title: Inflammasome-driven catecholamine catabolism in macrophages blunts lipolysis during ageing

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

summary: We performed whole transcriptome profiling on sorted tissue macrophages from the spleen or from visceral adipose tissue (VAT) of wild-type mice that are 3-month or 24-month of age or from 24-month Nlrp3-/- mice

overall_design: Profiles were generated on fluorescence-activated-cells (FACs) sorted F480+CD11b+ cells from spleen or adipose tissue, using sequencing analysis

first: Christina

last: Camell

first: Jil

last: Sander

first: Olga

last: Spadaro

first: Aileen

first: Kim

middle: Y

last: Nguyen

first: Allison

last: Wing

first: Emily

middle: L

last: Goldberg

first: Yun-Hee

last: Youm

first: Chester

middle: W

last: Brown

first: John

last: Elsworth

first: Matthew

last: Rodeheffer

first: Vishwa

last: Dixit


title: RNA-SEQ analysis of the superficial, intermediate and basal cell layers of the bladder urothelium 24h after infection with UTI89 strain of E.coli and their adult female non-UTI controls.

status: Public on Sep 30 2017

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

type: Expression profiling by high throughput sequencing

summary: Dissection and FACS cell sorting techniques were used to isolate the superficial, intermediate and basal cell types from the bladder urothelium of adult female mice following UTI infections, and their controls. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific noncoding RNAs.

overall_design: Total RNA was obtained from FACS isolated superficial, intermediate and basal cell layers of the adult female bladder urothelium 24h after infection with UTI89 strain of E.coli and also from their non-UTI controls. Tg(Upk3a-GFP/cre/ERT2)26Amc x Gt(ROSA)26Sor<tm2.1(mix1b-mCherry)Mgn>  and Tg(KRT5-cre/ERT2)2Ipc x Gt(ROSA)26Sor<tm2.1(mix1b-mCherry)Mgn>) transgenic mice were used to isolate the intermediate and basal cells, respectively.  The long term goal is to generate a transcriptional atlas of bladder urothelium following UTI infections.

first: Steven

last: Potter

first: Spenser

last: Souza

first: Kerry

last: Schneider

first: Ekaterina

last: Batourina

first: Tammer

last: Yamany

first: Cathy

last: Mendelsohn


title: Analysis of genes differencially expressed depending on Myc expression

status: Public on Sep 29 2017

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

summary: The goal is to examine the transcriptome of ESCs with different Myc levels

overall_design: In order to analyse the transcriptome, mESC population was sorted in 3 groups depending on Myc levels

first: Covadonga

last: Diaz

first: Miguel

last: Torres

first: Cristina

last: Claveria


title: Diversity amongst trigeminal neurons revealed by high throughput single cell sequencing

status: Public on Sep 28 2017

city: Bethesda

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

country: USA

institute: NIDCR/NIH

summary: Single cell RNA-seq was performed on the mouse trigmeminal ganglia.

overall_design: Trigeminal ganglia from mice were dissociated into single cell and scRNA-seq were carried out using the Drop-seq method.

first: Lars

last: von Buchholtz

first: Nick

last: Ryba


city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

type: Non-coding RNA profiling by high throughput sequencing

summary: small RNA-seq of  embryonic samples of N. furzeri.

overall_design: 7 embryonic samples, two weeks post-fertilization, of Nothobranchius furzeri either in diapause or non-diapause.

first: Mario

last: Baumgart

first: Emanuel

last: Barth

first: Philipp

last: Koch

first: Manja

last: Marz

first: Matthias

last: Platzer

first: Alessandro

last: Cellerino


title: small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages) and Brain samples of 6 other killifish species

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
The RNA-seq data contain 3 tissues (brain, liver, skin) of N. furzeri strains MZM-0410 and GRZ plus 2 biological replicates of brain of 6 other killifish species.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

sample_organism:
Iconisemion striatum
Nothobranchius furzeri
Nothobranchius kuhntae
Nothobranchius rachovii
Nothobranchius pienaari
Nothobranchius kadleci
Nothobranchius korthausae

overall_design: 162 samples: 4-5 biological replicates per tissue and N. furzeri strain (N=150) plus 2 biological replicates of brain of 6 other killifish species.


title: Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [RNA-seq I]

city: Cambridge

first: Sandra

last: Cortijo

address: Bateman Street

institute: Sainsbury Laboratory, Cambridge University

summary: Plants are sessile organisms and therefore must sense and respond to changes of their surrounding conditions such as ambient temperature, which vary diurnally and seasonally. It is not yet clear how plants sense temperature and integrate this information into their development. We have previously shown that H2A.Z-nucleosomes are evicted in response to warmer temperatures. It is not clear however, whether the link between transcriptional responsiveness and changes in H2A.Z binding in context of temperature shifts is a global trend that can be seen throughout the genome, or the phenomenon is specific to a specialised set of temperature-responsive genes. In addition to the role of H2A.Z-nucleosome dynamics in the transcriptional response to temperature, it was shown that genes strongly misregulated in the h2a.z mutant are enriched for gene categories involved in response to multiple environmental cues. This suggests that H2A.Z could be implicated in the transcriptional response to various environmental inputs, raising the question: What brings the specificity of H2A.Z dynamics in response to temperature? To address this question we have profiled H2A.Z-nucleosome occupancy genome wide (using ChIP-seq) during a time course after temperature variation and compared its dynamics to transcriptional changes. We identified a fast, targeted and transient eviction of H2A.Z associated with transcriptional activation in response to temperature for a few hundreds genes. This eviction is associated with a reduction of the stability of the nucleosome. Moreover the genes with a fast H2A.Z eviction were strongly enriched in heat shock elements in their promoter and we observed a strong association between HSF1 binding and H2AZ eviction at warm temperature. These results highlight the importance of the interplay between transcription factors and chromatin to allow a controlled and dynamics response to temperature.

overall_design: RNA-seq were generated in duplicate for seedlings shifted to warm temperature

first: Phil

last: Wigge

first: Varodom

last: Charoensawan


title: Genome-wide analysis of transcription, H2A.Z, nucleosomes and HSF1 dynamics in response to temperature increase in Arabidopsis thaliana [ChIP-seq & Mnase-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: HTA11, H3, H2B and HSF1 ChIP-seq as well as MNase-seq were generated in seedlings shifted to warm temperature


title: De novo characterization of alligator weed (Alternanthera philoxeroides) transcriptome shedding light on gene expression under potassium deprivation

city: Chengdu

first: li

middle: li

last: qin

state: sichuan province

address: wenjiang district huiming 211road

country: China

institute: Sichuan Agricultural University

summary: We use solexa sequencing technology to analysis root transcriptome of alligator weed during 7 d potassium deficiency. Further analysis suggested that 9,253 differentially expressed genes (DEGs) were up-regulated and 2,138 DEGs were down-regulated after potassium deficiency for 7 days, including 121 transcription factors, 108 kinases, 146 transporters, and 178 genes that were related to stress. Our results afford a valuable resource for genetic and genomic research on plant potassium deficiency.

overall_design: Examination of 2 different root samples (control and treatment)

first: Liqin

last: Li

first: Liming

last: Lu


title: Analysis of gene expression changes by knock-down of hace1 tumour suppressor in zebrafish

city: Ottawa

first: Sergey

middle: V

last: Prykhozhij

state: Ontario

address: Room 318/319 | CAREG, 20 Marie-Curie Private

country: Canada

institute: CHEO Research Institute/University of Ottawa

summary:
Background:  In this study we reveal a previously undescribed role of the HACE1 (HECT domain and Ankyrin repeat Containing E3 ubiquitin-protein ligase 1) tumor suppressor protein in normal vertebrate heart development using the zebrafish (Danio rerio) model.  We examined the link between the cardiac phenotypes associated with hace1 loss of function to the expression of the Rho small family GTPase, rac1, which is a known target of HACE1 and promotes ROS production via its interaction with NADPH oxidase holoenzymes.
We examined expression changes induced by knock-down of hace1 in zebrafish at 48 hpf, the stage when heart abnormalities are observed. This was done by collecting duplicate samples of control and hace1 morphant embryos and performing RNA sequencing on them.
Conclusions:  Our study demonstrates that HACE1 is critical in the normal development and proper function of the heart via a ROS-dependent mechanism.

overall_design: 2 samples of control and hace1 morphant zebrafish embryos at 48 hpf were analyzed

first: Babak

last: Razaghi

first: Shelby

last: Steele

first: Jessica

last: Hill

first: Nicolas

last: Crapoulet

first: Jason

last: Berman

first: Stephen

last: Lewis


title: Calcium treatment can delay tomato (Solanum lycopersicum L.) fruit senescence

city: beltsville

first: Tianbao

last: Yang

state: MD

address: 10300 BALTIMORE AVENUE

department: BARC

institute: USDA-ARS

summary: In the present study, we demonstrated that application of CaCl2 to ‘Micro Tom’ tomato fruit (mature green stage) delayed fruit senescence and mature.

overall_design: Examination of Ca2+ and water injected tomato fruit

first: Lingfei

last: Shangguan


title: Genetic circuit 0x58 replicates and modified

city: Bristol

first: Thomas

middle: Edward

last: Gorochowski

address: 24 Tyndall Avenue

department: Biological Sciences

institute: University of Bristol

summary: We report the characterization of the 0x58 circuit, a modified version and wild-type cells not containing any circuit. Data is collected for all input inducer combinations and cells harboring the circuit are grown in culture tubes.

overall_design: Examination of two replicates of the 0x58 circuit and 1 modified circuit grown for different combinations of inducer in culture tubes.

middle: E

first: Yongjin

last: Park

first: Alec

last: Nielsen


title: MYCL and EP400 are required for Max and MCPyV mediated gene activation

city: Boston

first: Jingwei

last: Cheng

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: To determine if MYCL or EP400 knockdown would affect Max target genes in Merkel cell carcinoma cell line MKL-1, we performed RNA-seq analyses of MKL-1 cells inducibly expressing shMYCL and two different EP400 shRNA -2, -3  and compared to ChIP-seq data using BETA analyses.

