity to understand the fundamental molecular mechanisms underpinning the therapeutic effects of telmisartan, and will contribute to the establishment of a novel pharmacological treatment for NASH patients.

overall_design: Total RNA was extracted from the frozen liver tissues with a RNeasy mini kit (Qiagen, Hilden, Germany). Following quantitative and qualitative evaluations performed with BioAnalyzer (Agilent, Santa Clara, CA, USA), RNA samples with an RNA integrity number (RIN) ≥ 6.7 and A260/A280 values ≥ 1.88 were subjected to cDNA synthesis, performed with the GeneChip WT cDNA synthesis and amplification kit (Applied Biosystems). Next, the cDNA was fragmented and biotin-labeled using GeneChip WT terminal labeling kit (Applied Biosystems), and approximately 5.5 μg of labeled cDNA was hybridized to the Affymetrix GeneChip Mouse Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) at 45°C for 16 h. The hybridized arrays were scanned on a GCS3000 Scanner (Affymetrix) and all data analyses were performed with the GeneChip Command Console Software (Affymetrix). All data were normalized using the robust multi-array average (RMA) approach and hierarchical clustering of the expressed probes was performed using GenePattern (https://genepattern.broadinstitute.org). The distance between clusters was computed with Pearson correlations and global gene expression profiling was conducted in triplicate for the vehicle control and telmisartan treatment groups.

first: Jung


title: F-actin dynamics regulates mammalian organ growth and cell fate maintenance

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: Cell function depends on the mechanical properties of the microenvironment. Cells probe these features by applying and transmitting forces to their surroundings, via their actomyosin cytoskeleton and adhesion complexes, and then transducing them into biochemical signals. Among these, the transcriptional coactivators YAP/TAZ recently emerged as key factors mediating some biological responses to actomyosin contractility in vitro. However, whether mechanical cues regulate YAP/TAZ activity in vivo, and whether this is relevant for adult tissue homeostasis, remains poorly understood. Here we show that the F-actin capping protein CAPZ is a critical regulator of actomyosin contractility, as its inactivation alters stress fiber and focal adhesion dynamics, leading to enhanced myosin activity and increased cellular traction forces. In vitro, this rescues YAP from inhibition by a small geometry; in vivo, inactivation of Capzb in the mouse liver induces YAP activation and hepatocyte proliferation, leading to striking organ overgrowth. Moreover, Capzb is essential for the maintenance of the differentiated hepatocyte state, and for the metabolic zonation of hepatocytes. In keeping with changes in tissue mechanics and activation of YAP, inhibition of ROCK or deletion of Yap1 reverse the phenotypes emerging in Capzb-null livers. These results indicate a previously unrecognized role for CAPZ in tuning the sensitivity of cells and tissues to mechanical signals, and a physiological function for F-actin dynamics in regulating organ growth and tissue homeostasis.

overall_design: Comparison of gene expression between wild-type adult mouse livers (Capzb-fl/fl tamoxifen injected, or uninjected Albumin-CreERT2;Capzb-fl/fl) and CAPZ KO livers (Albumin-CreERT2;Capzb-fl/fl tamoxifen injected)

first: Mattia

last: Forcato

first: Arianna

last: Pocaterra

first: Sirio

last: Dupont


title: Gene expression, chromatin state and DNA methylome in retinal pigment epithelium (RPE)

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

overall_design: Refer to individual Series


title: ARR1 regulated genes in the lateral root cap

city: la jolla

first: Wolfgang

last: Busch

state: CALIFORNIA

address: Salk institute, 10010 n torrey pines rd

institute: Salk Institute for Biological Studies

summary:
We sorted for GFP+ cells using the enhancer trap line J2632 with the UAS promoter driving the expression of an inducible  (by dexamethasone - Dex) constitutive active version of the ARR1 gene (ARR1ΔDDK).
We obtained the transcriptional profile of lateral root cap cells

overall_design: Seedlings were grown for 5 days.  Time-course expression profiling at 3 time points: J2632-UAS::ARR1ΔDDK-GR untreated (T0), 1 hour (T1) and 4 hour (T2) Dex-treated. J2632-UAS::ARR1ΔDDK-GR sorted fluorecent cells were harvested for RNA extraction.

first: Riccardo

last: Di Mambro

first: Rosangela

last: Sozzani

first: Sabrina

last: Sabatini

first: Philip

middle: N

last: Benfey


title: R-loops and PRC1 repress Polycomb-target genes in mouse embryonic stem cells

city: Berlin

first: Elena

last: Torlai Triglia

state: Deutschland

address: Robert Rössle Str 10

department: BIMSB

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: R-loops are three-stranded nucleic acid structures that form naturally during transcription, especially over unmethylated CpG-rich promoters. In mESC, such promoters of developmental regulator genes are occupied by the Polycomb-repressor complexes PRC1 and PRC2. Here we have explored the possibility that R-loops form over Polycomb-repressed genes and play a role in their transcriptional silencing. Using single gene and genome-wide analyses, we show that R-loops form at a specific subset of PRC-target genes and contribute to Polycomb occupancy on chromatin. Removal of R-loops leads to an up-regulation of nascent and processed transcripts and the appearance of the elongating form of RNA polymerase II. In contrast, removal of PRC2 does not influence R-loop formation, transcriptional repression and PRC1 recruitment. We finally show that R-loops and PRC1 can repress Polycomb-target genes in the absence of PRC2. Our results uncover an unanticipated synergy between R-loops and PRC1 in Polycomb repression mechanisms.

overall_design: Genome-wide distribution of PRC2 subunits EZH2 and SUZ12 in mESC in presence or absence of R-loops

first: Konstantina

last: Skourti-Stathaki

first: Adrian

last: Bird

first: Ana

last: Pombo


title: Expression data from Sus scrofa ventricle

city: Taipei

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

summary: Regulatory Mechanisms of complete AV-block Pigs

overall_design: This study enrolled 12 pigs (age: 13 months) and divided into two groups: Sham group (n = 6; 6 females sacrificed 6 months after surgery), pacing group(EXP) (n = 6; 6 females age-matched to Sham group sacrificed 6 months after surgery).  Pacing group was implanted with pacemaker with VDD setting after creating atrioventricular block. We sought to systemically elucidate critical differences in the alteration of RNA expression pattern between the LV free wall and septal tissues at the papillary muscle level using high-density oligonucleotide microarrays and functional network enrichment analysis.

