title: CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [RNA-seq]

country: USA

overall_design: Four exons were targeted by CRISPR-SKIP. Targeted exons and their flanking exons were sequenced. Transcripts with inclusion and exclusion of targeted exon were quantified. Two control samples and two treated samples were used for each exon targeted.


title: Potential role of hoxb1b in zebrafish development

status: Public on Jul 15 2018

city: Worcester

first: Charles

middle: G

last: Sagerstrom

state: MA

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: UMass Medical School

type: Expression profiling by high throughput sequencing

summary: identification of differentially expressed genes in hoxb1b homozygous mutant hindbrain when compared to wildtype in zebrafish

overall_design: Total RNA was extracted from pools of dechrionated, deyolked of hoxb1b homzygous mutants and wildtype embryos at 18hpf using the RNeasy Mini Kit (Qiagen). Three libraries from wildtype embryos and three libraries from hoxb1b mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). All libraries were analyzed for quality on a bioanalyzer prior to sequencing (Agilent 2100 BioAnalyzer).

first: Priyanjali

last: Ghosh


title: Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes

status: Public on Jul 03 2018

city: Boston

first: Harm-Jan

last: Westra

address: 77 Avenue Louis Pasteur

department: Center for Data Sciences

institute: Brigham and Women's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We investigated whether variants fine-mapped for Rheumatoid Arthritis (RA) and Type 1 Diabetes overlap with open chromatin regions specifically after stimulation. We show that rs117701653, a potentially causal variant for RA near CD28, overlaps open chromatin regions only after stimulation. We futhermore observe a small increase in enhancer activity for this variant under stimulatory conditions using a luciferase assay. Reads were anonimized prior to upload.

overall_design: Examination of chromatin accesibility in CD4+ T-cells from a single individual at 8 timepoints after stimulation with anti-CD3/CD28 beads

first: Soumya

last: Raychaudhuri


title: CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 3]

city: BOSTON

first: Suvi

last: Jain

address: 300 LONGWOOD AVE

department: Molecular Medicine

institute: Boston Children's Hospital

summary: RAG endonuclease initiates antibody heavy chain variable region exon assembly from V, D, and J segments within a chromosomal V(D)J recombination center (RC) by cleaving between paired gene segments and flanking recombination signal sequences (RSSs).  The IGCR1 control region promotes DJH intermediate formation by isolating Ds, JHs, and RC from upstream VHs in a chromatin loop anchored by CTCF-binding elements ("CBEs").  How VHs access the DJHRC for VH to DJH rearrangement was unknown.  We report that CBEs immediately downstream of frequently rearranged VH-RSSs increase recombination potential of their associated VH far beyond that provided by RSSs alone.  This CBE activity becomes particularly striking upon IGCR1 inactivation, which allows RAG, likely via loop extrusion, to linearly scan chromatin far upstream.  VH-associated CBEs stabilize interactions of D-proximal VHs first encountered by the DJHRC during linear RAG scanning and, thereby, promote dominant rearrangement of these VHs by an unanticipated chromatin accessibility-enhancing CBE function.

overall_design: We performed 3C-HTGTS (high throughput, genome-wide translocation sequencing) on v-Abl kinase transformed pro-B cell lines using different baits to examine the interaction profiles of different loci and their dependence on VH-CBEs. All lines analyzed were RAG2-deficient derived from a parental WT line that harbors a non-productive VDJH rearrangement involving a distal VHJ558 (VH1-2P) which deletes the entire proximal VH domain on one allele while the other allele harbors a DHFL16.1 to JH4 rearrangement (DJH allele). The DJ allele was genetically manipulated to derive the various mutants.

first: Zhaoqing

last: Ba

first: Frederick

middle: W

last: Alt


title: Post-transcriptional knockdown of Dnmt1 demonstrates a functional role for insect cytosine methylation

status: Public on Jul 05 2018

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

summary: Despite considerable speculation for the role of cytosine (DNA) methylation in biological and molecular processes in insects, direct functional tests are lacking. Here we provide evidence for the functional role of the maintenance DNA methyltransferase 1 (Dnmt1) in an insect using experimental manipulation. Through RNA interference (RNAi) we successfully post-transcriptionally knocked down Dnmt1 in ovarian tissue of the hemipteran Oncopeltus fasciatus (the large milkweed bug). Individuals depleted for dnmt1, and subsequently DNA methylation, failed to reproduce. Manipulating the levels of DNA methylation did not result in changes in overall gene expression. Furthermore, reductions in levels of DNA methylation at transposable elements (TEs) did not lead to large-scale reactivation of TE transcription. Despite the lack of a causal relationship between reduced DNA methylation and gene expression in the tissue we surveyed, eggs were inviable revealing an important function of DNA methylation in O. fasciatus. Our work provides direct experimental evidence for a functional role of Dnmt1 and DNA methylation in insects and presents O. fasciatus as a tractable model for further exploration of the function of DNA methylation in other tissues and life history circumstances for insects.

sample_organism:
Blattella germanica
Oncopeltus fasciatus

overall_design: DNA methylation. MethylC-seq libraries for a single Oncopeltus fasciatus DNMT1 knocked down and dsRED control individual were prepared according to the protocol described in Urich et al. (2015; doi:10.1038/nprot.2014.114) using genomic DNA extracted from ovaries of post-mated females. Libraries were single-end 75 bp sequenced on an Illumina NextSeq500 machine. Un-methylated lambda phage DNA was used to as a control for sodium bisulfite conversion, and an error rate of ~0.05% was estimated. Blattella germanica was additionally sequenced to generate equal numbers of hemi- and holometabolous insects investigated in this study. However, DNA was extracted from whole-body minus gastrointestinal tract. MethylC-seq libraries were prepared and sequenced identically to O. fasciatus. An error rate of ~0.14% was estimated from un-methylated lambda phage DNA. Gene expression. RNA-seq libraries for RNA extracted from three O. fasciatus DNMT1 knocked down and three control (RED) individuals were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity. Libraries were single-end 75 bp sequenced on an Illumina NextSeq500 machine.

first: Adam

last: Bewick


title: CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 2]

overall_design: We performed HTGTS on v-Abl kinase transformed pro-B cell lines using a JH4 coding end primer as bait to examine the relative utilization of different VH segements in WT and mutant lines. All lines analyzed were derived from a parental WT line that harbors a non-productive VDJH rearrangement involving a distal VHJ558 (VH1-2P) which deletes the entire proximal VH domain on one allele and is inert for V(D)J recombination. The other allele harbors a DHFL16.1 to JH4 rearrangement (DJH allele) and can actively undergo VH to DJH recombination upon G1 arrest induced by STI-571 treatment. The DJ allele was genetically manipulated to derive the various mutants.

first: Yu

last: Zhang

first: Hai-Qiang

last: Dai


title: CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 1]

summary: RAG endonuclease initiates antibody heavy chain variable region exon assembly from V, D, and J segments within a chromosomal V(D)J recombination center (RC) by cleaving between paired gene segments and flanking recombination signal sequences (RSSs). The IGCR1 control region promotes DJH intermediate formation by isolating Ds, JHs, and RC from upstream VHs in a chromatin loop anchored by CTCF-binding elements ("CBEs").  How VHs access the DJHRC for VH to DJH rearrangement was unknown.  We report that CBEs immediately downstream of frequently rearranged VH-RSSs increase recombination potential of their associated VH far beyond that provided by RSSs alone.  This CBE activity becomes particularly striking upon IGCR1 inactivation, which allows RAG, likely via loop extrusion, to linearly scan chromatin far upstream.  VH-associated CBEs stabilize interactions of D-proximal VHs first encountered by the DJHRC during linear RAG scanning and, thereby, promote dominant rearrangement of these VHs by an unanticipated chromatin accessibility-enhancing CBE function.

overall_design: We performed high-throughput, genome-wide translocation sequencing (HTGTS) on pro-B cells derived from the bone marrow of 4- to 6-week-old mice using a JH4 coding end primer as bait to examine the relative utilization of different VH segments in WT and mutant (VH81X-CBEscr/scr) mice.


title: CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors

status: Public on Jul 06 2018

city: Urbana

first: Alan

last: Luu

state: Illinois

address: 1110 W Green St.

department: Physics

institute: University of Illinois at Urbana Champaign

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

overall_design: Refer to individual Series


title: CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [off-targets]

summary: CRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes in vivo by introducing mutations at target sites in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for introducing mutations at off-target sites, technologies capable of introducing targeted changes with increased precision, such as cytidine deaminase single-base editors, are preferred. We here present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program de-novo exon skipping by mutating target DNA bases within splice acceptor sites. Given its simplicity and precision, CRISPR-SKIP will be broadly applicable in gene therapy and synthetic biology.

overall_design: Examination of the on-target and off-target editing rates of a single base editor directed to splice acceptor sequence.

first: Michael

last: Gapinske

first: Jackson

last: Winter

first: Wendy

middle: S

last: Woods

first: Kurt

last: Kostan

first: Nikhil

last: Shiva

first: Jun

last: Song

first: Pablo

last: Perez-Pinera


title: Effect of STMN1 knockdown on prostate cancer cell lines

status: Public on Jun 30 2018

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

summary:
STMN1 is is a highly conserved 18 KDa cytosolic phosphoprotein, involved in the control of cell proliferation, differentiation, motility, clonogenicity and survival.
Over-expression of STMN1 has been shown to be a marker of poor outcome in nasopharyngeal, ovarian, estrogen receptor positive tamoxifen treated early breast and oral squamous cell carcinomas. Limited studies have shown overexpression of STMN1 in higher grade localized prostate cancers; however its association with outcome and metastatic disease is unclear. Here, we investigate role and regulation of STMN1 during prostate cancer progression.

overall_design: Two-color experiment.

first: B

middle: V

last: Chakravarthi

first: D

last: Chandrashekar

first: S


title: DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [amplicon-Seq]

status: Public on Jun 26 2018

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Mouse embryonic stem cells (ESCs) primed for differentiation display dynamic heterogeneity characterised by stochastic switching between transcriptional states, and recent advances have highlighted the heterogeneous and dynamic nature of DNA methylation in these. Using single cell sequencing we report global oscillations in ESC DNA methylation that affect particularly CpG poor regions including distal enhancers. These oscillations are dependent on DNA methylation turnover by Dnmt3 and Tet enzymes and influence the probability of transcriptional state switching. Our observations suggest that regulated DNA methylation heterogeneity may contribute to lineage priming in cells poised for differentiation.