overall_design: MYCL or EP400 was inducibly reduced with shRNA in MKL-1 cells to analyze gene regulation.


title: Determination of astrocyte transcripts regulated by neuronal contact

city: Portland

first: James

middle: Christopher

last: McGann

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Vollum Institute

institute: Oregon Health and Science University

summary: We co-cultured P0 TdTomato-expressing hippocampal neurons with wild type cortical astrocytes for 2, 4 or 7 days in vitro and then separated the populations using FACS. We then compared transcripts from co-cultured with those from astrocytes cultured alone

overall_design: Astrocytes were grown in culture until confluent on 15cm plates and then switched to N2 media. 1x10^6 P0 hippocampal neurons were plated on experimental plates and grown for indicated time (2, 4 or 7 days in vitro). At the indicated time, cells were trypsanized and underwent FACS sorting using the TdTomato emission peak of 581nm. Control astrocytes were used to set TdTomato- gates. Total RNA was extracted with Trizol and rRNA was removed using the Ribogone kit. cDNA synthesis and indexed Illumina libraries were made using the SMARTer Universal Low Input RNA kit for Sequencing and the SMARTer Low Input Library Prep Kit and sequenced on HiSeq 2000

middle: C

first: Gail

last: Mandel


title: Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

city: Nijmegen

first: Simon

last: van Heeringen

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

summary: Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates.The most recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago.  Here we generated epigenetic profiles and determined gene expression in X.laevis  embryos to study the consequences of this duplication at the level of the genome, the epigenome and gene expression.

sample_organism:
Xenopus laevis
Xenopus tropicalis
Xenopus tropicalis x Xenopus laevis

overall_design: Genomic DNA of Xenopus tropicalis and Xenopus laevis; RNA-seq (two replicates) in stage 10.5 Xenopus laevis embryos; ChIP-seq for H3K4me3 and p300 (each two replicates) in Xenopus laevis (LELS), Xenopus tropicalis (TETS) and Xenopus tropicals x laevis (hybrid; LETS) embryos.

first: Sarita

middle: S

last: Paranjpe

first: Georgios

last: Georgiou

first: Ila

last: van Kruijsbergen

first: Romain

last: Gibeaux

first: Rebecca

last: Heald

middle: J

first: Gert

last: Veenstra


title: Filamentation involves two overlapping, but distinct, programs of filamentation in the pathogenic fungus Candida albicans

city: Omaha

first: Jill

middle: R

last: Blankenship

state: NE

address: 6001 Dodge St, AH114

department: Biology

institute: University of Nebraska at Omaha

summary:
The ability of the human pathogenic fungus Candida albicans to switch between yeast-like and filamentous forms of growth has long been linked to pathogenesis. Numerous environmental conditions, including growth at high temperatures, nutrient limitation, and exposure to serum, can trigger this morphological switch and are frequently used in in vitro models to identify genes with roles in filamentation. Previous work has suggested that differences exist between the various in vitro models both in the genetic requirements for filamentation and transcriptional responses to distinct filamentation-inducing media. We compared 10 in vitro models for filamentation and found broad genetic and transcriptomic differences between model systems.
Methods: Total RNA was extracted from yeast or filamentous cells grown in liquid media or on solid plates. Samples were tested in biological triplicates. RNASeq libraries were generated beginning with 1.8 ng of total RNA following standardized protocols with the TruSeq RNA v2 kit (Illumina, San Diego).  Libraries were diluted to a concentration of 6.0 picomoles and sequenced on a HiSeq2500 and 100 bp single reads were generated. Two lanes were used for each sample.

overall_design: Total RNA profiles of Candida albicans cells grown for 3 hours in inducing and non-inducing solid and liquid media were generated in triplicate on an Illumina HiSeq2500.


title: Expression profiles of nine Fusarium fujikuroi strains revealed common and different sets of up-regulated genes

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

summary: We provide genome sequences of altogether 9 F. fujikuroi and one F. oxysporum (outgroup) strains, all isolated from rice plants in different geographical regions of the world, and searched for differences in genome structure, chromosome size, secondary metabolite production, virulence on rice, and in vitro and in planta transcriptome profiles. Despite their high relatedness on genome level, they differ significantly in their ability to infect rice, to form asexual spores (micro-and macroconidia), and to produce secondary metabolites. To gain insight into these differences, we compared the transcriptome of the ten strains in infected rice roots with that of liquid culture at low and high nitrogen (6 mM and 60 mM Gln) in vitro conditions by a RNA sequencing approach.

sample_organism:
Fusarium fujikuroi
Fusarium oxysporum

platform_organism:
Fusarium fujikuroi
Fusarium oxysporum

overall_design: RNA-sequencing of 10 Fusarium strains; 3 conditions (rice roots 7 days post infection; synthetic liquid media with 6 mM or 60 mM glutamine after 3 days of cultivation) ,

first: Martin

last: Münsterkötter

first: Eva-Maria

last: Niehaus

last: Güldener

first: Bettina

last: Tudzynski


title: Randomized CRISPR-Cas Transcriptional Perturbation Screening Reveals Protective Genes against Alpha-Synuclein Toxicity

status: Public on Oct 01 2017

first: Timothy

middle: K

last: Lu

address: 77 Mass. Avenue

institute: Massachusetts Institute of Technology

summary: We compared transcriptome profile of ITox2C strain expressing dCas9-VP64 (aka screen strain) that express gRNA 9-1 with those expressing no gRNA

overall_design: mRNA profiles of Saccharomyces cerevisiae W303 expressing SNCA and dCas9-VP64 (screen strain) with gRNA 9-1 or no gRNA (negative control) were generated by deep sequencing, in duplicates, using Illumina HiSeq.

first: Ying-Chou

last: Chen

first: Fahim

last: Farzadfard

first: Nava

last: Gharaei

first: Chien-Wen

first: Jicong

last: Cao


title: Poised RNA polymerase II co-localises with Polycomb repression at multi-lineage developmental regulator genes in differentiated neurons

city: Berlin

first: Elena

last: Torlai Triglia

state: Deutschland

address: Robert Rössle Str 10

department: BIMSB

institute: Max Delbrück Center for Molecular Medicine

summary: Polycomb repression is tightly associated with promoter co-occupancy of poised RNA polymerase II (RNAPII) in mouse Embryonic Stem Cells (ESCs). However, it remains unclear whether poising is a specific feature of ESCs or also associated with Polycomb during cell differentiation. Here, we show that RNAPII poising at Polycomb repressed genes is found in five stages of ESC differentiation to dopaminergic neurons. We find that key transcription factor genes of non-neuronal lineages are kept silent in the neuronal lineage through Polycomb repression in co-association with poised RNAPII in the absence of DNA methylation within DNA Methylation Valleys (DMVs). This group of poised transcription factors are preferential candidate master regulators for trans-differentiation of neurons into different lineages. We conclude that RNAPII poising is a general feature of Polycomb repression and cell plasticity in pluripotent stem cells and terminally differentiated neurons.

overall_design: Genome wide mapping of RNAPII post-translational modifications (S5p and S7p) together with Polycomb mark H3K27me3 in five time points during neuronal differentiation

first: Carmelo

last: Ferrai

first: Tiago

last: Rito

first: Alexander

last: Kukalev

first: Ines

last: de Santiago

first: Ana

last: Pombo


title: RNA sequencing quantitative analysis of RNA editing levels in ADAR1, ADAR2, AIMP2 overexpression and wild type HEK293 cells

city: STANFORD

first: Jin

middle: Billy

last: Li

state: CA

address: 300 Pasteur Dr.

department: Genetics

institute: Stanford University

summary: We overexpressed ADAR1, ADAR2 and AIMP2 in HEK293 cells and examined editing using RNA-seq.

overall_design: mRNA profiles of wild type (WT) and ADAR1, ADAR2 and AIMP2 overexpression HEK293 cells were generated by deep sequencing using Illumina HiSeq 2000.

first: Meng

middle: H

last: Tan

first: Qin

first: Raghuvaran

last: Shanmugam

middle: B


title: Transcriptional responses induced by controlled human malaria infection (CHMI)

city: Seattle

first: Carl

last: Murie

state: Washington

address: 1100 Fairview Ave. N

department: VIDD

institute: Fred Hutch Cancer Research Center

summary: Whole blood RNA-Seq was applied to investigate gene expression kinetics in Tanzanian males who underwent controlled malaria infection by intradermal injection with aseptic, purified, cryopreserved Plasmodium falciparum sporozoites.

overall_design: 10 volunteers injected intradermally with a total of 25'000 infectious Plasmodium falciparum sporozoites (PfSPZ).

first: Julian

last: Rothen


title: Cold-induced protein RBM3 regulates neocortical development via Yap1 in maternal hypothermia

status: Public on Sep 27 2017

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression. The goals of this study are to compare the different transcripts between control or RBM3 knockdown in the neural stem cells when the maternal hypothermia was induced.

overall_design: Methods: the in utero electroporation was employed to introduce the RBM3 knockdown plasimds or control plasmids into the E13 embryonic cortex. and then the GFP+ Neural stem cell isolated from E15 mice by using FACS. RNA used for global transcriptome analysis were extracted from these GFP+ neural stem cells and sequenced by Hiseq 2500. Significantly differentially expressed genes were identified when we compared Normalized Reads Count between groups with p < 0.05 and |Log2FoldChange| > 1.

first: Wenlong

last: Xia

first: Libo

last: Su


title: EP400 is required for Max and MCPyV mediated gene activation

first: Jingwei

last: Cheng

summary: To determine if EP400 knockdown would affect Max target genes in Merkel cell carcinoma cell line MKL-1, we performed RNA-seq analyses of MKL-1 cells inducibly expressing EP400 shRNA and compared to ChIP-seq data using BETA analyses.