first: Yu-Sheng

last: Lin

first: Chung-Sheng

last: Shi

first: Yi-Zhen

last: Wang

first: Wan-Chun

last: Ho

first: Hsien-Da

last: Huang

first: Shih-Tai

first: Kuo-Li

last: Pan

first: Mien-Cheng

last: Chen


title: Autocrine Motility Factor Modulates Proliferation Signaling Mediated By GPER

city: shanghai

first: yiran

last: li

address: Gaoke West Road 2699

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China

summary: Traditional surgery plus radiotherapy or chemotherapy, existing targeted therapies failed to significantly improve the survival rate of recurrent endometrial cancer, so suggesting that mechanism  of recurrence and progression that modulates in endometrial cancer is clinically important. Here, we show that GPER(G protein-coupled estrogen receptor 1) was binded to AMF, and the complex were translocation form plasma to cytoplasmic. Mechanistic investigations elucidated that interaction of AMF with GPER triggers phosphoinositide-3-kinase (PI3K) signaling activating and accelerating the ability of endometrial cancer cells growth. Furthermore, we found that AMF may contribute to GPER-mediated endometrial cancer progression using animal experiments and human histological experiments which be consistent with the above conclusions. On the basis of these evidences including invivo and invitro, our findings suggest that AMF–GPER interaction might be novel key molecular targets for therapeutic management of patients with endometrial cancer, whose disease were progression and recurrence.

overall_design: endometrial cancer was used in this experiment and data analysis of the  4  samples have been completed.spec-2/shAMFR VS spec-2, Ishikawa/shAMFR VS Ishikawa

first: xiaoping

last: wan


title: Differential expression of mRNAs in MDA-MB-231 cells transfected with microRNA negative control and miR-4306 mimic

city: Beijing

first: yongmei

last: song

institute: State Key Laboratory of Molecular Oncology

summary: The possible downstream pathways of miR-4306 were analyzed, using Agilent mRNA microarray. MDA-MB-231 cells treated with miR-4306 mimic were used to compare with the control group.

first: Yongmei

last: Song

first: Zitong

last: Zhao


title: Chromatin capture defines AHCY as regulator of pluripotent stem cells proliferation

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

summary: Profiling of the proteome bound to the chromatin in a simple, direct and reliable manner might result key to uncover the role of unpredicted chromatin factors in physiology and disease. We have developed a biochemical strategy named iChrock to capture the chromatin in a single purification step that provides a global view of the cellular chromatome and enables the identification of chromatin-bound proteins de novo. Integrating iChrock with genomic and functional data, we have unveiled the unexpected chromatin function of Adenosylhomocysteinase (AHCY), a major one-carbon pathway metabolic enzyme, in gene activation. Our study reveals a new regulatory axis between the metabolic state of pluripotent cells, ribosomal protein production and cell division during early phase of embryo development, by favoring the metabolic flux of methylation reactions in a local milieu.

overall_design: List of ChIPseq and RNAseq samples (Wt and Ahcy mutant).

first: Anna

last: Alcaine

first: Sergi

last: Aranda

first: Luciano

last: DiCroce


title: Differential expression of mRNAs in CAL-51 cells transfected with microRNA negative control and miR-4306 mimic

summary: The possible downstream pathways of miR-4306 were analyzed, using Agilent mRNA microarray. CAL-51 cells treated with miR-4306 mimic were used to compare with the control group.


title: Loss of RNA-binding protein Sfpq causes long-gene transcriptopathy in skeletal muscle and severe muscle mass reduction with metabolic myopathy (skeletal muscle, mRNA-seq)

status: Public on Mar 18 2019

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

summary: Growing evidences are suggesting that extra-long genes in mammals are vulnerable for full-gene length transcription and dysregulation of long genes is a mechanism underlying human genetic disorders. Skeletal muscle expresses Dystrophin which is 2.26 Mbp in length; however, how long-distance transcription is achieved is totally unknown. We had discovered RNA-binding protein SFPQ preferentially binds to long pre-mRNAs and specifically regulates the cluster of neuronal genes > 100 kbp. Here we investigated the roles of SFPQ for long gene expression, target specificities, and also physiological functions in skeletal muscle. Loss of Sfpq selectively downregulated genes >100 kbp including Dystrophin and caused progressive muscle mass reduction and metabolic myopathy characterized by glycogen accumulation and decreased abundance of mitochondrial oxidative phosphorylation complexes. Functional clustering analysis identified metabolic pathway related genes as the targets of SFPQ. These findings indicate target gene specificities and tissue-specific physiological functions of SFPQ in skeletal muscle.

overall_design: We analyzed polyA-tailed RNA profiles including transcribing RNAs in gastrocnemius skeletal muscle ( from 3 control and 3 Sfpq-/- P35 male mice) using Ion-proton.

first: Motoyasu

last: Hosokawa

first: Akihide

last: Takeuchi

last: Iida

first: Masatoshi

last: Hagiwara


title: Gene expression in the mesenteric arteries of SHR and SHRSP compared with WKYs treated with 2K1C or 1K1C, or without operation for 3 weeks at 6 weeks of age

city: Suita

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: We examined gene expression profiles in the rat mesenteric arteries using genome-wide microarray technology, and determined gene expression profiles in 3 rat strains and treated ones: spontaneously hypertensive rats (SHR), stroke-prone SHR (SHRSP), and normotensive WKYs treated with 2K1C or 1K1C, or without operation for 3 weeks at 6 weeks of age. To identify candidate genes involved in the genesis of hypertension in the SHR strains in comparison to renal hypertensive WKY, we compared the gene expression levels at 6 weeks of age, isolated genes showing a more than 4-fold increase or a less than 1/4-fold compared with WKY treated with 2K1C, 1K1C or none.

overall_design: The rat mesenteric arteries derived from spontaneously hypertensive rats (SHR), stroke-prone SHR (SHRSP), normotensive WKYs treated with 2K1C or 1K1C, or without operation for 3 weeks at 6 weeks of age were examined. Each group of rats was run in N=4.