overall_design: 2i ES cells transferred into serum media and collected at 48 time points. Control cells were 2i ES cells collected at the same time points (i.e. without changing to serum media)

first: Steffen

last: Rulands

first: Heather

last: Lee

first: Stephen

last: Clark

first: Christof

last: Angermueller

first: Sebastien

middle: A

last: Smallwood

first: Gavin

last: Kelsey

first: Oliver

last: Stegle

first: Benjamin

middle: D

last: Simons

first: Wolf

last: Reik


title: MicroRNA array analysis from infected and uninfected PBMC samples

status: Public on Jun 23 2018

city: Montpellier

first: Laurent

last: MANCHON

address: 1919 Route de Mende

country: France

institute: CNRS

summary:
ABX464, a new drug for curing HIV and treating inflammatory diseases induces upregulation of the anti-inflammatory miR-124.
We used microarrays to show the implication of ABX464 in the biogenesis of small noncoding RNAs. So, we decided to evaluate if miRNAs or small nucleolar RNAs (snoRNAs) were differentially regulated by ABX464.

overall_design: We performed a microarray analysis for these RNAs from the PBMCs of 6 donors. Cells that were infected with the YU2 strain, followed by treatment with ABX464 were compared with uninfected and untreated controls. A total of 104 human miRNAs and 40 snoRNAs were significantly differentially expressed in infected PBMCs, when compared to uninfected PBMCs (data file S4), with a false discovery rate lower than 0.05 and fold change higher than 1.5.

last: Manchon

first: Jamal

last: Tazi


title: Three autoinducer molecules act synergistically to control virulence gene expression in Vibrio cholerae

status: Public on Jun 25 2018

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

country: Germany

institute: Friedrich-Schiller-Universität Jena


title: The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing

status: Public on Jun 21 2018

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

type: Non-coding RNA profiling by high throughput sequencing


title: CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning

first: Suvi

last: Jain


title: RNA-seq and FA-CLIP studying ECT2 function in Arabidopsis

first: Lianhuan

last: Wei

address: Chengfu road 202

department: College of chemistry and Molecular Engineering

institute: Peking university


title: The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing [smallRNA-Seq]

summary: We found PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing.

overall_design: Examination of the smallRNA expression in Arabidopsis

first: Lianmei

last: Tan

first: Cuijun

last: Zhang

first: Xinjian


title: RNA-seq of WT (Col-0) and ect2 in Arabidopsis

summary: RNA-seq of WT (Col-0) and ect2 to study the differentially expressed genes.

overall_design: Standard RNA-seq.

first: Zhike

last: Lu

first: Guifang

last: Jia


title: The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing [RNA-Seq]

overall_design: Examination of the mRNA expression in Arabidopsis


title: The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing [ChIP-Seq]

overall_design: Examination of histone modification in Arabidopsis.


title: Chemotherapy induced terminal muscle differentiation in WT1 mutant Wilms tumors is associated with cell cycle exit and a loss of growth potential

status: Public on Jun 17 2018

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

summary: Patients with Wilms tumors are efficiently treated by chemotherapy; however, tumors with mutant WT1 genes show a poor volume response. Here we used an unbiased gene expression profiling approach and identified a novel mechanism of conventional chemotherapy that explains how the cure of these patients is brought about. Transcription profiling of an untreated WT1 mutant Wilms tumor (Wilms10) and a corresponding lung metastasis that was detected after long-term chemotherapy, revealed the induction of a myogenic transcriptional network with concomitant down-regulation of cell cycle genes. Cell culture experiments showed convincingly that the Wilms10 tumor cells from this lung metastasis had lost their growth potential due to an induction of terminal skeletal muscle differentiation by chemotherapy. These results were confirmed using a set of Wilms tumors with mutant WT1 genes that were treated by preoperative chemotherapy. We conclude here that chemotherapy-induced terminal skeletal muscle differentiation of Wilms tumors with concomitant loss of growth potential enables the cure of Wilms tumor patients with WT1 mutations in the clinical setting. We have shown before that cell lines derived from Wilms tumors with WT1 mutations have characteristic features of mesenchymal stem cells and it will be of great interest to evaluate whether other tumor types with stem cell features show a differentiation reponse to chemotherapy.

overall_design: Array expression experiment of direct Wilms tumor and lung metastasis tissue

first: Artur

last: Brandt

first: Manfred

last: Beier

first: Carmen

last: Torres

first: Jaume

last: Mora

first: Barbara

last: Leube


title: Formaldehyde-crosslinking and immunoprecipitation (FA-CLIP) sequencing to identify ECT2 targets in Arabidopsis

summary: Developed an efficient method to identify RNA binding sites for RNA-binding proteins in plants.

overall_design: Formaldehyde-crosslinking enhance the binding affinity of RNA-binding protein of RNA, while RNaseT1 digestion can improve the resolution of targets site. We combined the two methods to generate FA-CLIP method in plant to identify RNA-binding protein targets.


title: PolyA+ expression profiling of tubulin Gal4 driven targeted DamID in Drosophila melanogaster adults and gonads

status: Public on Jun 13 2018

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: Targeted DamID (TaDa) measures gene expression using a DNA adenine methyltransferase (Dam) fused to RNA polymerase II (Dam Pol II) to methylate DNA as the genome is transcribed (Southall, Gold et al. 2013, PMID: 23792147). Here we use traditional Illumina RNA-Seq to determine if a cell’s expression profile is affected by Dam Pol II expression. Twenty-four hours prior to collection, we ubiquitously drove UAS Dam or UAS Dam Pol II using a tubulin (tub) GAL4 regulated by a temperature sensitive tub GAL80[ts] (McGuire et al. 2003, PMID: 14657498) in adult Drosophila melanogaster (taxon: 7227) whole males, whole females, testes, and ovaries.

overall_design: There were a total of 24 samples: 2 conditions (Dam or Dam Pol II), 4 tissues (whole female, whole male, testis, and ovary), and 3 biological replicates. Each sample contained a pool of individuals. We collected samples on different days, but extracted RNA and constructed RNA-Seq libraries at the same time in a 96 well plate. We used Dam expression as the control to look at transcriptional changes caused by Dam Pol II.

first: Miriam

last: Akeju

first: Yijie

last: Li

first: Justin

middle: M

last: Fear

first: Maria

last: Jaime

first: Erika

last: Matunis


title: One color Agilent experiment of T. cruzi (Dm28C)infected and control human primary cardiomyocyte

status: Public on Jun 15 2018

city: Montevideo

first: Gabriela

last: Libisch

address: Mataojo 2020

department: Montevideo

country: Uruguay

institute: Institut Pasteur Montevideo

summary: The main objective of the study is to compare the differeneces in gene expression of the T.cruzi (Dm28C) infected and control cardiomyocytes at different times post infection.

overall_design: Human cardiomyocytes (Celprogen) derived from adult cardiac tissue were grown in Human Cardiomyocyte Cell Culture medium (Celprogen) supplemented with 10% (v/v) fetal bovine serum. Dm28C T. cruzi strain of TcI lineage was used throughout this work. For infection assays, semi-confluent cardiomyocytes were infected with cell-derived trypomastigotes (10: 1 parasite: cell ratio), centrifuged for 5 minutes at 1500 rpm, and incubated for 2 hours to allow invasion, at 37°C, 5% CO2 in the cardiomyocyte medium without serum. After the interaction period, parasites were removed, and cells were washed 5-times with PBS and incubated with complete cardiomyocyte medium. Cell samples were taken at 0, 3, 6 and 12 hours after the interaction period henceforth named t0, t3, t6, and t12, respectively. Three biological replicates were performed for t0 and t3 time-points (infected and control cells), and two each for t6 and t12 time-points (infected and control cells).

first: María

first: Paula

last: Faral-Tello

first: Nisha

last: Garg

first: Rafael

last: Radi

first: Lucía

last: Piacenza

first: Carlos

last: Robello


title: Stretch growth does not alter gene expression

status: Public on Jun 08 2018

city: Pisa

first: Vittoria

last: Raffa

state: Please Select

address: S.S. 12 Abetone e Brennero, 4

department: Department of Biology

country: Italy

institute: Università di Pisa

summary: Differentiated PC12 cells were magnetically labeled with magnetic nanoparticles (MNP). External magnetic fields were used to mechanically stretch the MNP-labeled neurites. We found that mechanical stretching of the neurites induces mass addition and neurite elongation. We performed RNAseq of MNP-labelled cells in stretched versus non-stretched conditions and we did not found gene expression dysregulation, confirming that the two conditions were identical and excluding cytotoxicity or involvement of nuclear mechanotransdution. Indeed, local mechanisms triggered by the stretching of the MNP-labelled neurite would be responsible for neurite elongation.

overall_design: mRNA profile in stretched versus non stretched  cells were generated by NGS, in triplicate, using Illumina.

first: Alfred

last: Cuschieri

first: Glasgow

last: Polyomics


title: Paneth cells acquire multi-potency upon Notch activation after irradiation

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

institute: Rutgers, the State University of New Jersey

summary: In murine models, we find that irradiation of Paneth cells caused a gain of a stem cell-like transcriptome and induced activation of the Notch signaling pathway. This study documents plasticity by Paneth cells, a fully committed cell population to participate in epithelial replenishment following stem cell loss.

overall_design: Single-cell dissociation was carried out as previously described (Li et al., 2016; Sato et al., 2011). Cell pellets were washed with cold PBS and re-suspended in FACS buffer. Cells were stained with DAPI, PerCP/Cy5.5-conjugated EpCAM, BUV395-conjugated CD45, and APC/fire 750-conjugated CD24. Cell suspensions were subjected to sorting by BD Biosciences Aria II Flow Cytometer. Single viable intestinal epithelial cells were gated by forward scatter, side scatter, and by negative staining for DAPI and CD45, and positive staining for EpCAM. Subpopulations were further gated based on CD24 and tdTomato (using R-phycoerythrin/PE channel). Paneth cells (tdT+CD24+) and derivative (tdT+CD24-) cells were FACS-sorted from irradiated (5 days after radiation) and non-irradiated 8-14 week old Lyz1CreER; R26R-tdT mice with one dose of tamoxifen adminstration (10mg/mouse), and subjected to total RNA extraction using Qiagen RNeasy Plus Micro kit.

first: Shiyan

last: Yu

first: Kevin

last: Tong

first: Yanlin

last: Zhao

first: Iyshwarya

last: Balasubramanian

first: George

last: Yap

first: Ronaldo

last: Ferraris

first: Edward

last: Bonder

last: Gao


title: Run or die in the evolution of de novo microRNAs

status: Public on Jun 14 2018

city: Cold Spring Harbor

first: Yixin

state: NEW YORK

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: MicroRNAs (miRNAs) are a class of small, endogenous RNAs that regulate mRNA expressions post-transcriptionally. To study their expression, we collected and sequenced small RNA libraries in Drosophila species. To survey their regulation divergence, we dissected testes from miR-983 mutant and control flies in two sibling species and performed an RNA-seq analysis.