overall_design: EP400 was inducibly reduced with shRNA in MKL-1 cells to analyze gene regulation.

first: Donglim

last: Park


title: MCPyV ST, MAX and the TRRAP complex cooperate to bind to Transcription Start Sites

summary: To determine if MCPyV ST was recruited to chromatin together with MAX and the TRRAP complex, we performed chromatin immunoprecipitation (ChIP) using the validated antibodies to MCPyV ST produced in our lab, HA tagged ST, MAX and EP400 followed by next generation sequencing. De novo DNA motif analysis revealed that the canonical E-box MYC target sequence was the most frequently observed motif. Metagene analysis revealed that antibodies to MAX, EP400, ST (Ab5) and HA tagged ST showed strong enrichment in transcription start site (TSS). H3K4me3 ChIP-seq confirmed that the peaks enriched with antibodies to MAX, EP400 and ST all centered on the H3K4me3 peaks with a high degree of overlap.

overall_design: Examination of the hypothesis that transcripton factors Max and TRRAP complex bind same DNA loci as a complex.

first: Rhamy

last: Zeid

first: Thomas

last: Westerling


title: Regulartory effect of HNRNPL and LARP on RNA expression in LNCaP prostate cancer cells

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

summary: Analysis of RNA expression in LNCaP prostate cancer cells treated with different siRNAs to define the regulatory effect of HNRNPL and LARP on RNA expression.

overall_design: LNCaP prostate cancer cells were treated with the control siRNA oligos and the siRNA oligos that knockdown the expression of HNRNPL and LARP. The polyA-RNA expression difference upon different siRNA oligo treatment was evaluted.

first: Teng

last: Fei

first: Chen

last: Yiwen

first: Shirley

last: Liu

first: Brown

last: Myles


title: CRISPR screen in LNCaP prostate cancer cells

summary: Genome-wide CRISPR screen was performed in LNCaP cells.

overall_design: Analysis of genome-wide CRISPR screen data enabled the identification of HNRNP family proteins that are essential to LNCaP cell growth/survival.

first: Xiao

last: Tengfei

first: Li

last: Wei


title: Malaria Host Pathogen Interaction Center Experiment 25: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi strain ceylonensis treated with artemether over 5 time points in a 61 day study.

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

summary: This project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC continues with ongoing support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC:  Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), and Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director).

sample_organism:
Macaca mulatta
Plasmodium cynomolgi ceylonensis

overall_design: Male rhesus macaques (Macaca mulatta), cleared of previous infection with  P. cynomolgi B strain via treatment with the anti-malarial drugs artemether, chloroquine, and primaquine,  approximately five years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment included, 8 pre-inoculation days, 49 experiment days, and 4 post-experiment days.  Pre- and post-experiment days were used to prepare subjects and administer post-experiment curative treatments respectively.  The anti-malarial drug artemether was subcuratively administered to subjects at the initial peak of infection, if subjects were not able to self-resolve their parasitemias.  Peak infection was determined clinically for each subject.  The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively.  Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood samples were collected at five time points for functional genomic, lipidomic, proteomic, and immunological analyses. Within the MaHPIC, this project is known as ‘Experiment 25’.  This is the third and final of a series of experiments that includes infection of malaria-naïve subjects (Experiment 23, P. cynomolgi B strain) and homologous challenge (Experiment 24, P. cynomolgi B strain) of individuals from the same cohort.  This dataset was produced by This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel, and Greg Tharp at the Emory University Yerkes Genomics Core.  To access other publicly available results from E25 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp .  This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).

first: John

last: Barnwell

first: Steve

last: Bosinger

first: Monica

last: Cabrera-Mora

first: Regina

last: Cordy

first: Jeremy

middle: D

last: DeBarry

first: Allison

last: Hankus

first: Jay

last: Humphrey

first: Jianlin

last: Jiang

first: Chester

last: Joyner

first: Nicolas

last: Lackman

first: Stacey

middle: A

last: Lapp

first: Alberto

last: Moreno

first: Mustafa

last: Nural

first: Suman

last: Pakala

first: Nirav

last: Patel

first: Hannah

middle: M

last: Stealey

first: Greg

last: Tharp


title: Regulartory effect of HNRNPL and LARP on circular RNA expression in LNCaP prostate cancer cells

first: Yiwen

last: Chen

summary: Analysis of circular RNA expression in LNCaP prostate cancer cells treated with different siRNAs to define the regulatory effect of HNRNPL and LARP on circular RNA expression.

overall_design: LNCaP prostate cancer cells were treated with the control siRNA oligos and the siRNA oligos that knockdown the expression of HNRNPL and LARP. The circular RNA expression difference upon different siRNA oligo treatment was evaluted.

first: Teng

last: Fei

first: Chen

last: Yiwen

first: Shirley

last: Liu

first: Brown

last: Myles


title: PU1 ChIP-seq in human monocytic THP-1 cells

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: ChIP-seq for PU1 (SPI1) in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

overall_design: THP-1 cells were treated for 24 h with 100 nM 1,25(OH)2D3 or vehicle before ChIP assay

first: Sabine

last: Seuter

first: Antonio

last: Neme


title: Developmental high binge ethanol exposure does not alter the transcriptome of visual cortical microglia as determined by mature mRNA RNA sequencing

city: Rochester

first: Anna

middle: Katarzyna

last: Majewska

state: NY

address: 601 Elmwood avenue box 603

department: Neuroscience

institute: University of Rochester

summary: This RNA-seq data was generated to determine the effects of developmental ethanol exposure on the microglial transcriptome in the visual cortex during adolescence.  This data reveals that there were no significant differences in expression levels for any of the genes detected, despite the reliable data quality and the fact that the most highly expressed genes detected were in fact also shown by other studies to be highly expressed by microglia.  Therefore, this data lends strong support to the conclusion that the phenotype of microglia in adolescent mouse visual cortex after developmental ethanol exposure is remarkably similar to the phenotype of comparable microglia in controls, and suggest that early ethanol exposure has limited effects on visual cortical microglia long-term.

overall_design: We examined 9 different samples of adolescent visual cortex microglia, freshly isolated from male C57BL/6 adolescent mice via fluorescence assisted cell sorting and lysed directly into RNA preserving buffer upon collection.  Mice from which the samples were obtained were either exposed to high binge levels of ethanol (n=4) or equivalent volumes of saline (n=5) daily from P4-P9 via dorsal subcutaneous injections.  Microglia were identified as the propidium iodide negative (live) CD11b positive CD45 low expressing cell population, using an identical gating strategy for all samples.

first: Elissa

middle: L

last: Wong

first: Helene

last: McMurray

first: Jason

last: Myers

first: John

last: Ashton

first: Ania


title: Transcriptomic profile of circulating naïve, TCM, TEM and TEMRA T cells in donors from Sri Lanka previously exposed to dengue virus and healthy controls from Sri Lanka [Cohort 1]

city: La Jolla

first: Mariana

last: Babor

address: 9420 Athena Cir

institute: La Jolla Institute for Allergy and Immunology

summary: Dengue virus is responsible for 400 million human infections each year . The characterization of exact molecular components of immune response associated may help design more effective therapeutic interventions. In this study, we aimed to characterize the immune signature of  T cells subtypes associated with previous exposure to dengue virus. Transcriptomic profiling using RNA sequencing was performed on naive, TCM, TEM and TEMRA CD4 T cells isolated from individuals with secondary dengue infections from Sri Lanka, an endemic area, as well as from dengue negative healthy controls.

overall_design: RNA-sequencing of sorted CD4 naïve, TCM, TEM and TEMRA T cells from cryopreserved PBMC of 9 subjects with secondary infection infection and 3 dengue virus negative healthy controls.

first: Daniela

last: Weiskopf

first: Yuan

last: Tian

first: Patrick

last: O'Rourke

first: Gregory

last: Seumois

first: Zheng

last: Fu

last: Greenbaum

first: Bjoern

last: Peters

first: Pandurangan

last: Vijayanand

first: Alessandro

last: Sette


title: Whole transcriptome sequencing data of GBSCC patients from India

city: Kolkata

first: BIDYUT

last: ROY

state: West bengal

address: 203 bt road

department: human genetics unit

country: India

institute: indian statistical institute

summary: Our study has elucidated the immunoregulatory gene expression landscape in primary tumors of Gingivo-Buccal Squamous Cell Carcinoma, as compared to their adjacent normal tissue and computationally estimated a relative composition of various immune cell classes in those tissues. A detailed portrayal of expression variation of immune evasion genes alongwith other potential therapeutic targets have been highlighted in the study.

overall_design: 12 pairs of tumor and adjacent normal from same patient have been included in the study

first: Bidyut

last: Roy


title: E. fischeriana root compound Dpo activates antiviral innate immunity

status: Public on Sep 26 2017

city: beijing

first: fuping

last: you

address: xueyuan street

institute: Peking University Health Science Center

summary: E. fischeriana has long been used as a traditional Chinese medicine.Recent studies reported that some compounds of E. fischeriana exhibited antimicrobial and immune enhance activity. Innate immune system is essential for the immune surveillance of inner and outer threats, initial host defense responses and immune modulation. The role of natural drug compounds, including E. fischeriana, in innate immune regulation is largely unknown. Here we demonstrate that E. fischeriana compound Dpo is involved in antiviral signaling. The genome wide RNA-seq analysis revealed that Dpo synergized the induction of ISGs by viral infection. Consistently, Dpo enhanced the antiviral immune responses and protected the mice from death during viral infection. Dpo however was not able to rescue STING deficient mice lethality caused by HSV-1 infection. The enhancement of ISG15 by Dpo was also impaired in STING, IRF3, IRF7 or ELF4 deficient cells, demonstrating that Dpo activates innate immune responses in a STING/IRFs/ELF4 dependent way. The STING/IRFs/ELF4 axis is therefore important for Dpo induced ISGs expression, and can be used by host to counteract infection.