first: Naohisa

last: Goto

first: Yuko

last: Watanabe

first: Momoko

last: Yoshida

first: Nobutaka

last: Okamura

first: Haruki

first: Kyosuke

last: Yamanishi

first: Hideaki

last: Higashino

first: Hiromichi


title: Genome-wide maps of H3K4me3 in C57BL6/J, DBA/2J, and BXD lines for male germ cells, hepatocytes, cardiomyocytes, and mouse ESCs

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: Here, we have explored how natural genetic variation in mice shapes the epigenome by studying levels of H3K4me3, a mark of active chromatin. We found tissue-specific trans-regulation in four diverse cell types: male germ cells, embryonic stem (ES) cells, hepatocytes and cardiomyocytes. Using recombinant inbred lines, we mapped six major trans-acting histone quantitative trait loci (hQTL) modulating hundreds of H3K4me3 sites in germ cells. These loci act dominantly to suppress H3K4me3, which at recombination hotspots reduces the likelihood of subsequent DNA double-strand breaks during meiosis. QTL locations match clusters of zinc finger genes, making these possible candidates that explain the dominant suppression of H3K4me3. Collectively, these data describe an extensive, tissue-specific set of chromatin regulatory loci that control functionally related chromatin sites.

overall_design: Measure H3K4me3 levels using ChIP-seq in founders and progeny of a genetic reference population of mice for QTL mapping


title: Loss-of-function of PTPN2 promotes pathogenic loss of FoxP3+ in RORgt+ Tregs [ATAC-seq]

city: La jolla

first: Mattias

last: Svensson

state: Ca

address: 9420 athena cir

institute: La jolla Institue for Allergey

summary: Genetic variants at the PTPN2 locus, which encodes the tyrosine phosphatase  PTPN2, cause reduced gene expression and are linked to rheumatoid arthritis  (RA) and other autoimmune diseases. PTPN2 inhibits signaling through the T cell  and cytokine receptors and loss of PTPN2 promotes T cell expansion and CD4  and CD8-driven autoimmunity. However, it remains unknown whether loss of  PTPN2 in FoxP3+ regulatory T cells (Treg) plays a role in autoimmunity. Here we  show that a reduction in Ptpn2 expression, comparable to that reported in human  carriers of autoimmune-predisposing PTPN2 variants, unexpectedly enhances the  severity of autoimmune arthritis through a Treg-intrinsic mechanism.  Mechanistically, we found that through dephosphorylation of STAT3, Ptpn2 inhibits  IL-6-driven pathogenic loss of FoxP3 after Tregs have acquired RORgt expression,  at a stage when chromatin accessibility for STAT3-targeted IL-17 associated  transcription factors is maximized. We conclude that PTPN2 promotes FoxP3  stability in RORgt+ Treg and that loss of function of PTPN2 in Treg contributes to the association between PTPN2 and autoimmunity.

overall_design: Chromatin Accessibility with ATAC-Sequencing for Th17 and Tregs in vivo and Tregs and exTregs isolated after in vitro culutre.

first: Karen

last: Doody

first: Benjamin

middle: J

last: Schmiedel

first: Sourya

last: Bhattacharyya

first: Bharat

last: Panwar

first: Florian

last: Wiede

first: Shen

last: Yang

first: Eugenio

last: Santelli

first: Dennis

last: Wu

first: Cristiano

last: Sacchetti

first: Ravindra

last: Gujar

first: Gregory

last: Seumois

first: William

last: Kiosses

first: Isabelle

last: Aubry

first: Gisen

last: Kim

first: Piotr

last: Mydel

first: Shimon

last: Sakaguchi

first: Mitchell

last: Kronenberg

first: Tony

last: Tiganis

first: Michel

middle: L

last: Tremblay

first: Ferhat

last: Ay

first: Pandurangan

last: Vijayanand

first: Nunzio

last: Bottini


title: Loss-of-function of PTPN2 promotes pathogenic loss of FoxP3+ in RORgt+ Tregs [RNA-seq]

first: Mattias

last: Svensson

overall_design: Gene expression analysis by RNA-Sequencing of Tregs and exTregs isolated during arthritis development in mice or after in vitro culutre.

first: Karen

last: Doody

first: Benjamin

last: Schmiedel

first: Sourya

last: Bhattacharyya

first: Bharat

last: Panwar

first: Florian

last: Wiede

first: Shen

last: Yang


title: RNA-seq in untreated and flagellin-treated Human Intestinal Myofibroblast cells (HIMF)

city: Cleveland

last: Rieder

state: OH

address: 9500 Euclid Ave

department: I & I

institute: Cleveland Clinic

summary: The goal of this experiment was to identify if there are any genes differentially expressed in flagellin-treated HIMF

overall_design: RNA was isolated, cDNA libraries (50 bp, single end) were made at the University of Chicago Genomics Facility, and sequenced on an Illumina HiSeq4000, in triplicates, according to standard protocols.

first: Shuai

last: Zhao


title: Next-gen RNA sequencing of Sleeping Beauty accelerated mouse brain tumors

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Expression profiling by high throughput sequencing

overall_design: 23 Tumor samples were obtained from a Sleeping Beauty forward genetic screen and sequenced using Illumina HiSeq 2000

first: David

last: Largaespada


title: Loss-of-function of PTPN2 promotes pathogenic loss of FoxP3+ in RORgt+ Tregs


title: Next Generation Sequencing upon siRNA-mediated knockdown of DRAIC in MCF-7 cells.

city: Copenhagen N

first: Imke

last: Tiessen

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Centre (BRIC)

country: Denmark

institute: University of Copenhagen

summary: The goal of this study is to examine the effect of DRAIC knockdown on the MCF-7 transcriptome.

overall_design: MCF-7 total RNA profiles upon siRNA-mediated knockdown of DRAIC or using a control siRNA (siCTRL) were generated by deep sequencing, in triplicate, using the Illumina TruSeq kit (RPHMR12126). Library products were sequenced on the Illumina NextSeq500 platform.


title: Expression based Intrinsic Glioma Subtypes are prognostic in low grade gliomas of the EORTC22033-26033 clinical trial.