sample_organism:
Drosophila erecta
Drosophila melanogaster
Drosophila sechellia
Drosophila simulans

overall_design: Two small RNA samples from D. erecta and D. sechellia testes as well as eight RNA-seq samples from D. melanogaster and D. simulans testes were analyzed. For RNA-seq, each genotype contains two biological replicates.

first: Hao

last: Yang

first: Pei

last: Lin

first: Zhongqi

last: Liufu

first: Guang-an

last: Lu

first: Jin

last: Xu

first: Tian

last: Tang

first: Haijun

last: Wen

first: Chung-I

last: Wu


title: Proteogenomic Analysis of Medulloblastoma [methylation array]

city: Washington

first: Samuel

last: Rivero-Hinojosa

state: District of Columbia

address: 111 Michigan Ave NW

department: Children’s Research Institute, Center for Cancer and Immunology Research

institute: Children’s National Health System

type: Methylation profiling by genome tiling array

summary: These methylation arrays were performed as part of a project aiming to integrate quantitative proteomic, gene expression and epigenetic data from the childhood brain tumor medulloblastoma.

overall_design: A total of 33 pediatric medulloblastoma and 5 normal cerebellum samples were analized

first: Rivero-Hinojosa

last: Samuel

first: Stampar

last: Mojca

first: Rood

middle: R

last: Brian


title: RNA-seq Analysis of the effect of Tfcp2l1 overexpression on Human ESC maintenace

status: Public on Jun 06 2018

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary: Purpose:The goals of this study are to analyze the candidate genes motified by Tfcp2l1 overexpression to regulated the human embryonic stem cell (ESC) self-renewal through RNA-seq approach.

overall_design: HES2 human ESCs transfected with Piggybac(PB) or PB-Tfcp2l1 plasmid were cultured in N2B27/10% KSR  supplemented with 10 ng/ml FGF2 and 10 ng/ml Activin A  for three passages and then were collected by using Trizol. These samples were sent to BGI (China) company to do deep sequencing by using BGISEQ-500.

first: Shoudong

last: Ye


title: Celll type specific gene expression from healthy human lung tissue infected with mycobacterium tuberculosis (ILC).

status: Public on Jun 04 2018

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

institute: MPIIB

summary: We have investigated the initial responses in human lung tissue explants to Mtb infection, focusing primarily on gene expression patterns in different tissue resident innate cell types

overall_design: Cells sorted from uninfected and infected lung tissue (24 hrs. post infection)

first: Hans

last: Mollenkopf

first: Stefan

middle: E

last: Kaufmann


title: Celll type specific gene expression from healthy human lung tissue infected with mycobacterium tuberculosis (innate).


title: Gene expression in human lung tissue infected with mycobacterium tuberculosis

status: Public on May 26 2018

summary: Differential gene expression in human lung tissue 24 hrs after infection compared to uninfected tissue from the same donor

overall_design: Gene expression analysis of RNA in whole lung tissue

middle: H


title: Expression data from pituitary of steers grazing endophyte-infected tall fescue and supplemented with different forms of Se

status: Public on May 25 2018

city: Lexington

first: James

last: Matthews

state: KY

address: 207 W.P. Garrigus Buidling

department: Animal and Food Sciences

institute: University of Kentucky

summary: The goal of this study was to test the hypothesis that sodium selenite (ISe), SEL-PLEX (OSe), vs. a 1:1 blend (MIX) of ISe and OSe in a basal vitamin-mineral (VM) mix would differetianlly alter pituitary transcriptome profiles in growing beef steers commonly grazing an endophyte-infected tall fescue pasture. Predominately-Angus steers (BW = 183 ± 34 kg) were randomly selected from herds of fall-calving cows grazing E+ pasture and consuming VM mixes that contained 35 ppm Se as ISe, OSe, and MIX forms. Steers were weaned, depleted of Se for 98 d, and subjected to summer-long common grazing of an E+ pasture (0.51 ppm total ergovaline per ergovalinine; 10.1 ha). Steers were assigned (n = 8 per treatment) to the same Se-form treatments upon which they were raised. Selenium treatments were administered by daily top-dressing 85 g of VM mix onto 0.23 kg soyhulls, using in-pasture Calan gates. We collected pituitary samples and examine for changes in global expression pattern by microarray analysis.

overall_design: 20 total samples were analyzed (n = 6 for ISe, and n=7 for both OSe and MIX).

first: Qing

last: Li

first: Phillip

last: Bridges

middle: C


title: de novo re-construction of the core genome from ChIP-Seq for large-genome organisms

status: Public on May 27 2018

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: Genetic diversity in plants is remarkably high. Recent whole genome sequencing (WGS) of 67 rice accessions recovered 10,872 novel genes. Comparison of the genetic architecture among divergent populations or between crops and wild relatives is essential for obtaining functional components determining crucial traits. However, many major crops have gigabase-scale genomes, which are not well-suited to WGS. Existing cost-effective sequencing approaches including re-sequencing, exome-sequencing and restriction enzyme-based methods all have difficulty in obtaining long novel genomic sequences from highly divergent population with large genome size. The present study presented a reference-independent core genome targeted sequencing approach, CGT-seq, which employed epigenomic information from both active and repressive epigenetic marks to guide the assembly of the core genome mainly composed of promoter and intragenic regions. This method was relatively easily implemented, and displayed high accuracy, sensitivity and specificity for capturing the core genome of bread wheat. 95% intragenic and 89% promoter region from wheat were covered by CGT-seq read. We further demonstrated in rice that CGT-seq captured hundreds of novel genes and regulatory sequences from a previously unsequenced ecotype. Together, with specific enrichment and sequencing of regions within and nearby genes, CGT-seq is a time- and resource-effective approach to profiling functionally relevant regions in sequenced and non-sequenced populations with large genomes.

sample_organism:
Oryza sativa
Triticum aestivum
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: We designed an experimental and computational pipeline for re-construction of wheat core genome. Briefly, ChIP-seq of different marks was performed, sequencing reads of each modification were assembled and further merged. Next, reads from all modifications were mapped to the assembled contigs derived from the previous step, and paired sequencing reads were used to join contigs into scaffolds. All reads were re-mapped to the scaffolds, gaps were filled and scaffolds were extended. The scaffolding and extension steps were repeated until the covered bases showed no apparent change.

first: Yijing

last: Zhang


title: Gene expression profiling of tumor-associated macrophages and in-vitro cultured macrophages

status: Public on Jun 01 2018

city: London

first: JONATHAN

last: CARON

state: Greater London

address: New Hunt's House, Newcomen St

department: Cancer Studies

institute: KING'S COLLEGE LONDON

summary: The aim of this study was to decipher gene expression of tumor-associated macrophage in the 4T1 mouse model of breast cancer.

overall_design: For M0 basal macrophages, Ly6C+ monocytes were isolated from splenocytes of 4T1-bearing mice using Miltenyi magnetic beads, seeded in a 6-wells plate at 1 million cells per wells in RPMI 10% FCS, penicillin/streptomycin, 50ng/ml M-CSF and cultured for 72h. F4/80+ TAMs were isolated from enzyme-digested 4T1 tumors using Miltenyi magnetic beads, and lysed directly in Ambion's PureLink™ RNA Mini Kit lysis buffer.

first: J

middle: N

last: Arnold

last: Caron


title: Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70 [II]

status: Public on May 18 2018

city: San Diego

first: Meng

last: Zhao

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute of Allergy and Immunology

summary: Various subsets of invariant natural killer T (iNKT) cells with different cytokine productions develop in the mouse thymus, but the factors driving their differentiation remain unclear.  Here we show that hypomorphic alleles of Zap70 or chemical inhibition of Zap70 catalysis lead to an increase of IFN-g-producing iNKT cells (NKT1 cells), suggesting  NKT1 cells may require a lower TCR signal threshold. Zap70 mutant mice develop IL-17-dependent arthritis. iNKT cells and therapeutic induction of IFN-g secretion by activating iNKT cells are protective in this model, but the representation of IFNg versus IL-17 secreting iNKT cells in the joint change in favor of IL-17 producers as disease worsened. NKT1 cells are also present in the synovial fluid of arthritis patients, where they could be beneficial. Our data therefore suggest that TCR signal strength during thymic differentiation may influence not only IFNg production, but also the protective function of iNKT cells in arthritis.

overall_design: Three subsets of iNKT cells from the thymi of WT control and SKG mice were analyzed. Three independent experiments were carried out. Triplicates of each sample were analyzed

first: Mattias

last: Svensson

first: Koen

last: Venken

first: Ashu

last: Chawla

first: Shu

last: Liang

first: Isaac

last: Engel

first: Piotr

last: Mydel

first: Jeremy

last: Day

first: Dirk

last: Elewaut

first: Nunzio

last: Bottini

first: Mitchell

last: Kronenberg


title: SWI/SNF subunit CHR2 remodels pri-miRNAs via microprocessor component SE to inhibit miRNA production

city: college station

first: Xiuren

state: Texas

address: 2123 tamu

department: biochemistry & biophysics

institute: texas a&m university

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

overall_design: Refer to individual Series


title: SWI/SNF subunit CHR2 remodels pri-miRNAs via microprocessor component SE to inhibit miRNA production (miRNA-Seq)

summary: We performed Illumina sequencing of sRNA libraries prepared from leaves of adult plants in Arabidopsis. Chromatin remodeling factor 2 (CHR2) positively regulates transcription of MIR loci whereas repressing microRNA (miRNA) accumulation in vivo. CHR2 can directly bind to and unwind primary miRNAs (pri-miRNAs) and inhibit their processing; and this inhibition entails its remodeling activity in vitro and in vivo.

overall_design: Non-coding RNA profiling by high throughput sequencing

first: Zhiye

last: Wang

first: Zeyang

last: Ma

first: Claudia

last: Castillo-González

first: Di

last: Sun

first: Yanjun

last: Li

first: Bin

last: Yu

first: Pingwei


title: Human Muscle Posses Epigenetic Memory

status: Public on May 23 2018

city: Liverpool

first: Robert

middle: Arthur

last: Seaborne

address: Byrom Street

department: SCAMP

institute: Liverpool John Moores University

summary: It is unknown if adult human skeletal muscle has an epigenetic memory of earlier encounters with growth. We report, for the first time in humans, genome-wide DNA methylation (850,000CpGs) and gene expression analysis after muscle hypertrophy (loading), return of muscle mass to baseline (unloading), followed by later hypertrophy (reloading). We discovered increased frequency of hypomethylation across the genome after reloading (18,816 CpGs) versus earlier loading (9,153 CpG sites). We also identified AXIN1, GRIK2, CAMK4, TRAF1 as hypomethylated genes with enhanced expression after loading that maintained their hypomethylated status even during unloading where muscle mass returned to control levels, indicating a memory of these genes methylation signatures following earlier hypertrophy. Further, UBR5, RPL35a, HEG1, PLA2G16, SETD3 displayed hypomethylation and enhanced gene expression following loading, and demonstrated the largest increases in hypomethylation, gene expression and muscle mass after later reloading, indicating an epigenetic memory in these genes. Finally, genes; GRIK2, TRAF1, BICC1, STAG1 were epigenetically sensitive genes demonstrating hypomethylation after a single bout of resistance exercise that was maintained 22 weeks later with the largest increase in gene expression and muscle mass after reloading. Overall, we identify an important epigenetic role for a number of largely unstudied genes in muscle hypertrophy/ memory.