overall_design: immortallized bone marrow derived macrophages were treated with medium (control) or Dpo at a concentration of 8ng/ul for 12 hours (Dpo)before harvest for RNA extraction.

first: Fuping

last: You

first: Jingxuan

last: Chen


title: Transcriptomic profile of circulating naïve, TCM, TEM and TEMRA T cells in donors from Sri Lanka previously exposed to dengue virus and healthy controls

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

overall_design: Refer to individual Series


title: Global gene expression profiling from LeuCAG3'tsRNA depleted- HeLa and HCT-116 cell lines through 50 base pair paired-end RNA-seq

city: Stanford

first: Mark

middle: M.

last: Davis

address: 279 Campus Drive

department: Department of Microbiology and Immunology

summary:
We sequenced mRNA expression from 3 HeLa and 3 HCT-116 cell lines transfected with LNA (Locked nucleic acid) GL2, LNA CAGMM, or LNA CAGPM respectively.
In order to dissect the biological role of 3?tsRNAs (type I tsRNAs) in mammals, we reduced the bioavailable abundance of specific tsRNA species using complementary locked nucleic acid/DNA-mixed antisense oligonucleotides (LNA). The LNA forms a highly stable complex with the target RNA in a sequence specific manner, essentially inhibiting its ability to interact with their biological targets.
In our tsRNA-knockdown experiments of HeLa and HCT-116 cell lines, we used three different LNA probes. GL2, is the LNA probe complementary to firefly luciferase gene from pGL2 vector (Promega, WI, USA), which serve as negative control. CAGPM, is the LNA probe perfect complementary to LeuCAG3?tsRNA. CAGMM, is the LNA probe complementary to LeuCAG3?tsRNA with 2 nt mismatches.
The sequences for LNA probes are as follows. LNA bases are upper-case letter and DNA bases are lower ?case letter.
GL2: GtaCgCgGaaTaCTtC
CAGPM: tGTcAGgAgTggGaT
CAGMM: tCTcACgAgTggGaT

overall_design: Examination of mRNA levels in individual HeLa and HCT-116 cell lines 24h after transfection of LNA GL2, LNA CAGMM, LNA CGPM respectively.

first: Hak

last: Kim

first: Yue

last: Zhang

last: Kay


title: Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.

first: Martin

last: Enge

address: James H. Clark Center, 318 Campus Drive,

department: Bioengineering

summary: As organisms age, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific age-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial age-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.

overall_design: Examination of single cells from primary human pancreas tissue

first: Efsun

last: Arda


title: Malaria Host Pathogen Interaction Center Experiment 23R: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi B strain treated with artemether over 7 time points in a 100 day study

first: Mary

last: Galinski

sample_organism:
Macaca mulatta
Plasmodium cynomolgi strain B

overall_design: Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for about 100 days, with pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. During the 100-day period subjects experienced periods of patent and sub-patent infection. The anti-malarial drug artemether was subcuratively administered to subjects after the initial peak of infection, if subjects were not able to self-resolve.  Blood-stage curative artemether was administered to all subjects following peak infection, and following a period of relapse infection.  All peaks were clinically determined for each subject.  The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively.  Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses.  E23 is an iteration of Experiment 04 with the same parasite-host combination.  E23 is the first in a series of experiments that includes subsequent homologous (Experiment 24, P. cynomolgi B strain) and heterologous (Experiment 25, P. cynomolgi strain ceylonensis) challenges of individuals from the E23 cohort.  Note that one E23 subject was not included in subsequent experiments due to persistent behavioral issues that prevented sample collection.  Within the MaHPIC, this project is known as ‘Experiment 23R’.  E23R is a 'resequencing' of all samples from E23, processed with SOPs and technology consistent with that used for E04R, E24, and E25 so that results from these experiments could be reliably compared.  Only E23R is intended for comparison with E04R, E24, and E25.  This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel, and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from E23R and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp. This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).

first: John

middle: W

last: Barnwell

first: Steven

last: Bosinger

first: Monica

last: Cabrera-Mora

first: Regina

last: Cordy

first: Jeremy

last: DeBarry

first: Allison

last: Hankus

first: Jay

last: Humphrey

first: Jianlin

last: Jiang

first: Chester

last: Joyner

first: Nicolas

last: Lackman

first: Stacey

last: Lapp

first: Alberto

last: Moreno

first: Mustafa

last: Nural

first: Suman

last: Pakala

first: Nirav

last: Patel

first: Hannah

last: Stealey

first: Greg

last: Tharp


title: High-resolution genome-wide dissection of transcriptional regulatory activity and function in human cells

city: Cambridge

first: Xinchen

last: Wang

address: 32 Vassar St, D514

institute: MIT

summary: Genome-wide profiling of epigenomic marks allows rapid prediction of transcriptional regulatory regions, including promoters and enhancers. However, experimental validation of predicted regions’ effect on gene expression, and high-resolution dissection of driver sequence elements within them, have remained infeasible on a high throughput scale. Here, we describe HiDRA (High-Definition Reporter Assay), a  high-throughput episomal assay for the high-resolution dissection of promoter and enhancer activity genome-wide. We applied HiDRA on millions of DNA fragments preferentially extracted from open chromatin. We applied HiDRA to the GM12878 lymphoblastoid cell line, generating a 6.83 million fragment library preferentially extracted from open chromatin, and revealed tens of thousands of genomic regions that significantly drive reporter gene transcription. These regions are enriched for H3K9ac, H3K27ac, other active histone marks, known regulatory motifs, and regions bound by immune regulators. We developed a new algorithm, SHARPR2, to deconvolve fragment-level activity measurements from regulatory regions tiled by dozens to hundreds of offset fragments to enable high-resolution maps of activity patterns, pinpointing individual driver regulatory motifs and predicting driver genetic variants underlying immune diseases. Our results indicate that HiDRA provides a general and scalable high-throughput and high-resolution strategy for experimental dissection of regulatory regions and nucleotides in the context of human biology and disease.

overall_design: Transfection of a transcriptional regulatory element plasmid library into GM12878 lymphoblastoid cells followed by collection and sequencing of RNA


title: Hippo reprograms the transcriptional response to Ras signalling

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

summary: Mutations that lead to hyperactivation of Ras signaling are hallmarks of carcinomas. During development, signaling via Ras mediates cell fate decisions and cellular differentiation without causing hyper-proliferation. What determines whether Ras activation leads to differentiation or proliferation remains unknown. Here we show that the Hippo pathway reprograms the cellular response to Ras signaling in Drosophila. While hyperactivation of Ras signaling alone promotes cellular differentiation, additional loss of Hippo signaling drives aggressive hyper-proliferation. Transcriptome analysis combined with ChIP-nexus confirmed that the magnitude and specificity of Ras target gene expression strongly depends on the activity status of the Hippo pathway. This is because Hippo signaling directly regulates the expression of two key downstream transcription factors of the Ras pathway: the ETS-domain transcription factor Pointed and the transcriptional repressor Capicua. Our results highlight how independent signaling pathways can impinge on each other at the level of transcription factors, thereby providing a safety mechanism to keep proliferation in check under normal developmental conditions.

overall_design:
RNA-seq on wing imaginal discs from 3rd instar Drosophila larvae with wild type control, cic or wts single mutant and cic wts double-mutant cell clones.
ChIP-Nexus-seq against Scalloped and Capicua on wing imaginal discs from 3rd instar Drosophila larvae with wild type control, wts single mutant and cic wts double-mutant cell clones.

first: F

last: Hamaratoglu

first: J

first: S

last: Aerts


title: The intestinal microbiota regulates body composition through NFIL3 and the circadian clock

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

summary: The intestinal microbiota has been identified as an environmental factor that markedly impacts energy storage and body fat accumulation, yet the underlying mechanisms remain unclear. Here we show that the microbiota regulates body composition through the circadian transcription factor NFIL3. Nfil3 transcription oscillates diurnally in intestinal epithelial cells and the amplitude of the circadian oscillation is controlled by the microbiota through type 3 innate lymphoid cells (ILC3), STAT3, and the epithelial cell circadian clock. NFIL3 controls expression of a circadian lipid metabolic program and regulates lipid absorption and export in intestinal epithelial cells. These findings provide mechanistic insight into how the intestinal microbiota regulates body composition and establish NFIL3 as an essential molecular link among the microbiota, the circadian clock, and host metabolism.

sample_organism:
Mus musculus
mouse gut metagenome

platform_organism:
Mus musculus
mouse gut metagenome

overall_design: 1. RNAseq analysis of epithelial cell transcripts in Nfil3fl/fl and Nfil3ΔIEC mice at 6 time points across a circadian cycle. Laser captured epithelial cells from 3 mice were pooled together for RNAseq at each time point. 2. 16s sequencing analysis of fecal bacterial composition in Nfil3fl/fl and Nfil3ΔIEC mice before and after switching from chow diet to high-fat diet.

first: Yuhao

first: Xiaofei

last: Yu

first: Kelly

last: Ruhn

first: Masato

last: Kubo

first: Lora

middle: V

last: Hooper


title: Transcriptomic profile of circulating naïve, TCM, TEM and TEMRA T cells in donors from Sri Lanka previously exposed to dengue virus and healthy controls from San Diego [Cohort 2 & Cohort 3]

first: Mariana

last: Babor

overall_design: RNA-sequencing of sorted CD4 naïve, TCM, TEM and TEMRA T cells from cryopreserved PBMC of 5 subjects with secondary infection infection and 6 dengue virus negative healthy controls.