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

institute: Erasmus MC

summary:
Introduction: The EORTC22033-26033 clinical trial investigated whether initial temozolomide (TMZ) chemotherapy confers survival advantage compared to radiotherapy (RT) in low grade glioma patients. In this study we performed gene expression profiling on tissues from this trial in order to identify markers associated with progression free survival and treatment response in this well-defined cohort of patients.
Methods: Gene expression profiling, performed on 195 samples, was used to assign tumors to one of six intrinsic glioma subtypes (IGS; molecularly similar tumors predefined by unsupervised gene expression analysis) and to extract the cellular composition of immune infiltrates. DNA copy number changes were determined on samples assigned to IGS-16.
Results: We confirm that IGS-subtypes are prognostic in EORTC22033-26033 clinical trial samples. Specific genetic changes segregate in distinct IGS subtypes: most samples assigned to IGS-9 have IDH-mutations combined with 1p19q codeletion, samples assigned to IGS-17 have IDH-mutations with intact 1p19q chromosomal arms and samples assigned to other intrinsic subtypes often are IDH-wildtype and 1p19q intact. A trend towards benefit from RT compared to TMZ was observed for samples assigned to IGS-9 (HR for TMZ is 1.90, 95% CI [0.95, 3.80], P=0.065), but not for samples assigned to IGS-17 (HR for TMZ vs RT is 0.87, 95% CI[0.50,  1.51], P=0.62). We did not identify genes significantly associated with progression free survival (PFS) within intrinsic subtypes, though follow-up time is limited. We also show that LGGs and GBMs differ in their immune-infiltrate with LGGs having higher suppressor and lower effector cell populations compared to GBMs. This suggests that LGGs are less amenable to checkpoint inhibitor type immune therapies than GBMs. Gene expression analysis and copy number analysis also identified one patient with a pilocytic astrocytoma (PA).
Conclusion: Intrinsic glioma subtypes are prognostic for PFS in EORTC22033-26033 clinical trial samples.

overall_design: The study presents gene expression data on 195 low grade glioma samples of patients treated in the EORTC22033-26033 clinical trial

first: Y

last: Gao

first: B

last: Weenink

first: M

last: van den Bent

first: L

last: Erdem-Eraslan

first: J

last: Kros

first: P

last: Smitt

first: K

last: Hoang-Xuan

first: A

last: Brandes

last: Vos

first: F

last: Dhermain

first: R

last: Enting

first: G

middle: F

last: Ryan

first: O

last: Chinot

last: Hassel

middle: E

last: van Linde

first: W

last: Mason

last: Gijtenbeek

first: C

last: Balana

last: von Deimling

first: T

last: Gorlia

last: Stupp

last: Hegi

last: Baumert


title: Global transcriptome analysis of Sclerotinia sclerotiorum following infection of resistant and susceptible soybean lines

city: Madison

first: Mehdi

last: Kabbage

state: Wisconsin

address: Department of Plant Pathology, 583 Russell Labs 1630 Linden Dr

department: Department of Plant Pathology

institute: University of Wisconsin Madison

summary: Sclerotinia sclerotiorum is a broad-host range necrotrophic pathogen which is the causative agent of Sclerotinia stem rot (SSR), and a major disease of soybean (Glycine max). A time course transcriptomic analysis was performed in both compatible and incompatible soybean lines to identify pathogenicity and developmental factors utilized by S. sclerotiorum to achieve pathogenic success.

overall_design: Four week old soybean plants of both a susceptible (S) and resistant (R) lines were infected with S. sclerotiorum by petiole inoculation using a 1 ml pipette tip agar plug of actively growing fungal hyphae. Plant tissue was sampled by cutting horizontally above and below (1.5 cm) the node of the inoculated petiole with a clean straight-edge razor. Tissue samples were then immediately frozen in liquid nitrogen prior to RNA extraction. The experimental design was completely randomized and consisted of three biological replicates for each of the treatments. For each of the experimental conditions, stem segments (∼3 cm, first internode) from 2 different plants were pooled together to form one of three biological replicates. Total RNA was extracted from soybean stem tissues and infecting S. sclerotiorum using a modified TRIzol™ Reagent protocol (Invitrogen Corp., Carlsbad, CA, USA).  Further, samples were cleaned using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). RNA concentration and purity was determined by Nanodrop (Thermo Fisher Scientific, Wilmington, DE) and sample quality was assessed using an Agilent Bioanalyzer 2100 and an RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA). Three biological replicates were generated per treatment. Library preparation was performed at the University of Wisconsin – Madison Biotechnology Centre (Madison, WI, USA). Individually indexed libraries were prepared using the TruSeq RNA Sample Preparation v2 kit according to the manufacturer’s instructions (Illumina, San Diego CA, USA). Library concentrations were quantified with the Qubit HS DNA kit (Thermo Fisher Scientific, Wilmington, DE). The size and quality of the libraries were evaluated with an Agilent Bioanalyzer 2100 and an Agilent DNA 1000 kit (Agilent Technologies, Santa Clara, CA) and the libraries were sequenced using Illumina HiSeq2500 (1X100bp) (Illumina, San Diego CA, USA). Illumina raw read data quality was verified with FastQC (http://www.bioinformatics.babraham.ac. uk/projects/fastqc/). The soybean and S.sclereotiorum genomes were collected from Phytozome v12.1  (https://phytozome.jgi.doe.gov/pz/portal.html#! bulk?org=Org_Gmax) and the Broad institute (https://www.broadinstitute.org/fungal-genome-initiative/sclerotinia-sclerotiorum-genome-project), respectively. Raw sequence reads were mapped to both genomes using the Subjunc aligner from Subread. Alignments were compared to the gene annotation GFF files for both organisms (Soybean: Gmax_275_Wm82.a2.v1.gene.gff3, S. sclereotiorum: sclerotinia_sclerotiorum_2_transcripts.gtf) and raw counts for each gene were generated using the feature Counts tool from Subread. The raw counts data were normalized with the trimmed mean of means (TMM) normalization method using edgeR package.  The normalized gene counts were transformed to log2 scale using the voom method from the R Limma package, then used to generate differential expression (log2FC) values [97, 98]. DEGs (log2FC >1 or <-1) were generated for S. sclereotiorum genes from the comparison of inoculated soybeans at different timepoints to the culture control (FDR<0.05), between early (24 and 48 hpi) and late (96 hpi) infection (FDR<0.05), and between the timepoints of resistant (R) and susceptible (S) line infections (p-value < 0.01).