overall_design: Using a within-subjects design, skeletal muscle samples from the vastus lateralis were analsyed at baseline ((control; N=9; subject 1 has a duplicate(rep2) all other subjects are in single (rep1)), immediately (30-mins) following one single bout of acute resistance exercise (N=8; where this session was the first session of the subsequent 7-week training intervention) after 7 weeks of chronic resistance exercise loading (N=8), following a further 7 weeks of unloading (N=8) and finally, following 7 weeks of chronic resistance exercise reloading (N=7). All samples are run in single unless otherwise stated.

first: Adam

last: Sharples


title: RNA sequencing of SRSF3 depleted pluripotent cells

status: Public on May 10 2018

city: Clayton

first: Minna-Liisa

last: Anko

state: VIC

address: 15 Innovation Walk

department: Department of Anatomy and Developmental Biology

country: Australia

institute: Monash University

summary: RNA seqeuncing was performed to identifiy changes in genes expression and alternative splicing following SRSF3 depletion in pluripotent stem cells.

overall_design: Induced pluripotent stem cells (iPSCs) generated from reprogrammable conditional SRSF3 knockout (SRSF3-KO/OKSM) mouse embryonic fibroblasts (MEFs) were induced for 24h to deplete SRSF3 and RNA seqeuncing was performed.


title: Myc and the Tip60 chromatin remodeling complex control neuroblast maintenance and polarity in Drosophila

status: Public on May 15 2018

city: Cologne

first: Andreas

last: Wodarz

address: Kerpener Str. 62, Building 37

department: Anatomy

institute: Uniklinik Cologne

summary: Transcriptomic analyses of wild type and Domino knockdown 3rd instar larval neural cells

overall_design: Transcriptional regulation by Domino in the Drosophila larval brain


title: Collaborative repressive action of the antagonistic ETS transcription factors Pointed and Yan fine-tunes gene expression to confer robustness in Drosophila

status: Public on May 08 2018

city: Chicago

first: Jemma

middle: L.

last: Webber

state: IL

address: 929 E 57th Street

department: Ben May Department for Cancer Research

institute: University of Chicago


title: The impact on reprogramming of Msx2

city: Guangzhou

first: lilong

last: Lin

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health，Chinese Academy of Sciences

summary: We report that we make the high-profiling for transcriptome to detect the impact on reprogramming of transcription factor Msx2 at different time points during reprogramming. Based on the technology of overexpression and Knock down for Msx2, we can observe the changes of transcriptomes in contrast with control group. We get the connections between Msx2 and BMP signaling, and other meaningful results, but we should make further validation.

overall_design: Examination of the impact on reprogramming of Msx2

first: Lilong

first: Hui

last: Zheng


title: TCR repertoire of effector CCR7-CD38+ cells accumulating during experimental infection with Typhoidal Salmonella

status: Public on May 13 2018

city: Oxford

first: Margarida

last: Rei

address: Headley Way

institute: University of Oxford

summary: In order to characterize pathogen specific T cell responses against Salmonella volunteers challenged with Salmonella enterica serovar Typhi (S. Typhi) or Salmonella Paratyphi A (S. Paratyphi). we used mass cytometry, to identify effector CD4+ T cells circulating during infection. We identified a population of CCR7-CD38+ cells accumulating during infection, and via unbiased single cell cloning and expansion we demonstrated that these CCR7-CD38+ cells are enriched in Salmonella specific T cells. In this experiment we performed TCR repertoire analysis of CCR7-CD38+ and CCR7-CD38- cells to determine the clonality of CCR7-CD38+ cells, the overlap between the repertoire of CCR7-CD38+ cells and of non-activated effector CCR7-CD38- cells, and to identify within CCR7-CD38+ and CCR7-CD38- cells the presence of the CDR3b TCR sequence of the pathogen specific T cell clones isolated from  CCR7-CD38+ cells

overall_design: Analysis of the TCR repertoire of CCR7-CD38+ and CCR7-CD38+ CD4 T cells isolated from frozen PBMC after diagnosis of enteric fever in one volunteer challenged with Salmonella Typhi and one challenged with Salmonella Paratyphi A

first: David

last: Miguel Susano Pinto

first: Giorgio

last: Napolitani


title: Detection of differentially-expressed genes in mouse embryonic fibroblasts (WT, MAVSko, STINGko, and LGP2ko MEFs) following exposure to ionizing radiation

first: Diana Rose

last: Ranoa

address: 900 E 57th St, KCBD, Rm 6160

department: Radiation and Cellular Oncology

summary:
Analysis of the impact of MAVS, STING, and LGP2 in MEFs in response to ionizing radiation at the gene expression level.
Results provide important information on the relative contribution to cellular funtions of each individual gene knock-outs in MEFs both at the basal level and in response to genotoxic stress.

overall_design: Total RNA was extracted from MEFs at 48 hours post-exposure to ionizing radiation (6Gy) and compared with unirradiated controls.

first: Diana-Rose

first: Nikolai

last: Khodarev

first: Ralph

last: Weichselbaum


title: Collaborative repressive action of the antagonistic ETS transcription factors Pointed and Yan fine-tunes gene expression to confer robustness in Drosophila [ChIP-Seq]

summary: Purpose: To understand how the Drosophila ETS transcription factors Yan and Pointed together with the corepressor Groucho are recruited to chromatin

overall_design: ChIP profiles of Yan, Pnt or Groucho from either stage 11 wildtype (WT) or mutant embryos were generated by deep sequencing, in duplicate using an Illumina Hi-seq instrument according to manufacturers protocols. Raw sequence data was aligned to the April 2006 Drosophila melanogaster genome and peak detection was perfomed using MACS software. SPP was used to generate Wig files that were normalized to total dataset size.

first: Jie

last: Zhang

first: Ilaria

last: Rebay


title: FACS validation dataset: An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray (III)

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

summary: DNA methylation assessments of peripheral blood DNA can be used to accurately estimate the relative proportions of underlying leukocyte subtypes. Such cell deconvolution analysis relies on libraries of discriminating differentially methylated regions that are developed for each specific cell type measured. The relationship between estimated cell type proportions can then be tested for their association with phenotypes, disease states, and subject outcomes, or used in multivariable models as terms for adjustment in epigenome-wide association studies (EWAS). We obtained purified neutrophils, monocytes, B-lymphocytes, natural killer (NK) cells, CD4+ T-cells, and CD8+ T-cells from healthy subjects and measured DNA methylation with the Illumina HumanMethylationEPIC array platform. In addition, we measured DNA methylation with the EPIC array in two sets of artificial DNA mixtures comprising the above cell types. We compared three separate approaches to select reference differentially methylated region libraries (DMR library), for cell type proportion inference. The IDOL algorithm identified an optimal DMR library consisting of 450 CpG sites for inferring leukocyte subtype proportions (average R2=99.2). Importantly, the majority of CpG sites (69%) in the IDOL DMR library were unique to the new EPIC methylation array, in that they were not present on the 450K array. Our new reference DMR library is available as a Bioconductor package, has the potential to reduce any unintended technical differences arising from the combination of different generations of array platforms, and may be helpful in generating larger DMR libraries that include novel cell subtypes. A  dataset of six whole blood samples were FACS sorted and the DNA was processed as a validation dataset.

overall_design: Bisulphite converted DNA from whole blood draw from six healthy subjects and the samples were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4

first: Devin

last: Koestler

first: Rondi

last: Butler

first: Helen

last: Hansen

first: John

middle: K

last: Wiencke

first: Karl

middle: T

last: Kelsey

first: Brock

last: Christensen


title: The effect of simulated night shift work on the circadian regulation of the human transcriptome

city: Montreal

first: Laura

last: Kervezee

state: Quebec

address: 6875 LaSalle Boulevard

department: Douglas Mental Health University Institute

country: Canada

institute: McGill University

summary: Eight healthy human subjects were enrolled in a 6-day simulated shift work protocol. Blood samples were collected during the two 24-hour measurement periods. Blood samples were collected every 4 hours during both measurement periods. Subjects entered the lab on Day 1. At the start of Day 2, the first 24-hour measurement period was started. Subjects slept according to their habitual sleep/wake schedule, followed by a 16-hour constant posture procedure. On days 3-6, the sleep period was delayed by 10 hours. Following the third night on this schedule, subjects underwent another 24-hour measurement period. During both measurement periods, 7 blood samples were collected and PBMCs were isolated. mRNA was extracted, labelled, and hybridized to microarrays.

overall_design: A total of 103 samples were collected from 8 subjects spread across two 24-hour measurement periods

first: L

first: M

last: Cuesta

first: N

last: Cermakian

first: D

middle: B

last: Boivin


title: Validation of systems biology derived molecular markers of donor organ status associated with long term allograft function

status: Public on May 04 2018

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

summary: Determinion of performance of a molecular marker panel - derived via a systems biology data integration approach reflecting renal transplant pre-implantation donor organ status - to predict post-transplant renal function in an independent cohort.

overall_design:
pre-implantation transcriptomics dataset of renal transplant donor organs plus network-based molecular model reflecting renal transplant donor organ status based on publicly available transcriptomics datasets
PMIDs: 19155987; 17452894; 22992769; reported set of transcripts was used as input for molecular model generation as described in PMIDs: 23144070; 26209734;

first: Paul

last: Perco

first: Andreas

last: Heinzel

first: Stefan

last: Schneeberger

first: Silvia

last: Wagner

first: Franziska

last: Engler

first: Gert

last: Mayer


title: Genome-wide chromatin maps in the liver from male and female Wistar rats

status: Public on May 01 2018

city: Edinburgh

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: We carry out H3K27pan-acetly chromatin imminoprecipitation (ChIP) and H3K4me1 ChIP prior to sequencing on the Illumina Nextseq 500 sequencing platform to report on the genome-wide epigenetic patterns in rat livers

overall_design: Genome-wide patterns were generate on Illumina Nextseq 500

first: Raffaele

last: Ottaviano

first: Angie

last: Fawkes

first: Richard

last: Clark

first: Lee

last: Murphy

last: Meehan


title: Kinetics and fidelity of the repair of Cas9-induced double-strand DNA breaks