first: Daniela

last: Weiskopf

first: Yuan

last: Tian

first: Patrick

last: O'Rourke

first: Gregory

last: Seumois

last: Fu

first: Jason

last: Greenbaum

first: Bjoern

last: Peters

first: Pandurangan

last: Vijayanand

first: Alessandro

last: Sette


title: Widespread activation of antisense transcription of the host genome during Herpes simplex virus 1 infection

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

summary: We show that Herpes simplex virus 1 (HSV-1) induces the expression of about 1000 antisense transcripts from the human host cell genome.

overall_design: Human WI-38 and HeLa cells were infected with Herpes simplex virus 1, and antisense transcripts on the host cell genome defined using a custom algorithm.

first: Jennifer

last: Menegatti

first: Vedran

last: Franke

first: Christine

last: Kocks

first: Anastasiya

last: Boltengagen

first: Kathrin

last: Theil

first: Thomas

last: Hennig

first: Carmelo

last: Ferrai

first: Andrzej

last: Rutkowski

first: Laura

last: Baer

first: Lisa

last: Kermas

first: Caroline

last: Friedel

first: Nikolaus

last: Rajewsky

first: Altuna

last: Akalin

first: Lars

last: Dölken

first: Friedrich

last: Grässer

first: Markus

last: Landthaler


title: Malaria Host Pathogen Interaction Center Experiment 24: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi B strain treated with artemether over 3 time points in a 46 day study.

first: Mary

last: Galinski

platform_organism:
Macaca mulatta
Plasmodium cynomolgi strain B

overall_design: Male rhesus macaques (Macaca mulatta), cleared of previous infection with  P. cynomolgi B strain via treatment with the anti-malarial drugs artemether, chloroquine, and primaquine,  approximately five years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, and metabolomic measurements. The experiment included, 1 pre-inoculation day, 35 experiment days, and 10 post-experiment days.  Pre- and post-experiment days were used to prepare subjects and administer post-experiment curative treatments respectively.  The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively.  Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood samples were collected at three time points for functional genomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as ‘Experiment 24’.  This is the second in a series of experiments that includes infection of malaria-naïve subjects (Experiment 23, P. cynomolgi B strain) and heterologous challenge (Experiment 25, P. cynomolgi strain ceylonensis) for the individuals from the same cohort.  This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel, and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from E24 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp .  This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).

first: John

last: Barnwell

first: Steve

middle: E

last: Bosinger

first: Monica

last: Cabrera-Mora

first: Regina

last: Cordy

first: Jeremy

last: DeBarry

first: Allison

last: Hankus

first: Jay

last: Humphrey

first: Jianlin

last: Jiang

first: Chester

last: Joyner

first: Nicolas

last: Lackman

first: Stacey

last: Lapp

first: Alberto

last: Moreno

first: Mustafa

last: Nural

first: Suman

last: Pakala

first: Nirav

last: Patel

first: Hannah

last: Stealey

first: Greg

last: Tharp


title: Actively translating transcriptome (Ribotag) profiling of mouse retinal endothelial cells during postnatal development

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: Angiogenesis, a process mediating the expansion of vascular beds in many physiological and pathological settings, requires dynamic changes in endothelial cell (EC) behavior. The molecular mechanisms governing EC activity during different phases of vascular growth, remodeling, maturation, and quiescence remain elusive. Here, we have employed actively translating transcriptome analysis of mouse retinal ECs for the characterization of dynamic gene expression changes during postnatal development and the identification of critical angiogenic factors. In silico computational analyses of these data enabled the identification of candidate regulators controlling EC behavior at different developmental checkpoints. The detailed characterization of Mafb, one of the identified candidates, established that this transcription factor controls endothelial sprouting in vitro and in vivo. Integrative analysis of RNA-Seq and ChIP-Seq data defined putative direct Mafb targets, which are repressed or activated by the transcriptional regulator. Together, our results identify novel cell-autonomous regulatory mechanisms controlling sprouting angiogenesis.

overall_design: 2 retinas from a mouse were used for single library / 3 biological replicates (individual mouse) per sample / 5 developmental stages of P6, P10, P15, P21 and P50 / EC-specific Mafb conditional KO

first: Ralf

last: Adams


title: Comparative Transcriptomic Profiling of Antimicrobial Resistant and Virulent   Escherichia coli of Poultry Origin

city: Guangzhou

first: Ganlin

last: Xu

address: CB

institute: shbiochip

summary: To characterize the differentially expressed genes between pathogenic avian E. coli and human E. coli ATCC 25922, Abstract   Escherichia coli (E. coli) is a harmless common bacterium of poultry intestine, but with a wide range of genomic flexibility, is also causative agent of many poultry diseases collectively called colibacillosis that is blamed for high economic loss in poultry sector worldwide. Numerous studies have been conducted to check the prevalence of pathogenic E. coli in poultry and poultry products, however limited data are available regarding their resistance and virulence associated genes expression profile. This study examined the pathogenomic content of poultry E. coli by antibiotic susceptibility, biofilm formation and adhesion, invasion and intracellular survivability assays in Caco-2 and Raw 264.7 cell lines along with the determination of median lethal dose in two-day old chickens. A clinical pathogenic multidrug resistant (MDR) isolate, E. coli 381, isolated from broilers was found to be highly virulent in cell culture and in chicken model. Transcriptome analysis has been skewed towards bacterial pathogens because of the prioritization of poultry diseases. Comparative gene expression profile of MDR E. coli 381 and the reference human strain E. coli ATCC 25922 was done using Illumina HiSeq2500 transcriptome  and results were verified by RT-qPCR analyses. A number of resistant encoding genes including multidrug transporters, multidrug resistance proteins, porins and autotransporters were identified. We also noticed overexpression of very important virulent genes (fimA, fimC, fimH and fimI) encoding the type-1 fimbrial proteins, curli fimbriae genes , invasin genes, toxin-encoding genes and biofilm forming regulatory genes . In addition, many types of stress  and metal homeostasis controlling genes were among up-regulated genes in E. coli 381 as compared to reference strain. GO and KEGG pathway analysis results revealed that genes controlling secondary metabolism, drug transport, adhesion and invasion proteins, and mobile genetic elements were over-expressed in E. coli 381. Several genes involved in cellular and metabolic processes such as carbohydrate metabolism were responsible for stress tolerance. Seminal description of the transcriptomic results and other unique features of E. coli 381 confirmed that it is highly virulent and MDR strain of poultry origin. This comparative study provides new avenues for further work on molecular mechanisms to prevent resistance development in bacteria and to ensure public health.

overall_design: We isolated E. coli from broilers having collibacillosis, RNA were extracted from poultry isolate and E. coli ATCC 25922 a reference strain, RNA-Sequencing was done for both strains and virulent and resistance DEGs characters were discussed.   Each sample had 2 biological replicates.

first: Hafiz

last: Hussain

first: Zahid

last: Iqbal

first: Mohamed

middle: N

last: Saleem

first: Adeel

last: Sattar

first: Haihong

last: Hao

first: Zonghui

last: Yuan


title: Interpreting reverse transcriptase termination and mutation events for greater insight into the chemical probing of RNA

city: West Haven

first: Matthew

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

summary: Chemical probing has the power to provide insight into RNA conformation in vivo and in vitro, but interpreting the results depends on methods to detect the chemically modified nucleotides. Traditionally, the presence of modified bases was inferred from their ability to halt reverse transcriptase during primer extension and the locations of termination sites observed by electrophoresis or sequencing. More recently, modification-induced mutations have been used as a readout for chemical probing data. Given variable propensity for mismatch incorporation and read-through with different reverse transcriptases, we examined how termination and mutation events compare to each other in the same chemical probing experiments. We found that mutations and terminations induced by dimethyl sulfate probing are both specific for methylated bases, but these two measures have surprisingly little correlation and represent largely non-overlapping indicators of chemical modification data. We also show that specific biases for modified bases depend partly on local sequence context, and that different reverse transcriptases show different biases toward reading a modification as a stop or a mutation. These results support approaches that incorporate analysis of both termination and mutation events into RNA probing experiments.

overall_design:
Chemical probing using dimethylsulfate reactivity with structured RNAs Xist and 18S in mouse, with analysis of modification induced reverse transcriptase mutations or stops.

This series contains only 18S samples.

first: Alec

last: Sexton

first: Peter

middle: Y

last: Wang


title: Rescue of Tet2 KO ES cells in primed or naïve state

status: Public on Sep 25 2017

city: London

first: Miguel

last: Branco

address: 4 Newark Street

institute: Blizard Institute

summary: Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential for ERV repression in embryonic stem cells (ESCs), with DNA methylation also playing an important role. It has been suggested that SETDB1 protects ERVs from TET-dependent DNA demethylation, but the relevance of this mechanism for ERV expression remains unclear. Moreover, previous studies have been performed in primed ESCs, which are not epigenetically or transcriptionally representative of preimplantation embryos. We used naïve ESCs to investigate the role of SETDB1 in ERV regulation and, in particular, its relationship with TET-mediated DNA demethylation. Naïve ESCs show an increased dependency on SETDB1 for ERV silencing when compared to primed ESCs, including at the highly mutagenic intracisternal A particles (IAPs). We found that, in the absence of SETDB1, TET2 activates IAP elements in a catalytic-dependent manner. Surprisingly, however, TET2 does not drive changes in DNA methylation levels at IAPs, suggesting that it regulates these transposons indirectly.

overall_design: Stable cell lines were established from Tet2 KO embryonic stem cells using PiggyBac vectors containing either wildtype TET2 or a catalytic mutant (H1304Y, D1306A). SETDB1 was depleted in cells cultured under primed or naïve conditions by shRNA. RNA was extracted to generate mRNA-seq libraries (3 replicates of each sample).