first: Nathaniel

last: Westrick

first: Ashish

last: Ranjan

first: Sachin

last: Jain

first: Craig

middle: R

last: Grau

first: Damon

last: Smith


title: Comprehensive analysis of transcriptomes reveals insight into the tolerance of Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) to alkaline stress

city: Wuhan

first: Juxun

last: Wu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

institute: Huazhong Agricultral University

summary: Alkaline stress has serious negative effects on citrus production. Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) (Cj) has been reported to be a rootstock that is tolerant to alkaline stress and iron deficiency. Poncirus trifoliata (Poncirus trifoliata (L.) Raf.) (Pt), the most widely used rootstock in China, is sensitive to alkaline stress. To investigate the molecular mechanism underlying the tolerance of Cj to alkaline stress, next-generation sequencing was employed to profile the root transcriptomes and small RNAs of Cj and Pt seedlings which were cultured in nutrient solution with three gradient pH. This two-regulation level data set provides a system-level view of molecular events with precise resolution. The data suggest that the auxin pathway may play a central role in inhibitory effect of alkaline stress on root growth, and the regulation of auxin homeostasis under alkaline stress was important for citrus adapting to alkaline stress. Moreover, the JA pathway shown an opposite response to alkaline stress in Cj and Pt may contributes to the differentials of root system architecture and iron deficiency tolerance between Cj and Pt. The data set provides a wealth of genomic resources and new clues for further studying the mechanisms underlying Cj that resist alkaline stress.

sample_organism:
Citrus trifoliata
Citrus junos

platform_organism:
Citrus trifoliata
Citrus junos

overall_design: The seeds of Cj and Pt were surface-sterilized and their germination accelerated. The seedlings were grown in a growth chamber until they had four leaves. Then, the seedlings were selected by uniform size and transferred into hydroponics with 4 L solution in a green house. Three different pH gradients (6.5, 8.0 and 9.5) were set up. Because most natural soils have a weak acidity, we set pH 6.5 as the normal condition. After 8 weeks of culture, three biological replicates (three seedling plants per replicate) were harvested randomly for each treatment. Cj1, Cj2 and Cj3 were represented the seedlings of Cj cultured in pH 6.5, 8.0 and 9.5 condition, respectively. And it was the same for naming the seedlings of Pt. The root tissues of Cj and Pt were used for RNA-seq. A total of six different samples, each with three replicates, were used for RNA-seq.

first: Hualin

last: Yi


title: RNA-seq of fruit of pear with a different on-tree maturity

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

institute: University of Trento

summary: The harveting of the fruit of a single cultivar are technically harvested over a period of time and the progression of the on-tree fruit maturity lead to important physiological modification and transcriptional signature able to impact the final quality of fruit and the management of the postharvest phase.

overall_design: RNA-seq analysis of 4 sample (H1, H2, H3, H4) with three replicates (R1, R2 and R3) each.

first: Nicola

last: Busatto

first: Brian

last: Farneti

first: Alice

last: Tadiello

first: Vicky

last: Oberkofler

first: Antonio

last: Cellini

first: Franco

last: Biasioli

first: Massimo

last: Delledonne

first: Alessandro

last: Cestaro

first: Christos

last: Noutsos


title: Gene expression changes after epinephrine treated in breast cancer tumor cell

city: Dalian

first: jinxin

last: lu

state: Liaoning

address: lvshunkou district lvshun south goad west sector No.9

institute: Dalian Medical University

summary:
Chronic stress triggers activation of the sympathetic nervous system (SNS) and drives malignancy. Using an immunodeficient murine system, we show that chronic stress promotes breast cancer stem-like properties via lactate dehydrogenase A (LDHA) dependent metabolic rewiring.
In this dataset, we used microarray to characterize the mRNA expression profiles from primary PBS and Epinephrine -treated MDA-MB-231 tumor cells.

overall_design: 6 Total samples were analyzed. Collection of primary PBS and Epinephrine treated breast cancer tumor cells in triplicates. Differencial expression was performed to identify significantly differencially expressed mRNA and corresponding pathways.

first: Bai

last: Cui

first: Quentin

last: Liu


title: Comprehensive analysis of transcriptomes and small RNAs reveals insight into the tolerance of Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) to alkaline stress

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

overall_design: Refer to individual Series


title: Inhibition of NF-κB-dependent signaling enhances sensitivity and overcomes resistance to BET inhibition in uveal melanoma

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

summary: Bromodomain and extra terminal protein inhibitors (BETi) are epigenetic therapies aimed to target dysregulated gene expression in cancer cells. Despite early success of BETi in a range of malignancies, the development of drug resistance may limit their clinical application. We evaluated the mechanisms of BETi resistance in uveal melanoma (UM), a disease with little treatment options, using two approaches: a high-throughput combinatorial drug screen with the clinical BET inhibitor PLX51107, and RNA sequencing of BETi-resistant cells. We found that the NF-kB inhibitors synergistically sensitized UM cells to PLX51107 treatment. Furthermore, genes involved in NF-kB signaling were upregulated in BETi-resistant cells and the transcription factor CEBPD contributed to the mechanism of resistance. These findings suggest that inhibitors of NF-kB signaling may improve the efficacy of BET inhibition in patients with advanced UM.

overall_design: We developed 4 BETi-resistant uveal and 1 BETi-resistant cutaneous melanoma cell lines by exposing chronically the cells to increasing doses of PLX51107(0.05-2 μM) for eight weeks. To search for mechanisms driving resistance, we compared transcriptomes of the parental and BETi-resistant cell lines under 2 conditions: either with DMSO treatment either with 0.5 μM PLX51107 for 24 hours. For each condition and cell line, RNA-seq (100 SE) was performed on 2 or 3 replicates.

first: Grazia

last: Ambrosini

first: Catherine

last: Do

first: Ronald

last: Realubit

first: Charles

last: Karan

first: Elgilda

last: Musi

first: Richard

middle: D

last: Carvajal

first: Vivian

last: Chua

first: Andrew

last: Aplin

first: Gary

middle: K

last: Schwartz


title: miR-7977 transfer alter the transcriptome in bone marrow mesenchymal stem cells.

city: Sapporo

first: Masayoshi

last: Kobune

state: Hokkaido

address: Chuo-Ku, South-1, West-16

department: Hematology

institute: Sapporo Medical University

summary:
Acute myeloid leukemia (AML) cells release abundant exosomal miR-7977 that transfer into bone marrow (BM) mesenchymal stromal cells (MSCs).
We have shown that exosomal miR-7977 was highly released from AML cells and was transferred into BM MSCs. It has been well known that  a microRNA has multiple targets. In fact, miRDB predicted 633 targets. Based on these findings, control and miR-7977mimic were transferred into BM MSCs. Subsequently, alteration of transcriptome was analyzed to gain insight into the role of miR-7977 in bone marrow micro environment.