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: The RNA-guided DNA endonuclease Cas9 is a powerful tool for genome editing. Little is known about the kinetics and fidelity of the double-strand break (DSB) repair process that follows a Cas9 cutting event in living cells. Here, we developed a strategy to measure the kinetics of DSB repair for single loci in human cells. Quantitative modeling of repaired DNA in time series after Cas9 activation reveals variable and often slow repair rates, with half-life times up to ~10 h. Furthermore, repair of the DSBs tends to be error-prone. Both classical and microhomology-mediated end-joining pathways contribute to the erroneous repair. Estimation of their individual rate constants indicates that the balance between these two pathways changes over time and can be altered by additional ionizing radiation. Our approach provides quantitative insights into DSB repair kinetics and fidelity in single loci, and indicates that Cas9-induced DSBs are repaired in an unusual manner.

overall_design: We transiently transfected K562#17 with a plasmid encoding a sgRNA. Twenty-four hours after transfection we stabilized Cas9 by adding Shield-1. We collected cells at various time points, isolated genomic DNA, amplified a ~300-bp region around the sgRNA target site by PCR and subjected the products to high-throughput sequencing to determine the intact and indel fractions. 8 replicates for sgRNA-LBR2, 6 replicates for sgRNA-AAVS1, 6 replicates sgRNA-LBR8, 5 replicates chr11, 2 replicates sgRNA LBR2/LBR8 combined. Double cut t=60 for sgRNA LBR2/LBR5, sgRNA LBR2/LBR6, sgRNA LBR2/LBR7,  sgRNA LBR2/LBR8, sgRNA LBR2/LBR9

first: Eva

last: Brinkman

first: Tao

last: Chen

first: Marcel

last: de Haas

first: Hanna

last: Holland

first: Waseem

last: Akhtar


title: A guide to single-cell transcriptomics in adult rodent brain: the medium spiny neuron transcriptome revisited

city: Menlo Park

first: Thomas

last: Portmann

address: 1505 O'Brien Dr

department: Neurobiology and Transcriptomics

institute: Circuit Therapeutics

summary: Recent advances in single-cell technologies are paving the way to a comprehensive understanding of the cellular complexity in the brain. Protocols for single-cell transcriptomics combine a variety of sophisticated methods in order to isolate heavily interconnected and heterogeneous neuronal cell types in a relatively intact and healthy state. The emphasis of single-cell transcriptome studies has thus far been on comparing library generation and sequencing techniques that enable measurement of the minute amounts of starting material from a single cell. However, in order for data to be comparable, standardized cell isolation techniques are essential. Here, we analyzed and simplified methods for the different steps critically involved in single-cell isolation from brain. These include highly region-specific cellular labelling compatible with use of stereotaxic coordinates, enzymatic digestion, tissue trituration, and improved methods for efficient fluorescence-activated cell sorting in samples containing high degree of debris from the neuropil. The methods are exemplified using medium spiny neurons (MSN) from dorsomedial striatum, a cell type that is clinically relevant for disorders of the basal ganglia, including psychiatric and neurodegenerative diseases. We present single-cell RNA sequencing (scRNA-Seq) data from D1 and D2 dopamine receptor expressing MSN subtypes. We illustrate the need for single-cell resolution by comparing to available population-based gene expression data of striatal medium spiny neuron subtypes. Our findings contribute towards standardizing important steps of single-cell isolation from adult brain tissue to increase comparability of data. Furthermore, our data newly define the transcriptome of medium spiny neurons at unprecedented resolution and identify novel subtype specific marker genes in this important cell type

overall_design: 40 Drd1 and 40 Drd2 expressing neurons from double-transgenic animals (Drd1a-TdTomato X Drd2-EGFP) were sequenced by scRNA-Seq. Cells were FACS sorted into single wells 96-well plates and selected based on their fluorescence intensity (TdTomato > Drd1 expressing, EGFP > Drd2 expressing). Single-cell Samples were processed with SMARTer Ultra Low Input RNA Kit for Sequencing – v3 (Clontech Laboratories) and sequenced on a MiSeq instrument (Illumina)

first: Hanson

last: Ho

first: Matt

last: De Both

first: Ashley

last: Siniard

first: Sasha

last: Sharma

first: James

last: Notwell

first: Michelle

last: Wallace

first: Dino

last: Leone

first: Amy

last: Nguyen

first: Eric

last: Zhao

first: Hannah

last: Lee

first: Daniel

last: Zwilling

first: Kimberly

last: Thompson

first: Steven

last: Braithwaite

first: Matthew

last: Huentelman


title: Whole transcriptomic analysis of AB1 tumor microenvironment 4 or 14 days after tumor inoculation

status: Public on Apr 30 2018

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

summary: Analysis of highly immunogenic, AB1 tumor environment at gene expression level.

overall_design: Total RNA obtained from tumor microenvironment tissues (at Day 4 and Day 14 after tumor inoculation) compared to control tissues.

last: NEHAR-BELAID

first: Phuong

last: Hang

first: David

last: KLATZMANN


title: RNA-seq on D5 C. elegans in WT(N2), alg-1(gk214), alg-2(ok304)

city: La Jolla

last: Pasquinelli

address: 9500 Gilman Drive

department: Biological Sciences

institute: University of California, San Diego

summary: In order to examine the misregulation of genes in loss of function alg-1 and alg-2 versus WT, RNA-seq was performed on D5 C.elegans in WT(N2), alg-1(gk214), alg-2(ok304)

overall_design: RNA-seq on adult day 5 (D5) C.elegans in WT(N2), alg-1(gk214), alg-2(ok304)

first: P

last: Aalto

first: J

middle: S

last: Chen


title: Cell of origin dictates aggression and stem cell activity in acute lymphoblastic leukemia

status: Public on Apr 29 2018

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

institute: Massachusetts General Hospital

summary: Subclassification of lymphoid neoplasms is often based on the presumed cell of origin based on T and B progenitor gene expression and the effect of cell lineage on influencing functional characteristics such as aggression and self-renewal capacity is largely unknown, accounted for in part, by lack of experimental models to address these questions. Here, we have used transgenic zebrafish to create the first models of Myc-induced B-ALL and mixed phenotypic B/T-ALL, opening new avenues for studying the these leukemias in the zebrafish. Our work has utilized syngeneic strain zebrafish, limiting dilution cell transplantation, and the widely reported rag2-Myc transgenic model to provide new understanding of how strain differences can underlie leukemia onset in the zebrafish model. Even more importantly, our work now for the first time, has allowed assessment of cell lineage on dictating aggression and leukemia stem cell frequency independent of the underlying oncogenic driver. In total, our work uncoveres that T-ALLs are more aggressive and have higher numbers of leukemia stem cells when compared with B-ALL and mixed phenotypic ALL. Furthermore, analysis of our biphenotypic B/T-ALL suggests that B cell pathways lock cells in less aggressive and lower stem cell fates and are dominant in regulating these processes when T cell pathways are co-regulated within ALL cells.

overall_design: The goal of our study is to determine the transcriptional profiles of high and low self-renewing capacity tumors. 20 samples total: 11 unique samples (9 samples with biological replicates), 6 high self-renewing tumors (>1% cells could initiate leukemia) and 5 low self-renewing tumors (<1% of cells could initiate leukemia).

first: Elaine

last: Garcia

last: Langenau


title: ALG-1 and ALG-2

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

overall_design: Refer to individual Series


title: Pure epicatechin and inflammatory gene expression profiles in circulating immune cells in (pre) hypertensive adults; a randomized double-blind, placebo-controlled, crossover trial

status: Public on Apr 25 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Introduction: There is increasing evidence that consumption of cocoa products have a beneficial effect on cardio-metabolic health, but the underlying mechanisms remain unclear. Cocoa contains a complex mixture of flavan-3-ols. Epicatechin, a major monomeric flavan-3-ol, is considered to contribute to the cardio-protective effects of cocoa. We investigated effects of pure epicatechin supplementation on whole genome gene expression profiles of circulating immune cells. Methods: In a randomized, double blind, placebo-controlled cross-over trial, 37 (pre)hypertensive (40-80y) subjects received two 4-week interventions; epicatechin (100mg/day) or placebo with a wash-out period of 4-week between both interventions. Whole genome gene expression profiles of peripheral blood mononuclear cells were determined before and after both interventions. Results: After epicatechin supplementation 1180 genes were significantly regulated, of which 234 were also significantly regulated compared to placebo. Epicatechin supplementation up-regulated gene sets involved in transcription/translation and tubulin folding and down-regulated gene sets involved in inflammation. Only a few genes within these regulated gene sets were actually significantly changed upon epicatechin supplementation. Upstream regulators that were shown to be inhibited were classified as cytokine or inflammatory type molecules. Conclusion: Pure epicatechin supplementation modestly reduced gene expression related to inflammation signalling routes in circulating immune cells. These routes are known to play a role in cardiovascular health

overall_design: Microarray analysis was performed on peripheral blood mononuclear cells (PBMC) from (pre)hypertensive men and women before, and after 4 weeks epicatechin (100mg/d) or placebo supplmentation. A total of 4 samples, from 32 subjects, were used for the microarray analysis.

first: Diederik

last: Esser

first: James

middle: I

last: Dower

first: Juri

last: Matualatupauw

first: Marianne

last: Gelejinse

first: Daan

last: Kromhout

first: Peter

last: Hollman

first: Lydia

middle: A

last: Afman


title: Cytosine methylation analysis of adult mixed phenotype acute leukemia (MPAL)

status: Public on Apr 24 2018

city: Houston

first: Koichi

last: Takahashi

state: TX

address: 1881 East Road

institute: UT MD Anderson Cancer Center

summary: Cytosine methylation analysis of genomic DNA from 31 MPAL patients  bone marrow samples was performed using Illumina’s Infinium MethylationEPIC Kit (EPIC) that covers approximately 850,000 CpG probes (Illumina, San Diego, CA).

overall_design: Bisulphite converted DNA from the 31 MPAL patient bone marrow  samples were hybridised to the Illumina Infinium MethylationEPIC array

first: Feng

last: Wang


title: Transcriptional profiling of sorted tumor cells from implanted T cell low and T cell high mouse pancreatic tumors

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

summary:
Purpose: Use RNA-seq strategy to characterize the differentially expressed genes in T cell low and high mouse pancreatic tumors in order to identify factors contributing to the differential abundance of tumor infiltrating T cells.
Methods: Subcutaneously implanted T cell low and high pancreatic tumors were utilized for the preparation of RNA-seq libraries from sorted tumor cells.

overall_design: Examination of differentially expressed genes between two biological groups (T cell low v.s. T cell high tumors).