first: Ozgen

last: Deniz

first: Lorenzo

last: de la Rica

first: Kevin

last: Cheng

first: Dominik

last: Spensbeger


title: SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells


title: Rapid chromatin switch in the direct reprogramming of fibroblasts to neurons

city: Singapore

first: Qian Yi

last: Lee

address: Biopolis Drive

department: R&D

country: Singapore

institute: Nuevocor

summary: How transcription factors (TFs) reprogram one cell lineage to another remains unclear. Here, we define chromatin accessibility changes induced by the proneural TF Ascl1 throughout conversion of fibroblasts into induced neuronal (iN) cells. Thousands of genomic loci are affected as early as 12 hours after Ascl1 induction. Surprisingly, over 80% of the accessibility changes occur between days 2 and 5 of the 3-week reprogramming process. This chromatin switch coincides with robust activation of endogenous neuronal TFs and nucleosome phasing of neuronal promoters and enhancers. Subsequent morphological and functional maturation of iN cells are accomplished with relatively little chromatin reconfiguration. Integrating chromatin accessibility and transcriptome changes, we built a network model of dynamic TF regulation during iN cell reprogramming, and identified Zfp238, Sox8 and Dlx3 as key TFs downstream of Ascl1. These results reveal a singular, coordinated epigenomic switch during direct reprogramming, in contrast to step-wise cell fate transitions in development.

overall_design: Examination of changes of the chromatin accessibility landscape during Ascl1-mediated reprogramming of mouse embryonic fibroblasts (MEFs) into neurons, at distinct timepoints during the reprogramming process. Chromatin changes were correlated with previously published RNA-seq data for control rtTA 48hr and Ascl1 48hr (GSE43916: GSM1074345-8), and newly generated RNA-seq data for Ascl1 7d.

first: Orly

last: Wapinski

first: Qian

first: Albert

middle: C

last: Chen

first: Marius

last: Wernig

first: Howard

last: Chang


title: SETDB1 depletion in primed or naïve ES cells

middle: R

overall_design: SETDB1 was depleted in primed or naïve embryonic stem cells by shRNA, using a non-targeting sequence (shScr) as a control. RNA was extracted to generate rRNA-depleted RNA-seq libraries (3 replicates of each sample).


title: RNA-seq and small RNA-seq analysis of BORIS/CTCFL knockdown in K562 cell line

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH


title: SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters [RNA-Seq]

city: Boston

first: Cigall

last: Kadoch

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: BAF complex perturbations contribute to over 20% of human cancer, yet the mechanisms by which these alterations drive oncogenesis remain poorly understood. The driving role for BAF complex mutations in cancer was first documented in malignant rhabdoid tumor (MRT), an aggressive pediatric cancer in which loss of SMARCB1 (also known as BAF47, INI1, hSNF5), a core BAF complex subunit, is the hallmark genetic alteration. We find that loss of BAF47 destabilizes the biochemical affinity of BAF complexes on chromatin without significantly impairing complex integrity or subunit composition. Rescue of BAF47 in BAF47-deficient sarcoma cell lines results in global increases in BAF complex occupancy, which mediates a major gain in enhancer activation. In addition, we find BAF47 targets BAF complexes to bivalent promoters, resolving bivalency to activation through opposition of polycomb-mediated repression. These findings demonstrate collaborative gene activation by the BAF complex through distinct mechanisms, highlighting specific BAF complex functions that are coopted or abated to drive human cancers and developmental disorders.

overall_design: Malignant rhabdoid tumor cell lines (G401 and TTC1240) were lentivirally infected with either an empty vector control or a constitutive vector expressing BAF47, selected for 48 hours with blasticidin, then grown for 5 days, at which point RNA was harvested in biological duplicate for sequencing.

first: John

last: Pulice


title: SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters [Hi-C]

overall_design: VA-ES-BJ epithelioid sarcoma cell lines were lentivirally infected with either an empty vector control or a constitutive vector expressing BAF47, selected for 48 hours with blasticidin, then grown for 5 days, at which point cells were harvested for chromatin capture followed by sequencing (Hi-C).


title: Network of nutrient sensing pathways and a conserved kinase cascade integrates osmolarity and carbon sensing in Neurospora crassa

city: Ithaca

first: Lori

last: Huberman

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

summary: Identifying nutrients available in the environment and utilizing them in the most efficient manner is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of carbohydrates, from simple sugars to the complex carbohydrates found in plant cell walls. The zinc binuclear cluster transcription factor CLR-1 is necessary for utilization of cellulose, a major, recalcitrant component of the plant cell wall; however, expression of clr-1 in the absence of an inducer is not sufficient to induce cellulase gene expression. We performed a screen for unidentified actors in the cellulose-response pathway and identified a gene encoding a hypothetical protein (clr-3) that is required for repression of CLR-1 activity in the absence of an inducer. Using clr-3 mutants, we implicated the hyperosmotic-response pathway in the tunable regulation of glycosyl hydrolase production in response to changes in osmolarity. The role of the hyperosmotic-response pathway in nutrient sensing may indicate that cells use osmolarity as a proxy for the presence of free sugar in their environment. These signaling pathways form a nutrient-sensing network that allows N. crassa cells to tightly regulate gene expression in response to environmental conditions.

overall_design: mRNA profiles of wild type and mutant N. crassa cells exposed to carbon starvation and cellulose. There are 14 different strains and conditions each done in biological triplicate, which includes wild type controls for a total of 42 samples.

first: Samuel

middle: T

last: Coradetti

first: N

last: Glass


title: Neural precursor cell-secreted TGF-β2 subverts the inflammatory program of invading monocyte-derived dendritic cells during CNS autoimmunity

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

summary: In Multiple Sclerosis, the pathological interaction of autoreactive helper T (TH) cells with mononuclear phagocytes in the central nervous system (CNS) drives initiation and maintenance of chronic neuroinflammation. Herein, we found that intrathecal transplantation of neural stem cells (NPCs) in mice with experimental autoimmune encephalomyelitis (EAE) impairs the accumulation of inflammatory monocyte-derived dendritic cells (moDCs) in the CNS leading to improved clinical outcome. NPCs treatment reduced in the CNS IL-23, IL-1 and TNF-α, cytokines required for terminal differentiation of TH cells and accordingly GM-CSF-producing pathogenic TH cells. In vivo and in vitro transcriptome analyses disclosed that NPC secreted factors induce an inhibition of DC differentiation and maturation, favoring a fate switch towards an anti-inflammatory phenotype. We identified TGF-β2 as the crucial mediator of NPC immunomodulation: TGFβ2 knockout NPCs transplanted in EAE are ineffective in impairing moDC accumulation within the CNS and fail to drive clinical improvement.  This study provides evidence that intrathecally injected NPCs interfere with CNS-compartmentalized inflammation of the effector phase of EAE, reprogramming, through the secretion of TGF-β2, inflammatory monocyte-derived DCs towards anti-inflammatory myeloid cells.

overall_design: mRNA profiles of monocyte derived-dendritic cells (moDCs) isolated by FACS sorting at 7 days post-treatment from the CNS (hindbrain and spinal cord) of quadruplicate pool of 4–7 MOG35-55-immunized C57Bl/6 mice either intrathecally injected with PBS or 1 million neural precursor cells (NPCs) at the peak of the disease (2-4 days after clinical onset).

first: Donatella

last: De Feo

first: Melanie

last: Greter

first: Linda

last: Ottoboni


title: Loss of imprinting mutations define both distinct and overlapping roles for misexpression of IGF2 and H19 lncRNA

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

summary: Imprinted genes occur in discrete clusters that are coordinately regulated by shared DNA elements. H19 and Igf2 are linked imprinted genes that play critical roles in development. Loss of imprinting at the IGF2/H19 locus is associated with Beckwith Wiedemann Syndrome (BWS). Here we use comprehensive genetic and genomic analyses to follow muscle development in a mouse model of BWS to dissect the separate and shared roles for Igf2 and H19 in the disease phenotype. We show that LOI results in defects in muscle differentiation and hypertrophy and we identify primary downstream targets of Igf2 (MAPK signaling) and of H19 (AKT/mTOR signaling). Moreover, we demonstrate instances where H19 and Igf2 misexpression work separately, cooperatively, and also antagonistically to establish the disease phenotype. This study underscores the fact that LOI phenotypes are multigenic and complex interactions contribute to disease outcomes.

overall_design: Total of 13 samples analyzed; RNA-Seq samples from 2 genotypes: wild type and dICR/dICR, 2 cell types: myoblasts and myotubes, 2-3 replicates each.

first: Ki

middle: S

last: Park

first: Kweekwang

last: Kim

first: Karl

last: Pfeifer


title: Comparative transcriptomics of Steinernema and Caenorhabditis single embryos reveals gene expression divergence during early embryogenesis

city: Minneapolis

first: Marissa

last: Macchietto

address: 117 Pleasant Street SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Minneapolis

summary: Abstract: Cells express distinct sets of genes in a precise spatio-temporal manner during embryonic development. There is a wealth of information about embryonic development in C. elegans, but much less is known about embryonic development at the molecular level in nematodes from other taxa. We are interested in insect pathogenic nematodes from the genus Steinernema as models of parasitism and symbiosis as well as a satellite model for evolution in comparison to C. elegans. We sequenced the transcriptomes of single embryos of two Steinernema species and two Caenorhabditis species at eleven specific stages during embryonic development for comparative analysis. We found that zygotic transcription initiates at different developmental stages in each species, with the Steinernema species initiating transcription at earlier developmental stages than Caenorhabditis. We found that ortholog expression conservation during development is highest at the later embryonic stages than at the earlier ones. Moreover, we found that the components of the neddylation pathway are highly upregulated during Steinernema early embryonic development contributing further to these early differences seen between the genera at the post-translational level. The surprisingly higher conservation of orthologous gene expression in later embryonic stages strongly suggests a funnel-shaped model of developmental gene expression divergence in nematodes. This work provides novel insight into embryonic development across distantly related nematode species and demonstrates that the mechanisms controlling early development are more diverse than previously thought at both the transcriptional and post-translational level.