overall_design: We performed transduction of control or miR-7977 mimic into MSCs, compared transcriptome in between control transduced (n=3) and miR-7977 transduced MSCs (n=3) using the Affymetrix Human Gene 2.0 ST platform.

first: Masahiro

last: Yoshida


title: Comprehensive analysis of small RNAs reveals insight into the tolerance of Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) to alkaline stress

first: Juxun

last: Wu

overall_design: The seeds of Cj and Pt were surface-sterilized and their germination accelerated. The seedlings were grown in a growth chamber until they had four leaves. Then, the seedlings were selected by uniform size and transferred into hydroponics with 4 L solution in a green house. Three different pH gradients (6.5, 8.0 and 9.5) were set up. Because most natural soils have a weak acidity, we set pH 6.5 as the normal condition. After 8 weeks of culture, three biological replicates (three seedling plants per replicate) were harvested randomly for each treatment. Cj1, Cj2 and Cj3 were represented the seedlings of Cj cultured in pH 6.5, 8.0 and 9.5 condition, respectively. And it was the same for naming the seedlings of Pt. The root tissues of Cj and Pt were used for miRNA-seq. A total of six different samples, each with three replicates, were used for miRNA-seq. The mix samples Cj (mixed with Cj1, Cj2 and Cj3) and Pt (mixed with Pt1, Pt2 and Pt3) were used for degradome sequencing.

first: Hualin

last: Yi


title: Epigenetic profiling of Fetal Alcohol Spectrum Disorder (FASD) Replication

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

institute: Academic Medical Center Amsterdam

summary: Genome wide DNA methylation profiling of FASD patients versus healthy unexposed controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs in peripheral blood samples. Samples included 28 healthy controls and7 FASD patients.

overall_design: Bisulfite converted DNA from the 103 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: J

middle: M

last: Cobben

first: I

last: Krzyzewska

first: A

last: Venema

last: Mul

last: Polstra

middle: V

last: Postma

first: R

last: Smigiel

first: K

last: Pesz

last: Niklinski

first: M

last: Chomczyk

first: P

last: Mannens


title: Crossovers from B6xCAST F1 PRDM9-Humanized/CAST testes

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

institute: Oxford University

type: Genome variation profiling by high throughput sequencing

summary: We report 2,649 crossover breakpoints identified by single-cell DNA sequencing of 217 sperm in a B6xCAST F1 mouse, which is heterozygous at Prdm9, with one wild-type CAST allele and one allele found in human populations (bred from a genetically engineered mother, Davies et al Nature 2012). Separately, we have reported testis DMC1 enrichment in the same mouse (GSE124991). We also infer H3K4me3 intensities at DMC1 hotspots, based on the raw H3K4me3 ChIP-seq data published under GSE119727 (Li et al).    We identify several factors, including PRDM9 binding on the repair-template homologue, telomere proximity and local GC-content, that affect the probability that a DSB is repaired as a crossover. We further show that these factors also influence the time it takes for the site of a DSB to find and engage its homologue, with rapidly-engaging sites being more likely to be repaired as crossovers.

overall_design: Identification of crossover breakpoints in the sperm of a (C57BL/6J x CAST/Eij)F1 PRDM9-Humanized/CAST mouse

last: Donnelly


title: Expression data from podocyte injured glomerulus

city: New Haven

first: Shuta

last: Ishibe

state: CT

address: 300 Cedar street

institute: Yale University

summary:
Glomerular diseases are most common cause of end stage kidney disease (ESKD). Although renin angiotensin system inhibitors are effective for progression of chronic kidney disease,
The number of ESKD increases in the world. To identify a new candidate drug for glomerular disease, differentially expressed genes are searched by glomerular RNA microarray.

overall_design: Glomerulus were isolated from control and proteinuric mice for RNA extraction and hybridization on Affymetrix microarrays

first: Kazunori

last: Inoue

first: Xuefei

last: Tian


title: Gene expression after 1 and 5 days of cigarette smoke exposure in mice with chronically inflamed or healthy lungs

city: Chapel Hill

first: Claire

last: Doerschuk

state: NC

address: 125 Mason Farm Rd. CB#7248

institute: UNC Chapel Hill

summary:
These studies tested the hypotheses that smoke induces changes in mRNA profiles that are dependent on sex and the health status of the lung, and that the effects of smoke are different after 1 day compared to 5 days of smoke exposure. The ways in which the lungs modulate their response to cigarette smoke after repeated exposures are important for understanding the toxicology of smoke, for developing biomarkers of chronic smoke exposure, and for understanding the therapeutic potential in regulatory signaling pathways that are beneficial or detrimental to lung health.
Sex-matched 5-7-week old wildtype (WT) and Scnn1b-overexpressing (BENaC) littermates were exposed to cigarette smoke or sham (room air) exposure. Exposure occurred in a plexiglass chamber attached to a smoke delivery device using an exposure chamber and smoking machine (inExpose Exposure System, SCIREQ, Chandler, AZ). Mice were exposed to mainstream + sidestream smoke from 6 reference cigarettes with filters removed per day (3R4F research cigarettes, University of Kentucky). Each cigarette was puffed for 2 sec every 25 sec, using the standard Federal Trade Commission smoking machine protocol. The sham-exposed control mice were exposed to room air in the exposure chamber for a time equivalent to that needed for active smoke exposure. Mice were exposed to cigarette or sham smoke for 1 day or 5 consecutive days. Samples were harvested 4 hours after the completion of the final smoke exposure. The right lung was used for gene expression analysis.

overall_design: Mice were exposed to cigarette smoke or sham (room air) for 1 day or 5 consecutive days. Samples were harvested 4 hours after the completion of the final smoke exposure. The right lung was used for gene expression analysis. Gene expression was measured using the Affymetrix moGene2.1 array.