first: Ben

middle: Z

last: Stanger

first: Robert

last: Vonderheide

first: Katelyn

last: Byrne


title: The influence of snRNA and ER stress on alternative splicing in B cells

status: Public on Apr 21 2018

city: Pittsburgh

first: Christine

last: Milcarek

state: PA

address: 200 Lothrop Street

department: Immunology

institute: University of Pittsburgh

summary: B cells treated with LPS undergo stress and Ire1 phosphorylation by 18 hours. We measured the effect of inhibiting the Ire1 phosphorylation with the drug 4u8c on gene expression and RNA splicing.

overall_design: We analyzed 10 wild type C57BL/6 mouse B cell samples. Four of these samples were replicates for wild type unstimulated B cells, three were stimulated with LPS and collected at 18 hours, and three were stimulated with LPS + the RIDD inhibitor 4u8c and collected at 18 hours.

first: Ashley

middle: M

last: Nelson

first: Nolan

last: Carew

first: Sage

last: Smith


title: The calmodulin-like protein, CML39, is involved in regulating seed development, germination, and fruit development in Arabidopsis

city: Kingston

first: Wayne

last: Snedden

state: Ontario

address: 116 Barrie St.

department: Biology

institute: Queen's University

summary: In addition to the evolutionarily-conserved Ca2+ sensor, calmodulin (CaM), plants possess a large family of CaM-related proteins (CMLs). Using a cml39 loss-of-function mutant, we investigated the roles of CML39 in Arabidopsis and discovered a range of phenotypes across developmental stages and in different tissues.  In mature plants, loss of CML39 results in shorter siliques, reduced seed number per silique, and reduced number of ovules per pistil. We also observed changes in seed development, germination, and seed coat properties in cml39 mutants in comparison to wild-type plants. Using radicle emergence as a measure of germination, cml39 mutants showed more rapid germination than wild-type plants. In marked contrast to wild-type seeds, the germination of developing, immature cml39 seeds was not sensitive to cold-stratification. In addition, germination of cml39 seeds was less sensitive than wild-type to inhibition by ABA or by treatments that impaired gibberellic acid biosynthesis. Tetrazolium red staining indicated that the seed-coat permeability of cml39 seeds is greater than that of wild-type seeds. RNA sequencing analysis of cml39 seedlings suggests that changes in chromatin modification may underlie some of the phenotypes associated with cml39 mutants, consistent with previous reports that orthologs of CML39 participate in gene silencing.  Aberrant ectopic expression of transcripts for seed storage proteins in 7-day old cml39 seedlings was observed, suggesting mis-regulation of early developmental programs.  Collectively, our data support a model where CML39 serves as an important Ca2+ sensor during ovule and seed development, as well as during germination and seedling establishment.

overall_design: Global gene expression profiles were compared between cml39 mutant and wild-type control seedlings (in duplicate).

first: Midhat

last: Ubaid


title: RNA splicing in the transition from B cells to antibody secreting cells

status: Public on Apr 19 2018

summary: The purpose of this study was to explore the splicing landscape in unstimulated versus stimulated B cells in both ELL2 sufficient and deficient mice.  This would allow us to see the magnitidue of splicing changes in the transition from unstimulated to stimulated B cells, as well as the importance of ELL2 in this process.

overall_design: We analyzed 15 mouse B cell samples.  Four of the samples were replicates for wild type unstimulated B cells, four were unstimulated ELL2-/- B cells, four were +LPS wild type stimulated B cells collected @ 72 hours, and the final three were +LPS ELL2-/- stimulated B cells collected @ 72 hours.


title: Characterization and therapeutic targeting of the miR-21/PPP2R2A/ERK molecular circuit in bladder cancer

city: Santa Monica

first: HSIAOWANG

last: CHEN

address: 2825 Santa Monica Blvd

department: Medicine

institute: UCLA

summary: MicroRNAs play an important role in the pathogenesis of different types of cancer including bladder cancer. MiR-21 has been identified to have an oncogenic function, while its inhibition suppresses tumor growth. Here, we followed an integrated bioinformatics and molecular analyses to identify the molecular mediators of miR-21 oncogenic function in bladder cancer and evaluate the therapeutic potential of a chemically-modified miR-21 inhibitor in bladder xenografts. MiR-21 expression was found to up-regulated in human bladder cancers relative to normal tissues and miR-21 inhibition suppressed bladder cancer cell properties, including growth, invasiveness and anchorage-independence. Intravenous administration of an antisense oligonucleotide against miR-21 harboring locked-nucleic-acid (LNA-miR-21) modifications blocked bladder tumor growth in vivo. Transcriptomic analysis of 28 bladder cancer cell lines revealed a gene signature that negatively correlated with miR-21 expression levels.  Bioinformatics and 3’UTR luciferase assay analyses revealed a direct interaction between miR-21 the 3’UTR of PPP2R2A gene. Inhibition of PPP2R2A expression induced bladder cancer growth, suggesting its tumor suppressor function. Gene profiling followed by IPA network analysis revealed that PPP2R2A regulates the ERK1/2 molecular network. Taken together, PPP2R2A is the functional mediator of miR-21 oncogenic activity on bladder cancer and LNA-miR-21 could have a therapeutic potential in bladder cancer patients.

overall_design:
The significantly different expressed genes are obtained by ANOVA using miR-21 levels as catagories in 28 Bladder Cancer cell lines based on the gene experssion microarray experiment.
PPP2R2A was found in the significantly different expressed genes in ANOVA analysis, having negative correlation with miR-21 expression levels.  This data provided the supportive evidence to be associated with the paper and suggests PPP2R2A function in tumor suppressor.

first: Alexandra

last: Drakaki

first: Hsiao-Wang

last: Chen

first: Judy

last: Dering

first: Dennis

last: Slamon


title: Circulating-cell free DNA pooled samples for epigenome-wide discovery of methylation biomarkers for colorectal cancer screening

status: Public on Apr 17 2018

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

summary: We explored the differential methylation patterns found in cfDNA between healthy controls (individuals with no colorectal findings, NCF) and patients with advanced neoplasia (advanced adenomas and colorectal cancer, AA andCRC) using pooled samples, to determine if pooled serum cfDNA samples can be used to search for non-invasive methylation biomarkers, as an affordable and efficient alternative to tissue biopsy. cfDNA was extracted from serum samples and methylation measurements were assessed with the Infinium MethylationEPIC BeadChip. Data was mainly preprocessed and analyzed with R/Bioconductor packages.

overall_design: Two independent pooled samples were constructed for each pathological group (NCF, AA and CRC) using equal amounts of cfDNA from 5 men and 5 women per pool. Genome-wide DNA methylation in the six pooled samples was analyzed with the Infinium MethylationEPIC BeadChip microarray, covering over 850,000 CpG sites across the genome.    Two independent pooled samples were constructed for each pathological group (NCF, AA and CRC) using equal amounts of ccfDNA from 5 men and 5 women per pool. Genome-wide DNA methylation in the six pooled samples was analyzed with the Infinium MethylationEPIC BeadChip microarray, covering over 850,000 CpG sites across the genome.

first: María

last: Gallardo-Gómez

first: Loretta

last: De Chiara


title: CG7358 mutant Drosophila melanogaster sequencing

status: Public on Apr 18 2018

city: Shanghai

first: Guo

last: Jian

address: Fenglin Road

department: Chinese Academy of Science

institute: Shanghai Institutes for Biological Sciences

summary: To understand the function of gene CG7358 in Drosophila melanogaster, including indentification of those genes whose expression levels or alternative splicing are affected by CG7358.

overall_design: 6 samples are analyzed, including 3 replicates for CG7358 mutant and the other 3 for wild type fly


title: Vex-seq: high-throughput identification of genetic variation impact on pre-mRNA splicing efficiency

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

summary: Vex-seq is a method developed to study the impact of genetic variants on pre-mRNA splicing efficiency

overall_design: Barcoded splice reporter plasmids are used to identify splicing efficiency using Illumina paired-end sequencing

first: Scott

last: Adamson

first: Lijun

last: Zhan


title: Circadian Clock- and Transcription-controlled Genome-wide Excision Repair of UV Damage in Arabidopsis

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

summary: We used the recently developed Excision Repair-sequencing (XR-seq) method to study genome-wide repair of UV-induced DNA damage in Arabidopsis. We found that the repair of cyclobutane pyrimidine dimers for a large fraction of the genome is controlled by the joint actions of the circadian clock and transcription by RNA polymerase II. Arabidopsis has a relatively compact genome, and a large fraction of the genes are controlled by the circadian clock. Our data on the interface of these two global regulatory systems reveal very strong repair preference of the transcribed strands of Arabidopsis genes, 10 to 30% of which are circadian time-dependent. Thus, throughout the day, Arabidopsis exhibits enormous dynamic range in repair to cope with exposure to sunlight.

overall_design: Examination of excision repair throughout the circadian cycle with 2 experiments each of which having 8 samples collected at ZT2, ZT5, ZT8, ZT11, ZT14, ZT17, ZT20, ZT23

first: Onur

last: Oztas

first: Christopher

middle: P

last: Selby

first: Aziz

last: Sancar


title: Alternate assembly of SDHA connects energy stress to metabolic checkpoint and DNA synthesis

status: Public on Apr 16 2018

city: Vestec by Prague

first: Jakub

last: Rohlena

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, CAS, v.v.i.

summary: Cell growth and survival depend on a delicate balance between energy production and synthesis of metabolites. We have discovered that an alternative mitochondrial complex II (CII) assembly, designated here as CIIlow, serves as a check-point for metabolite biosynthesis under bioenergetic stress, with cells suppressing their energy utilization by modulating DNA synthesis and cell cycle progression. Depletion of CIIlow leads to an imbalance in energy utilization and metabolite synthesis, as evidenced by recovery of the de novo pyrimidine pathway and unlocking cell cycle arrest from the S-phase. In vitro experiments are further corroborated by analysis of paraganglioma tissues from patients with sporadic, SDHA and SDHB mutations. These findings uncover a new core complex inside mitochondria that provides homeostatic control of cellular metabolism to reflect availability of energy, with SDHA being its central molecule.