sample_organism:
Caenorhabditis elegans
Steinernema carpocapsae
Steinernema feltiae
Caenorhabditis angaria

overall_design: We sequenced the transcriptomes of single embryos of two Steinernema species and two Caenorhabditis species during embryonic development at eleven specific stages (zygote, 2-cell, 4-cell, 8-cell, 24-44-cell, 64-78-cell, comma, 1.5-fold, 2-fold, moving, and L1) for comparative analysis.

first: Dristi

last: Angdembey

first: Negar

last: Heidapour

first: Lorrayne

last: Serra

first: Bryan

last: Rodriguez

first: Nicole

last: El-Ali

first: Ali

last: Mortazavi


title: Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenografts

city: Waltham

first: ZiYang

last: Yu

state: MA

address: 950 Winter Street

institute: Radius Health

summary: These data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression.

overall_design: HBCx-22 PDX were treated with RAD140 or vehicle and snap frozen tumor samples were subjected to RNA-seq analysis at the end of the study

first: Dannie

last: Wang

first: Suqin

last: He

first: Ziyang


title: Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis

first: Chen

last: Chen

address: 723 Xinke Rd.

institute: South China Botanical Garden, Chinese Academy of Science

summary: Acetyl-Coenzyme A (acetyl-CoA) is a central metabolite and the acetyl source for protein acetylation, particularly histone acetylation that promotes gene expression. However, the effect of acetyl-CoA levels on histone acetylation status in plants remains unknown. Here, we show that malfunctioned cytosolic acetyl-CoA carboxylase1 (ACC1) in Arabidopsis leads to elevated levels of acetyl-CoA and promotes histone hyperacetylation predominantly at lysine 27 of histone H3 (H3K27). The increase of H3K27 acetylation (H3K27ac) is dependent on ATP-citrate lyase which cleaves citrate to acetyl-CoA in the cytoplasm, and requires histone acetyltransferase GCN5. A comprehensive analysis of the transcriptome and metabolome in combination with the genome-wide H3K27ac profiles of acc1 mutants, demonstrate the dynamic changes of H3K27ac, gene transcripts and metabolites occurring in the cell by the increased levels of acetyl-CoA. This study suggests that H3K27ac is an important link between cytosolic acetyl-CoA level and gene expression in response to the dynamic metabolic environments in plants.

overall_design: Examination of 9 different histone modifications in WT and acc1-5 seedlings and of H3K27 acetylation in acla-1i acc1-5 before and after treating with β-estrodial.

first: Chenlong

last: Li

first: Ying

first: Justin

last: Renaud

first: Gang

last: Tian

first: Shrikaar

last: Kambhampati

first: Behnaz

last: Saatian

first: Vi

last: Nguyen

first: Abdelali

last: Hannoufa

first: Frederic

last: Marsolais

first: Ze-Chun

last: Yuan

first: Kangfu

first: Ryan

last: Austin

first: Jun

last: Liu

first: Susanne

last: Kohalmi

first: Keqiang

last: Wu

first: Shangzhi

last: Huang

first: Yuhai

last: Cui


title: RNA-seq analysis of BORIS/CTCFL knockdown in K562 cell line

first: Alexander

last: Strunnikov

summary:
The study involved transcriptome analysis using RNA-seq knockdown of BORIS/CTCFL gene expression in K652 cancer cell line using inducible shRNA.
The K562 cell line is the only cancer cell line that is known to be dependent on BORIS for proliferation and self-renewal of stemness.
The goal of the study was to investigate the early/immediate transcriptional response to BORIS downregulation (over 10-fold reduction in protein level) using an inducible shRNA.

overall_design: The K562 cells were stably infected with pLKO-Tet-On-neo vector (empty vector, EV, 3 control replicates) or with the same vector expressing anti-BORIS shRNA (knockdown, KD, 4 independent replicates).

first: Evgeny

last: Teplyakov

first: Qiongfang

first: Jian

first: AbdelHalim

last: Boukaba


title: A novel Drosophila injury model reveals severed axons are cleared through a Draper/MMP-1 signaling cascade

city: Portland

first: Sean

middle: David

last: Speese

state: Oregon

address: 3181 SW Sam Jackson Road

department: Neurology

institute: OHSU-Jungers Center for Neurosciences Research

summary: The goal of this project was to assess differential gene expression in the Ventral Nerve Cord (VNC) of adult Drosophila 5 hours after severing of the legs, wings and head.

overall_design: Gene expression was assessed in 2 conditions (No Injury and 5-hrs after Injury) in the w1118 strain of Drosophila melanogaster.  5 independent biological replicates were used for each condition. RNA was isolated from the adult Ventral Nerve Cord (VNC) for the gene expression analysis (RNAseq).

middle: D

first: Mary

last: Logan


title: Small RNA (sRNA) RNA-seq analysis of BORIS/CTCFL knockdown in K562 cell line

summary:
The study involved transcriptome analysis using RNA-seq knockdown of BORIS/CTCFL gene expression in K652 cancer cell line using inducible shRNA.
The K562 cell line is the only cancer cell line that is known to be dependent on BORIS for proliferation and self-renewal of stemness.
The goal of the study was to investigate the early/immediate small RNA transcriptional response to BORIS downregulation (over 10-fold reduction in protein level) using an inducible shRNA.

overall_design: The K562 cells were stably infected with pLKO-Tet-On-neo vector (empty vector, EV, 2 control replicates) or with the same vector expressing anti-BORIS shRNA (knockdown, KD, 4 independent replicates).


title: Transcriptome analysis of calcium-regulated genes in relation to broccoli hypocotyl cell expansion

city: beltsville

first: Tianbao

last: Yang

address: 10300 BALTIMORE AVENUE

department: BARC

institute: USDA-ARS

summary: We report the application of RNA-seq to uncover the underlying mechanism of 10 mM calcium chloride spray on broccoli seedlings (Brassica oleracea var. italic) boosted the hypocotyl elongation and delayed the senescence.

overall_design: Examination of Ca2+ and water spray broccoli microgreens

first: Lingfei

last: Shangguan


title: Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone [H3K27Ac ChIP-Seq]

status: Public on Sep 24 2017

city: Rehovot

first: Yehoshua

last: Enuka

address: Herzl 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

summary: Growth factors (GFs) suppression by steroid hormones  recurs in embryology and is co-opted in pathology. While studying mammary cell migration, which is stimulated by GFs and antagonized by glucocorticoids (GCs), we found that GCs inhibit positive feedback loops activated by GFs and stimulate the reciprocal negative loops. Although no alterations in DNA methylation accompany the transcriptional events instigated by either stimulus, forced demethylation of distal regions broadened the repertoire of inducible genes. Our data indicate that the crosstalk involve transcription factors like p53 and NF-kB, along with reduced pausing (and traveling) of RNA polymerase II (RNAPII) at the promoters (and bodies) of GF-inducible genes. In addition, while GFs hyper-acetylated chromatin at unmethylated promoters and enhancers of genes involved in motility, GCs hypo-acetylated the corresponding regions. In conclusion, stably unmethylated genomic regions that encode feedback regulatory modules and differentially recruit RNAPII and acetylases/deacetylases underlie suppression of growth factor signaling by glucocorticoids.

overall_design: H3K27Ac ChIP-Seq – time course of EGF, DEX or EGF + DEX treatment


title: Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone [IMR90_MCF7_RNA-Seq]

overall_design: RNA-Seq – EGF or dexamethasone (DEX) treatemnt for 60 min of MCf7 and IMR90 cells


title: Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone [HCT RNA-Seq]

overall_design: RNA-Seq – EGF treatemnt for 60 min of WT and DNMT1a and DNMT3b double-knockout HCT116 cells


title: Thrombospondin1 replacement prevents cerebral cavernos malformations

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: California/San Diego

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

summary: We have purified primary brain microvascular endothelial cells (BMEC) from mice bearing floxed alleles of Krit1 (Krit1fl/fl) and an endothelial specific tamoxifen-regulated Cre recombinase (Pdgfb-iCreERT2), and used these to delete Krit1 in a time-controlled manner (Krit1ECKO). To elucidate the pathogenesis of cerebral cavernous malformations (CCM) we used genome-wide RNA sequencing (RNA-seq) to characterize the transcriptome of primary BMEC following acute genetic inactivation of Krit1.

overall_design: Treatment of Krit1f/f-Pdgfb-iCreERT2  BMEC with 5 µM-hydroxy-tamoxifen deleted Krit1 (Krit1ECKO) reduced KRIT1 mRNA and protein by >90% within 5 days compared to hydroxy-tamoxifen-treated Krit1fl/fl controls. Three independent biological replicates were used for the analysis.

middle: A

first: Gregory

last: Fonseca

first: Mark

middle: H

last: Ginsberg


title: Next-Generation Sequencing Supports Quantitative Analysis of Wild Type and Runx2+/- Calvarial Transcriptomes With or Without Administration of MS-275

city: Seoul

first: Han-sol

last: Bae

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Molecular Genetics

country: South Korea

institute: School of Dentistry, Seoul National University

summary: Because insufficiency of the Runt-related transcription factor 2 (Runx2) limits skeletal growth, there is a great deal of effort to activate Runx2 for clinical use. In this study, we found that MS-275, the class I-specific HDAC inhibitor, activates Runx2 both transcriptionally and translationally. Therefore, we performed NGS analysis to gain accurate patterns of gene expression in mouse calvaria tissue through MS-275 administration. As a result, we could get insight that treatment of MS-275 increases genes related with osteoblast differentiation and cell proliferation, and decreases genes in field of causing apoptosis.

overall_design: Mice calvarial mRNA profiles of embryonic day 17.5 wild type (WT) and Runx2+/- mice were generated by deep sequencing using Illumina NextSeq 500. Mice were administered MS-275 or vehicle. Three replicates per group.

first: Hyun-mo

last: Ryoo


title: Transcriptome profiling of ER+ breast cancer primary tumor and its tumorsphere derivative