first: Michelle

last: Engle

first: Hong

last: Dang

first: Joel

middle: S

last: Parker


title: Gene Expression Data from WT and Ifitm-/-  CD4 T cells

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

institute: UCL

summary: We used Affymetrix microarrays to understand the genome wide differences in gene expression between WT and Ifitm-/-  CD4 T cells

overall_design: Fresh single splenocyte suspensions were re-suspended in Ammonium Chloride solution (Stem Cell Technologies Inc, US) and CD4+ T cells were separated using negative selection EasySep system (Stem Cell Technologies Inc, US) according to the manufacturer’s protocol. Microarrays were performed on the purified naïve (resting) CD4 T cells from Ifitm-/- and WT controls. These arrays were done twice with independent biological replicates.

first: Hemant

last: Sahni


title: Deciphering the biological processes underlying tomato biomass production and composition.

status: Public on Mar 17 2019

city: Portici

first: Daniela

last: D'Esposito

address: Via Università 100

department: Department of Agriculture

institute: University of Naples Federico II

summary: After tomato fruits harvesting huge amounts of biomass residues, including plant and immature fruit, remaining in the field can be utilized to produce bioenergy. Little is known about the molecular aspects underlying tomato plant biomass production and hydrolysis. To identify genes involved in the regulation of plant biomass accumulation and composition, two Solanum pennellii introgression lines (ILs) with contrasting phenotypes for plant architecture and biomass characteristics, were analyzed. A multiple approach aimed to characterize such near-isogenic lines was carried out for studying gene expression dynamics, microscopy cell traits and qualitative and quantitative cell wall chemical compounds variation. Transcriptomic analysis showed that the enhanced biomass production observed in IL2-6 line is due to a more effective coordination of chloroplast and mitochondria energy fluxes (photosynthesis, cell division, cell wall and hormone metabolism activation). In parallel, microscopy analysis revealed a higher number of cells and chloroplasts in leaf epidermis in the high biomass line whilst chemical measurements on the two lines pointed out striking differences in the cell wall composition and organization.  Taken together, our findings shed light on the mechanisms underlying the tomato biomass production and open new routes for improving the tomato lignocellulosic processability.

sample_organism: Solanum lycopersicum x Solanum pennellii

overall_design:
Transcriptome profiles of two tomato introgression lines, IL2-6 and IL3-2 (in triplicate), and the control M82 (one replicate) were generated by RNA sequencing.
Please note that the 'M82 Rep 2'  (through the variant calling) was used as control to confirm that IL2-6 and IL3-2 were, at genotype level, as expected.  After checked this, the IL2-6 and IL3-2 samples were used for differentially expression analysis that is the central part of the current study.

last: D’Esposito

first: Elisa

last: Cappetta

first: Giuseppe

last: Andolfo

first: Francesca

last: Ferriello

first: Camilla

last: Borgonuovo

first: Gianluca

last: Caruso

first: Antonino

last: De Natale

first: Luigi

last: Frusciante

first: Maria

last: Ercolano


title: Differential lncRNA and mRNA expression profiles of 8 pairs of metastastic and non-metastastic CRC tissues

city: GUANGZHOU

first: Liang

last: Zhao

state: GUANGDONG

address: 1838 Guangzhou Avenue North

department: Department of Pathology

institute: Nanfang Hospital, Southern Medical University

summary: To further study the mechnisms behind CRC metastasis, we employed microarray expression profiling as a discovery platform to identify differential expressed lncRNAs and mRNAs in non-metastastic and metastastic CRC tissues. Eight non-metastic CRC tissues and eight metastatic CRC tissues are collected and total RNA were extracted and purified. Differential lncRNA and mRNA expression profiles  of non-metastatic and metastatic CRC tissues were obtained.

overall_design: LncRNA and mRNA expression profile was detected in eight non-metastastic and eight metastastic CRC tissues.

first: Xuegang

last: Sun


title: Genome-wide SNP data of Chinese indigenous horse breed (additional horse samples)

status: Public on Mar 16 2019

city: Beijing

first: Hongying

last: Ma

address: yuanmingyuan road NO.2

institute: China agriculture university

summary: The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data

sample_organism:
Equus asinus
Equus caballus
Equus przewalskii

overall_design: We used Equine SNP70 Bead Array technology to genotype 312 Equus samples  to study the relationships between them. This is the 'additional horse samples' data set.

first: Chunjiang


title: Genome-wide SNP data of Chinese indigenous horse breed (Jinjinag horse samples)

overall_design: We used Equine SNP70 Bead Array technology to genotype 312 Equus samples  to study the relationships between them. This is the 'Jinjinag horse samples' data set.


title: Genome-wide SNP data of Chinese indigenous horse breed


title: Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition

status: Public on Mar 26 2019

city: Boston

first: Andrew

last: Hong

state: MA

address: 450 Brookline Avenue, DA1514

department: Pediatric Oncology

institute: Dana-Farber / Boston Children's / Broad Institute

type:
Expression profiling by array
Third-party reanalysis

summary: Whole gene expression arrays for primary and metastatic cell lines derived from patients with RMC

overall_design: To compare patient derived RMC models with other publically available Whole Gene Expression Arrays from patients with SMARCB1 deficient cancers or other cancer cell lines.

first: William

middle: C

last: Hahn


title: Genome-wide SNP data of Chinese indigenous horse breed (264 Chinese horse breeds)

overall_design: We used Equine SNP70 Bead Array technology to genotype 312 Equus samples  to study the relationships between them. This is the 'Chinese horse breeds' data set.


title: Epigenetic signatures of chronic social stress in stress-susceptible animals

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

summary: Susceptibility to depression-like behavioral abnormalities in mice is studied with a well-established social defeat stress model. Responses to social defeat are associated with widespread transcriptomic changes in several brain regions. Here we present the first study of genome-wide cytosine methylation patterns of mice susceptible to social defeat stress using whole-genome bisulfite sequencing on DNA from the nucleus accumbens, a key brain reward region implicated in depression. We find a greater proportion of CpG hypermethylation than hypomethylation in susceptible mice compared to controls, with an opposite trend in the CHG and CHH contexts. Among the genes with the largest extent of differential methylation we find several which have been identified in earlier studies of gene expression changes related to social defeat, including estrogen receptor alpha (encoded by Esr1) and the deleted in colorectal cancer (Dcc) gene. Genes exhibiting differential methylation are enriched in GO terms of nervous system development, neurogenesis and structure development, which associated with learning memory and stress response. Our data provide a new evidence of the association of DNA methylation profiles and susceptibility to chronic stress.