overall_design: Parental MDAMB231 (MDA_) cells (duplicate) were compared with SDHB knockout (SDH_) cells (triplicate) and SDHB knockout cells with additional knockdown of SDHA (SH1_) cells (triplicate)

first: Pavel

last: Abaffy

first: Ravindra

last: Naraine

first: Silvia

last: Novais


title: microRNa expression profiling in adrenal myelolipoma, adrenocortical carcinoma and adrenocortical adenoma

status: Public on Apr 07 2018

city: Budapest

first: Abel

last: Decmann

address: Korányi str. 2a

department: Department of Internal Medicine and Oncology

country: Hungary

institute: Semmelweis University

summary: Background: Adrenal myelolipoma (AML) is a relatively common and invariably benign tumor composed of adipose tissue and hematopoietic elements. Due to the variable proportion of fat and hematopoietic elements, it is sometimes challenging to differentiate AML from adrenocortical carcinoma (ACC). MicroRNAs have been identified as promising biomarkers in many tumors, including adrenocortical neoplasms, but the microRNA expression of adrenal myelolipoma has not been investigated, yet. Aims: To perform a large scale microRNA expression profiling in adrenal myelolipoma, benign and malignant adrenocortical tumors to identify potential microRNA biomarkers. Methods: Next-generation sequencing (NGS) on 30 formalin-fixed paraffin-embedded archived tissue samples (discovery cohort: 10 adrenocortical adenoma (ACA), 10 ACC and 10 myelolipoma) was performed by Illumina MiSeq. Significantly differentially expressed microRNAs were validated by real-time RT-qPCR in an independent validation cohort comprised of 10 ACA, 10 myelolipoma and 9 ACC samples. Results:  We have found relative overexpression of miR- 451a, miR-486-5p, miR-363-3p and miR-150-5p in myelolipoma compared to the other two tumor groups by NGS. For ACC, we have found  up-regulation of miR-184, miR-483-5p, miR-431-5p and miR-183-5p compared to myelolipoma and ACA. Validation by RT-qPCR, confirmed significant overexpression of miR-451a, miR-486-5p and miR-150-5p in myelolipomas relative to ACA and ACC, whereas  significant overexpression of miR-184 and miR-183-5p was confirmed in ACC relative to the other 2 groups. The overexpression of miR-483-5p has not turned out to be significant in ACC relative to myelolipomas in the validation cohort. Conclusions: Overexpressed miR-451a, miR-486-5p and miR-150-5p might be potential tissue markers of adrenal myelolipoma. The lack of significance in the expression of miR-483-5p between ACC and myelolipoma is remarkable, as miR-483-5p has been considered to be the best marker of adrenal malignancy to date.

overall_design: Altogether 30 samples were investigated by high-throughput microRNA expression profiling

first: Peter

last: Igaz


title: Extensive profiling of Foxk1 binding in genomic DNA

status: Public on Apr 05 2018

first: Long

last: He

department: cancer center

institute: WCMC

summary: We report DNA binding of a  transcription factor Foxk1 in globle genomic DNA

overall_design: Chromosome Immunoprecipitation was performed with Foxk1 and IgG antibody and the DNA fragment were subjected to NGS

first: John

last: Blenis

first: Xin

last: Wang


title: Correlated metabolomic, genomic, and histologic phenotypes in histologically normal breast tissue

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Dr

department: Epidemiology

institute: UNC

summary: By the integrated analyses of histological, metabolomic and transcriptional data, we characterized two distinct subtypes of non-malignant breast tissue

overall_design: Unsupervised analysis of normal breast tissue from patients with invasive breast cancer and reductions

first: Xuezheng

last: Sun

first: Delisha

last: Stewart

first: Susan

last: Sumner


title: HOXA5 is a survival locus associated with chromosome 7 gain in IDH-wildtype glioblastoma

status: Public on Apr 09 2018

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Glioblastomas (GBMs) are divided into CpG Island Methylator Phenotype (CIMP) and non-CIMP tumors. Non-CIMP GBMs derive from cells with non-disjunction of chromosome (chr7) and chromosome 10 (chr10), resulting in chr7 gain and chr10 loss, while CIMP GBMs have mutations in isocitrate dehydrogenase 1 or 2 (IDH1/2). Gain of chr7 is largely driven by PDGFA, but other genes on chr7 are likely to contribute to fitness gains and aggressiveness of these GBMs. We computationally investigated genes on chr7 whose gene expression correlated with survival, identifying HOXA5 as a potential driver of proneural gliomagenesis. Using a combination of human GBM cells and mouse PDGF-driven gliomas, we showed that HOXA5 drives increased proliferation and radiation resistance in culture and in vivo. These phenotypes appear to be in part due to effects on p53 and other apoptosis-related genes.

overall_design: In order to determine whether elevated HOXA5 gene expression is causally related to aggressiveness of non-CIMP PN GBM, we used a PDGF-driven PN GBM mouse model based on the RCAS/tva system to perform gain of function analysis for HOXA5.

first: Patrick

middle: J

last: Cimino

first: Youngmi

last: Kim

first: Hua-Jun

last: Wu

first: Jes

last: Alexander

first: Hans-Georg

last: Wirsching

first: Frank

last: Szulzewsky

first: Ken

last: Pitter

first: Tatsuya

last: Ozawa

first: Jiguang

first: Julio

last: Vazquez

first: Raul

last: Rabadan

first: Ross

last: Levine

first: Franziska

last: Michor

first: Eric

last: Holland


title: Epigenome analysis of CD4 T cells from treated and untreated patients with multiple sclerosis (MS)

status: Public on Apr 03 2018

city: NY

first: Achillefs

last: Ntranos

address: 5 E 98th St, CGD MS Center, 1st floor

institute: Icahn School of Medicine at Mount Sinai

summary: Genome wide DNA methylation profiling of CD4 T cells from treated and untreated patients with multiple sclerosis. The Illumina InfiniumEPIC methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs of CD4 T cells from patients with multiple sclerosis.

overall_design:
Bisulphite converted DNA from CD4 T cells that were positively isolated with magnetic beads from treated and untreated patients with multiple sclerosis.

Therapy abbreviations:

Naive=untreated/treatment naive MS patients
FAE=MS patients treated with fumaric acid esters, such as dimethyl fumarate
GA=MS patients treated with glatiramer acetate

first: Achilles

first: Vasilis

first: Ye

last: He

first: Valentina

last: Bonnefil

first: Jia

last: Liu

first: Yunjiao

last: Zhu

first: Rachel

last: Brandstadter

first: Corey

last: Watson

first: Andrew

last: Sharp

first: Ilana

last: Sand

first: Patrizia

last: Casaccia


title: Regulation of brown fat homeostasis by H19 lincRNA [II]

status: Public on Jun 26 2018

city: Cologne

first: Jan-Wilhelm

last: Kornfeld

state: NRW

address: Gleueler Strasse 50

institute: Max-Planck-Institute for Metabolism Research

summary: Increases in organismal energy expenditure, as during cold exposure or exercise training, can improve metabolic health. This process is dependent also on brown adipose tissue (BAT) thermogenesis in mice and humans. Understanding and harnessing the molecular circuits activating BAT function is thus of great interest to devise novel approaches to counteract obesity and type 2 diabetes (T2D). In contrast to protein-coding genes, the role of long noncoding RNAs (lncRNAs) during BAT differentiation and function remains poorly understood. To address this, we performed RNA-Seq and identified the maternal allele-specific (imprinted) lncRNA H19 increased upon cold-mediated BAT activation and decreased upon chronic diet-induced obesity (DIO) BAT dysfunction. An inverse correlation of H19 expression with body-mass indices (BMI) was observed in a cohort of >160 lean and obese humans. H19 silencing impaired adipogenesis and oxidative metabolism in brown but not white adipocytes, while H19 gain-of-function increased nutrient oxidation and mitochondrial respiration, thus supporting a BAT-regulatory role for H19. In vivo H19 overexpression protected against DIO, improved insulin sensitivity and rescued DIO-mediated defects in energy expenditure in conjunction with improved mitochondrial biogenesis. In contrast, BAT-selective H19 loss decreased energy dissipation and sensitized towards high fat diet-induced body weight gains. When investigating other parent-of-origin specific, monoallelically expressed genes, we strikingly observed that paternally expressed genes (PEGs) were largely absent from BAT and coordinately downregulated during brown adipogenesis, whilst the same gene set was robustly expressed in white fat stores, a phenomenon not observed for maternally expressed genes (MEGs). Using H19 loss- and gain-of-function in primary adipocytes, we demonstrate that H19 acts as ‘PEG gatekeeper’ in brown, not white adipocytes, potentially due to recruitment of PEG-inactivating H19-MBD1 complexes in mature brown adipocytes. The exclusive PEG expression in white adipose tissuer could underly the observed susceptibility of mice exhibiting high PEG abundances towards DIO-evoked weight gain. Collectively, we here define novel roles for the imprinted lncRNA H19 in brown adipocyte differentiation and function in vitro, control of energy expenditure in vivo and repression of paternal allele-specific gene expression in BAT. This has far-reaching implications for our understanding of how monoallelical gene expression affects metabolic eustasis in both rodent models and, potentially, human patients.

overall_design: Examination of the effects of H19 silencing in adipose stromal cells derived from two different adipose depots (brown and white fat), in triplicates, by Illumina-based RNA-Seq

first: M

last: Bilban

last: Jeitler


title: Gene expression profiling of porcine skeletal muscle satellite cells after challenge with poly I:C

status: Public on Mar 31 2018

city: Wuhan

first: Thuy Nhien

last: Tran Thi

state: Hubei

address: Shizishan

institute: Huazhong Agricultural University

summary: Porcine satellite cells play a vital role in the construction, development, and self-renewal of skeletal muscle. In this study, porcine satellite cells were exposed to mimic viral infection poly (I:C) during proliferation and differentiation phases at 0h, 12h, 24h and 48h time points. The untreated and treated porcine satellite cells during proliferation and differentiation phases were further analyzed by RNA sequencing technology. In the proliferation and differentiation phases of porcine satellite cells grown under poly (I:C), 88, 119, 104 and 95 genes were differentially expressed in 0h – 12h treated, 12h – 24h treated, 0h – 24h treated and 24h – 48h untreated comparison libraries, respectively. The GO terms analysis results showed that in the proliferation phase of treated porcine satellite cells, the up-regulated genes related to the immune system were highly expressed. In addition, the gene expression associated with muscle structure development, response to growth factor emerged in the differentiation phase of untreated porcine satellite cells. The biological pathways associated with Influenza A, Toll-like signaling as well as chemokine signaling were revealed through poly (I:C) stimulation of porcine satellite cells. The differentially expressed genes were confirmed by quantitative real-time PCR. Our findings expanded the understanding of gene expression and signaling pathways about the infiltrated mechanism of the virus into porcine skeletal muscle satellite cells.

overall_design: total RNA profiles of untreated and treated poly (I:C) conditions were generated by sequencing, in triplicate, using Illumina Hiseq 4000 platform.

first: Thuy

last: Nhien

first: Tran

last: Thi

first: Shuhong

last: Zhao


title: PCALCL cell line Mac1:vehicle control vs.shEZH2

city: Beijing

first: Yi

last: Shengguo

address: No.1 Xi anmen Street

institute: the first hospital of Peking University

summary: Transcriptional profiling of human PCALCL cell line Mac1 comparing cells transfected with vehicle control with shEZH2 cells. Previous study have shown the involvements of EZH2 in T cell development and hematopoietic malignancies of T-cell origin. Objective was to explore the action of EZH2 in the pathogenesis of cutaneous T-cell lymphoma(CTCL).