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

institute: Genome Institute of Singapore

summary: We profiled RNA expression in the ER+ primary tumor and the matching tumorspheres. The objective was to find genes differentially expressed between the tumorspheres and bulk tumor.

overall_design: 12 pairs of matching ER+ bulk tumor and its tumorspheres

first: Min

last: Feng

last: Oguz

first: Jian Yuan

last: Goh


title: mRNA-Seq of the CA1 hippocampal subregion from 3 month old animals injected with JQ1 (50mg/kg) i.p. and mRNA-Seq of CA1 of 8-10 month old APP/PS1-21 transgenic animals injected with JQ1 (50mg/kg) i.p.

city: Goettingen

first: Eva

last: Benito Garagorri

state: Niedersachsen

address: Von Siebold Strasse 3A

department: Epigenetics of Aging

institute: DZNE Goettingen

summary: Histone acetylation is essential for memory formation and provides a drug target to treat dementia. The histone acetylation landscape is shaped by chromatin writer and eraser proteins. In contrast, little is known about the neural activity of chromatin readers that link chromatin state to cellular function. Here, we tested the effect of JQ1 – a small molecule inhibitor of the chromatin readers BRD2, BRD3, BRD4 and BRDT – on associative and spatial memory tasks and on synaptic plasticity and found that it is able to enhance cognitive performance and long-term potentiation in wildtype animals and in a mouse model for amyloid deposition. JQ1 elicited a hippocampal gene expression program associated with ion channel activity, transcription and DNA repair. Our findings suggest that JQ1 could be used as a therapy against dementia and should be further tested in the context of learning and memory.

overall_design: mRNA profile from the CA1 hippocampal subregion from adult (3 month old) WT and aged (8-10 month old) APP/PS1-21 animals treated with 50mg/kg JQ1 i.p. for 10-13 days

last: Benito-Garagorri

first: Andre

last: Fischer


title: RNAseq data on HDAC Class IIa inhibitor (CHDI-00390576) dosed R6/2 mice.

status: Public on Sep 23 2017

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: R6/2 and WT mice treated orally twice a day with vehicle (10% HPβCD), and R6/2 mice treated with either 30 or 100 mg/kg orally twice a day  CHDI-00390576. CHDI-00390576 is a Class IIa HDAC inhibitor.  Mice were dosed from 4 - 12 weeks of age.

overall_design: Tibialis, striatum, cortex, heart and liver collected N = 8 per group (4M/4F).

first: Jim

last: Rosinski


title: Genome-wide Transcriptome Analysis of Hippocampus, Frontal cortex and Pituitary gland in Rats Elucidated the Pathogenisis  of  Depressive Disorder Induced by Chronic Restraint

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary:
Objective: To elucidate the potential effects of stressful factors for depression on the hippocampal, frontal cortex and pituitary gland genome-wide transcriptomes at the molecular level, we evaluated the transcriptomic profiles of depression rats under chronic restraint stress (CRS).
Methods: Forty-eight rats were randomly divided into control, model, fluoxetine and acupuncture groups. Experimental period was 28 days. Open-field test, Sucrose preference and body weight were investigated respectively at the experiment before and after the experiment. The experiment having been finished, solexa sequencing technology (Illumina Nextseq 500/151nt) was applied to investigate and verify the altered hippocampal, frontal cortex and pituitary gland  genome-wide transcriptome analysis in rats of all groups.
Results: Based on the data from RNA-seq analysis, it revealed that compared the expression of genes in the control group with model group in the respective of three brain tissues, 101, 134, 148 differential expression genes were found in the hippocampus, frontal cortex and pituitary gland, respectively; compared the expression of genes in the fluoxetine group with model group in the respective of three brain tissues, 41, 46, 87 differential expression genes were found in the hippocampus, frontal cortex and pituitary gland, respectively; compared the expression of genes in the acupuncture group with model group in the respective of three brain tissues, 107, 89, 179 differential expression genes were found in the hippocampus, frontal cortex and pituitary gland, respectively. Furthermore, we used the GO (Gene ontology) analysis and KEGG (Kyo-To conservation of Genes and Genomes) pathway analysis for these differentially expressed genes. We found that the results of these two analyses were consistent, both mainly related to monoamine neurotransmitters, inflammation and immune response in control group VS model group. It is noted that this phenomenon also appears in fluoxetine group compared  with model group, acupuncture group VS model group. Importantly, the antidepressant effect of acupuncture was more extensive, which was more consistent with the pathogenesis of depression induced by CRS in rats.
Conclusions: Our study represents the first detailed analysis of the hippocampal, frontal cortex and pituitary gland  genome-wide transcriptomes in depression rats under CRS by RNA-seq technology. The results of this study revealed multiple DEGs and possible mechanisms specifying the function of hippocampal, frontal cortex and pituitary gland in depression rats induced by CRS. These results provide a basis for further investigation of the signaling mechanisms that affect central nervous system output related to stress-sensitive depressive disorder development.

overall_design: Forty-eight rats were randomly divided into control, model, fluoxetine and acupuncture groups. The rat model of depression was established by subjecting to chronic restraint stress (6h/day) for 28 days. Rats in acupuncture group were acupunctured at GV20 (Baihui) and GV29 (Yintang) one hour before the CRS procedures every day. Rats in fluoxetine group were administered with fluoxetine (10mg/kg) by gavage one hour before the CRS procedures every day. Open-field test, Sucrose preference and body weight were investigated respectively at the experiment before and after the experiment. The experiment having been finished, the hippocampal, frontal cortex and pituitary gland were harvested, and their RNA profiles were generated by deep sequencing, in triplicate, using  Illumina Nextseq 500/151nt.

first: Tuya

last: Bao

first: Yu

last: Wang

first: Huili

last: Jiang


title: Decreased Fgf8 gene dosage on gene expression

city: Calgary

first: Benedikt

last: Hallgrimsson

state: AB

address: 3330 Hospital Dr NW

department: Cell Bio and Anatomy

institute: University of Calgary

summary: Robustness to perturbation, or canalization, is a fundamental and required feature of complex organisms.1 Mutations are the raw material for evolution, but robustness to their effects is required for organisms to tolerate mutational loads.1  Similarly, robustness to environmental perturbations, or limiting environmental responses to an adaptive range, is necessary for organisms to tolerate environmental variation. Robustness is heritable2-4, but the mechanisms that produce it are poorly understood. Explanations range from the role of specific processes such as heat shock proteins to more general embedded features of developmental systems. Nonlinearities are an embedded, ubiquitous feature of development that may modulate how variation in development relates to phenotypic robustness.5,6 Here, we show that variation in Fibroblast Growth Factor 8 (Fgf8) expression across an allelic series has a nonlinear relationship to phenotypic variation, predicting the magnitude of variation within genotypes. These differences in phenotypic variance are independent of genetic variance and so reflect differential robustness to minor environmental variation. Differences in robustness are not related to differences in the variance of gene expression within genotypes. However, mean gene expression levels do vary across genotypes, particularly in genes downstream to FGF8 signaling. Gene expression changes thus explain the genotype-phenotype curve but not the changes in robustness along the curve. This suggests that mechanisms above the gene-regulatory network are important determinants of robustness. Our results show that nonlinearities in developmental mechanisms can persist from genotype to phenotype to produce variation in robustness between genotypes.  This suggests that embedded features of development rather than specific canalizing mechanisms explain robustness.  How such features vary among individuals in natural populations and relate to genetic variation more generally are key questions for unravelling the origin and evolvability of this fundamental feature of organismal development.

overall_design:
Mouse breeding and embryo generation:
The Fgf8 neo series is a 5 member series generated from a combination of the neomycin insertion into the intron between exon  2 and 3 of the Fgf8 locus and a null allele generated from loss of exon 2.  Fgf8 mice were generated from the Fgf8 flp/ floxed allele originally developed by (Meyers et al., 1998). The neo cassette was maintained in the Fgf8Neo mice.  Deletion constructs were developed by crossing with β-actin cre (FVB/N-Tg(ACTB-cre)2Mrt/J), to delete exons 2 and 3 from all cells.

To generate the neo series, crosses were performed between mice that were heterozygous for and mice that were homozygous for the Neo (flp) allele. Genotyping was performed as in (Meyers et al., 1998).

For embryos, pregnant dams were sacrificed at embryonic day (E) 10.5 based on visualization of a post-coital plug at E0.5. E10.5 embryos were dissected into PBS on ice and snap frozen at -80C. RNA was extracted in batch preps using Trizol. TapeStation analysis was used to select samples for RNAseq, all samples tested had a RIN number of between 9.0 and 10. Single end reads were performed to a read depth of 40 million reads/ sample on an illumina NextSeq 5000.

first: Ralph

last: Marcucio

first: Jennifer

middle: L

last: Fish

first: Rebecca

middle: M

last: Green


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CsDML OX Transcriptomes

city: Pozuelo de Alarcón (Madrid)

first: Daniel

last: Conde

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo 28223

institute: Centre for Plant Biotechnology and Genomics U.P.M. – I.N.I.A

summary:
Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between CsDML OX transgenic lines Wild Type
Methods: Expression profiles were examined by RNA sequencing (RNA-Seq) in SD-induced (for 28 days) shoot apices of CsDML over-expressor and wild-type hybrid poplars. For RNA extraction, 25 apices from 25 trees of each WT, CsDML OX1 and CsDML OX3 genotypes were dissected under a binocular loupe to remove leaflets surrounding the shoot apical meristem
Results: Using an optimized data analysis workflow, 318 differentially expressed genes (DEG) were identified in CsDML OX, among which 79 were found upregulated and 239 downregulated

first: Alicia

last: Moreno-Cortés

first: Christopher

last: Dervinis

first: José

first: Matias

last: Kirst

first: Mariano

last: Perales

first: Pablo

last: González-Melendi

first: Isabel

last: Allona