overall_design: Whole-genome bisulfite sequencing on nucleus accumens DNA from mice exposed to social defeat

last: O’Toole

first: Tieyuan

last: Zhang


title: Comparative transcription profiling of mRNA and lncRNA related to C75 effect on pulmonary arterial hypertension

city: shanghai

first: cuilan

last: hou

address: luding road

institute: shanghai jiaotong university

summary: Investigated the expression profile and potential roles of mRNA and long non-coding RNAs (lncRNAs) in pulmonary arterial hypertension (PAH) mice induced by monocrotaline.

overall_design: Control (n=2), MCT (n=2), and MCT-C75 (n=2) were examined by high throughput sequencing (HTS). Bioinformatics analyses were carried out to predict the roles of aberrantly expressed mRNA and lncRNAs.

first: Cuilan

last: Hou


title: Small non-coding RNA profiling in human biofluids from healthy individuals

city: Turin

first: Alessio

last: Naccarati

address: Via Nizza 52

institute: Italian Institute for Genomic Medicine

summary:
The role of non-coding RNAs in different biological processes and diseases is continuously expanding. Next-generation sequencing together with the parallel improvement of bioinformatics analyses allows the accurate detection and quantification of an increasing number of RNA species. With the aim of exploring new potential biomarkers for disease classification, a clear overview of the expression levels of common/unique small RNA species among different biospecimens is necessary. However, except for miRNAs in plasma, there are no substantial indications about the pattern of expression of various small RNAs in multiple specimens among healthy humans. Overall, the data reported hereby provide an insight of the constitution of the human miRNome and other small non-coding RNAs in various specimens of healthy individuals. This dataset was submitted by the Extracellular RNA Atlas (http://exrna-atlas.org/exat/datasets/EXR-ANACC1S6lJ1C-AN), and the selected raw and processed data for this dataset corresponds to what is available in that resource.

Submitter indicates: "The publication associated with the citation below refers to a slightly larger set of samples (includes cervical scrape samples) and contains an alternative analysis to the processed data files provided here."

overall_design: Small RNA-Seq data of RNA extracted from exosomes from 123 plasma samples of healthy donors derived from three different studies. Additionally, sequencing was performed on RNA from 39 faecal samples and 47 urine samples.

first: Barbara

last: Pardini

last: Cordero

first: Giulio

last: Ferrero

first: Sonia

last: Tarallo

first: Maddalena

last: Arigoni

first: Federica

last: Riccardo

first: Gaetano

last: Gallo

first: Guglielmo

last: Ronco

first: Marco

last: Allasia

first: Neha

last: Kulkarni

first: Giuseppa

last: Matullo

first: Paolo

last: Vineis

first: Raffele

last: Calogero


title: The Integrity of piRNA Clusters is Abolished by Insulators in the Drosophila Germline

status: Public on Mar 15 2019

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

summary: Piwi-interacting RNAs (piRNAs) control transposable element (TE) activity in the germline. piRNAs are produced from single-stranded precursors transcribed from distinct genomic loci, enriched by TE fragments and termed piRNA clusters. The specific chromatin organization and transcriptional regulation of Drosophila germline-specific piRNA clusters ensure transcription and processing of piRNA precursors. TEs harbour various regulatory elements that could affect piRNA cluster integrity. One of such elements is the suppressor-of-hairy-wing (Su(Hw))-mediated insulator, which is harboured in the retrotransposon gypsy. To understand how insulators contribute to piRNA cluster activity, we studied the effects of transgenes containing gypsy insulators on local organization of endogenous piRNA clusters. We show that transgene insertions interfere with piRNA precursor transcription, small RNA production and the formation of piRNA cluster-specific chromatin, a hallmark of which is Rhino, the germline homolog of the heterochromatin protein 1 (HP1). The mutations of Su(Hw) restored the integrity of piRNA clusters in transgenic strains. Surprisingly, Su(Hw) depletion enhanced the production of piRNAs by the domesticated telomeric retrotransposon TART, indicating that Su(Hw)-dependent elements protect TART transcripts from piRNA processing machinery in telomeres. A genome-wide analysis revealed that Su(Hw)-binding sites are depleted in endogenous germline piRNA clusters, suggesting that their functional integrity is under strict evolutionary constraints.

overall_design: The fractions of small RNAs (19-29 nt) from ovaries of four transgenic strains of Drosophila melanogaster were sequenced using Illumina HiSeq 2000.

first: Elizaveta

last: Radion

first: Alla

last: Kalmykova


title: Genistein treatment effects upin human prostate

city: Portland

first: Ryan

last: Gordon

state: OR

address: 3181 SW Sam Jackson Park Road, BRB519

institute: Oregon Health & Science University

summary: Prior studies support the notion that the experimental chemopreventive agent, genistein, inhibits prostate cancer (PCa) cell movement in humans and that this in turn inhibits metastatic spread, thereby preventing PCa-specific death. As many effects have been ascribed to genistein, it has been considered a non-specific agent. However, its effects are concentration-dependent, and the vast majority of studies use concentrations greater than 3 logs above those associated with dietary consumption. Genistein is found in soy, and individuals consuming soy-based diets have blood concentrations of free genistein in the low nanomalar range. Using dosing guided by phase I pharmacokinetic studies in US men, prospective treatment of men on a phase II trial with genistein for one month prior to radical prostatectomy for localized PCa. Here we conducted an unbiased screening for effects of genistein in prostate as well as evaluate changes between normal and cancer cells.

overall_design: To evaluate the performance of LCM coupled to linear amplification and array-based gene profiling across multiple patient samples, normal prostate epithelial cells (N) to prostate cancer cells (T) in prostate tissue from individuals who had undergone radical prostatectomy for localized PCa. Evaluation of gene expression in genistein treated (NG) versus untreated control subjects (N), using tissue obtained as part of a prospective pre-prostatectomy trial. These studies focused upon normal prostate epithelial cells. This population of cells is present in a cancer containing gland, representing an at risk population and constitutes an important target cell population for pharmacologic targeting with chemoprevention agents. Three-condition experiment, N vs. T samples and N vs. NG. No biological replicates samples: 14 N, 10 T, and 10 NG. In total 17 slides were used.

first: Yongzeng

last: Ding

first: Hu

last: Zhang

first: Raymond

last: Bergan