overall_design: Two-condition experiment, EZH2-VC Mac1 vs. shEZH2 Mac1 cells. Biological replicates: 3 control replicates, 3 shEZH2 replicates.

first: Shengguo

last: Yi

first: Yang

last: Wang


title: Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay in E. coli

status: Public on Apr 01 2018

city: Los Angeles

first: Guillaume

last: Urtecho

state: CA

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

summary: We built and tested a library of 10,898 σ70 promoter variants consisting of all combinations of a set of eight -35 elements, eight -10 elements, three UP elements, eight spacers, and eight backgrounds. Using a Massively Parallel Reporter Assay, we measure expression of all promoters and evaluate how individual promoter elements contribute to expression.

overall_design: We measure expression of all promoters and evaluate how individual promoter elements contribute to expression.

first: Arielle

middle: D

last: Tripp

first: K

last: Insigne

first: Hwangbeom

last: Kim

first: Sriram

last: Kosuri


title: Gene expression analisys of GD2+ cells from metastatic NB, unselected bone marrow from metastatic NB, primary tumors from stage 4 NB (alive and dead at 5 years of follow-up) and primary tumor from localized NB

status: Public on Mar 29 2018

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

institute: IRCCS AOU San Martino-IST

summary: Metastases in the bone marrow (BM) are grim prognostic factors in patients with neuroblastoma (NB). In spite of extensive analysis of primary tumor cells from high- and low-risk NB patients, a characterization of freshly isolated BM-infiltrating metastatic NB cells is still lacking. Our aim was to identify proteins specifically expressed by metastatic NB cells, that may be relevant for prognostic and therapeutic purposes. Metastatic NB cells were freshly isolated from patients’ BM by positive immunomagnetic bead manipulation using anti-GD2 monoclonal antibody. Unselected BM samples from patients with metastatic NB were also included. Gene expression profiles were compared with those obtained from archived NB primary tumors from patients with 5y-follow-up. After validation by RT-qPCR, expression/secretion of the proteins encoded by the up-regulated genes in the BM-infiltrating NB cells was evaluated by flow cytometry and ELISA.  Compared to primary tumor cells, BM-infiltrating NB cells down-modulated the expression of CX3CL1, AGT, ATP1A2 mRNAs, whereas they up-regulated several genes commonly expressed by various lineages of BM resident cells. BM-infiltrating NB cells expressed indeed the proteins encoded by the top-ranked genes, S100A8 and A9 (calprotectin), CD177 and CD3, and secreted the CXCL7 chemokine. BM-infiltrating NB cells also expressed CD271 and HLA-G. We have identified proteins specifically expressed by BM-infiltrating NB cells. Among them, calprotectin, a potent inflammatory protein, and HLA-G, endowed with tolerogenic properties facilitating tumor escape from host immune response, may represent novel  biomarkers and/or targets for therapeutic intervention in high-risk NB patients.

overall_design: This is an update of the previous GEO submission (GSE25623). We performed a gene expression analysis on 57 samples: 11 GD2 positive cells from metastatic NB,  9 bone marrow from metastatic NB, 13 primary tumors from stage 4 NB alive at 5 years of follow-up, 14 primary tumors from stage 4 NB dead at 5 years of follow-up, and 10 primary tumors from NB patients with localized disease

first: Paola

last: Scaruffi

first: Luca

last: Persico

first: Corrado

last: Lagazio

first: Fabio

last: Morandi

first: Maria

middle: V

last: Corrias


title: Expression data from RH30 vector and RH30 IκBα SR cells

status: Public on Mar 30 2018

city: Columbus

first: Peter

last: Yu

state: OH

address: 460 W 12th Ave

institute: Ohio State University

summary:
Classical NF-κB activity can be inhibited by overexpression of the IκBα super repressor (SR). To determine the role of NF-κB in rhabdomyosarcoma cells, we overexpressed the IκBα SR in RH30 rhabdomyosarcoma cells.
IκBα SR was overexpressed in RH30 cells. RH30 vector cells were used as control group.

overall_design: Triplicates of each group were cultured. Total RNA was isolated by Trizol extractions (Invitrogen, Carlsbad, CA). Analysis used Affymetrix Human Transcriptome 2.0 Array

middle: Y

first: Denis

middle: C

last: Guttridge


title: Gene expression profiles of RALD iPSCs cultured with or without bFGF

city: Tsukuba

first: Kenji

last: Kubara

state: Ibaraki

address: Tokodai 5-1-3

department: Tsukuba Research Laboratories

country: Japan

institute: Eisai Co., Ltd.

summary: We investigated roles of KRAS on stemness maintenance in the context of induced pluripotent stem cells (iPSCs) using isogenic KRAS mutant (G13C/WT) and wild-type (WT/WT) iPSCs from the same RAS-associated autoimmune lymphoproliferative syndrome-like disease (RALD) patients. Microarray analysis was conducted to compare gene expression profiles of WT/WT and G13C/WT iPS cells cultured with or without bFGF. Expression of stemness markers including POU5F1 and NANOG, which is indicative of an undifferentiated state, was highly maintained in G13C/WT iPSCs, but not in WT/WT iPSCs, under bFGF depletion, indicating enhanced self-renewal of iPSCs by the oncogenic KRAS.

overall_design: To investigate the changes of undifferentiation and differentiation markers between KRAS mutant and wild-type iPSCs under the presence or absence of bFGF, the iPSCs were cultured with or without bFGF for 5 days. Two clones were used for each genotype, resulting in total 8 conditions.

first: Kazuto

last: Yamazaki

first: Yasuharu

last: Ishihara

first: Huan

last: Lin

first: Masashi

last: Ito

first: Kappei

last: Tsukahara

first: Masatoshi

last: Takagi

first: Makoto

last: Otsu


title: Development of plasma cell-prone germinal center B cells

city: Suita

first: Eri

last: Nishiyama

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research

institute: Riken

summary: Higher- or lower-affinity GC B cells are directed to plasma cell or recycling GC cell fates; however, how commitment to the plasma cell fate takes place is unclear. By using the level of Bcl6 as a marker, we found that a population of light zone (LZ) GC cells, Bcl6loCD69hi with IRF4 and higher-affinity BCRs or Bcl6hiCD69hi with lower- affinity BCRs, favored the plasma cell or recycling GC cell fate, respectively. Mechanistically, CD40 acted as a dose-dependent regulator for Bcl6loCD69hi cell formation. Furthermore, we found that ICAM1 and SLAM levels on Bcl6loCD69hi cells were higher than on Bcl6hiCD69hi cells, thereby affording more stable TFH-GC B cell contacts, while attenuating this contact down-regulated IRF4. These data support the model that commitment to the plasma cell begins in the GC, and suggest that stability and possibly duration of TFH-GC B cell contacts are key for formation of plasma cell-prone precursor GC cells.

overall_design: mRNA profiles of GC B cell subsets and GC-derived plasmablast were generated by barcode-based digital RNA sequencing.

first: Wataru

last: Ise

first: Katsuyuki

last: Shiroguchi

first: Tomohiro

last: Kurosaki


title: An Intermediate Pluripotent State Controlled by microRNAs is Required for the Naïve to Primed Stem Cell Transition

city: Boston

first: Peng

last: Du

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

summary: The embryonic stem cell (ESC) transition from naive to primed pluripotency is marked by major changes in cellular properties and developmental potential. ISY1 is implicated in miRNA biogenesis yet its widespread role and relevance to ESC biology remain unknown. Here we find that highly dynamic ISY1 expression during the naïve to primed ESC transition defines a unique phase of ‘poised’ pluripotency characterized by distinct miRNA and mRNA transcriptomes and widespread poised cell contribution to mouse chimeras. Loss- and gain-of-function experiments reveal that ISY1 promotes exit from the naïve state, is necessary and sufficient to induce and maintain poised pluripotency, and that persistent ISY1 overexpression inhibits the transition from the naïve to the primed state. We identify a large subset of ISY1-dependent miRNAs that can rescue the inability of miRNA-deficient ESCs to establish the poised state and transition to the primed state. Thus, dynamic ISY1 regulates poised pluripotency through miRNAs to control ESC fate.

overall_design: mouse ESCs with ISY1 overexpression and depletion were used for EB and EpiLC differentiation. PolyA(+) RNA-seq and small RNA-seq were then performed from the samples at different time points to measure the mRNA and miRNA transcriptome changes during differentiation.

first: Richard

last: Gregory


title: Microprocessor depends on hemin to recognize the apical loop of primary microRNA

status: Public on Mar 26 2018

city: Seoul

first: Joha

last: Park

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Microprocessor, which consists of a ribonuclease III DROSHA and its cofactor DGCR8, initiates microRNA (miRNA) maturation by cleaving primary miRNA transcripts (pri-miRNAs). We recently demonstrated that the DGCR8 dimer recognizes the apical elements of pri-miRNAs, including the UGU motif, to accurately locate and orient Microprocessor on pri-miRNAs. However, the mechanism underlying the selective RNA binding remains unknown. In this study, we find that hemin, a ferric ion-containing porphyrin, enhances the specific interaction between the apical UGU motif and the DGCR8 dimer, allowing Microprocessor to achieve high efficiency and fidelity of pri-miRNA processing in vitro. Furthermore, by generating a DGCR8 mutant cell line and carrying out rescue experiments, we discover that hemin preferentially stimulates the expression of miRNAs possessing the UGU motif, thereby conferring differential regulation of miRNA maturation. Our findings reveal the molecular action mechanism of hemin in pri-miRNA processing and establish a novel function of hemin in inducing specific RNA-protein interaction.

overall_design: 17 Samples

first: Tuan

last: Nguyen

first: Narry

last: Kim


title: Microarray data of osteoblast from sham, ovariectomized mice (OVX) with and without treadmill training

status: Public on Mar 10 2018

city: Pu-Tzi

first: Wei-Bin

last: Hsu

state: Chia-Yi

address: No. 6, West Section, Chia-Pu Road

department: Sports center

country: Taiwan

institute: Chang Gung Memorial Hospital, Chiayi,

summary: Physical exercise has a positive effect on increasing or maintaining BMD in both pre-menopausal and postmenopausal women. The underlying mechanisms of physical exercise on the osteoblast (OB) in estrogen deficiency are not well understood. We used microarray to analyze the transcriptome of OB in ovariectomized mice, with or without physical exercise. intervention.

overall_design: Six-week-old C57BL/6J female mice were applied to  sham or ovariectomy surgery.The sham surgical procedures were the same as those used in ovariectomy, with the exception of leaving the ovaries intact. The ovariectomized mice were randomly divided into an exercise group (OVX+T) and a non-exercise group (OVX). Mice assigned to the exercise group (OVX+T) were given treadmill training 5-days/week for 8 weeks, with each training session lasting 60 minutes. The treadmill was run at 10 m/min with an incline angle of 10 degrees.

first: Robert

middle: W