title: Investigating the mechansisms associated with Folfiri-induced muscle wasting in normal mice

status: Public on May 18 2016

city: Aurora

first: Andrea

last: Bonetto

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary:
Purpose of the study: the goal of this study was to use Next-generation sequencing to investigate the gene expression profile of skeletal muscle from mice exposed to chemotherapy (Folfiri) for up to 5 weeks.
Methods: Standard methods were used for polyA mRNA-seq library construction, EZBead preparation and Next-Gen sequencing, based on Life Technologies SOLiD5000xl system. Briefly, one microgram total RNA per sample was applied for library preparation. PolyA mRNA was first captured using the standard protocol of Dynabeads® mRNA DIRECT™ Micro Kit (Life Technologies, #61021). Following the enrichment of polyA mRNA, the cDNA library was prepared and barcoded per sample using the standard protocol of SOLiD Total RNA-seq Kit (Life Technologies, #4445374). Each barcoded library was quantified by Bioanalyzer High Sensitivity DNA chip (Agilent, #5067-4626) and pooled in equal molarity. EZBead preparation, bead library amplification, and bead enrichment were then conducted using Life Technologies EZ Bead™ E80 System (Life technologies, #4453095). Approximately four hundred forty million library-enriched beads per lane were deposited onto a SOLiD5500xl FlowChip (6 lanes/chip). Finally sequencing by ligation was carried out using standard single-read, 5’-3’ strand-specific sequencing procedure (75b-read) on SOLiD5500xl Sequencer. The resulting 75 bp solid reads were mapped to Mus musculus mm9 reference genome using in-house mapping pipelines that utilizes bfast-0.7.0a [67]. In brief, using our RNA-seq pipeline, low quality reads and reads mapped to rRNA/tRNAs were first discarded. The remaining reads were mapped to reference genome mm9 and a splice-junction library, respectively; the genomic and splice-junction library mapping were merged at the end. The gene based expression levels were calculated using bamutils from NGSUtils based on the RefSeq gene annotation of mm9. Differential expression of genes across different treatments was determined with edgeR
Results: Gene expression profiling, performed by means of RNA-Sequencing analysis, identified a limited number of genes that were significantly modulated (False Discovery Rate < 0.05) following Folfiri administration. Interestingly, the pathway analysis showed marked down-regulation of the regulators of mitochondrial metabolism Ucp1, Cidea1 and Acot2, as well as the marker of muscle cell proliferation/pluripotency Fhl3 . Further, we found increased expression of regulators of lipid metabolism and transport (such as Fabp1, Apoa1, Apob, Apoa2, Alb, Prkcz and Scd2) as well as acute phase response proteins (such as Alb, Fga and Fgb), and members of the PPAR signaling and markers of the Energy metabolism (such as Dnah5) were reported .
Conclusions: Our study represents the first gene expression profiling of muscle from mice exposed to chemotherapy. The findings from our study identified several signaling pathways that were modulated following chemotherapy administration. These results will contribute to identify new modulators of muscle wasting associated with Folfiri administration, that might also represent putative new targets of interventions.

overall_design: Next-generation sequencing of RNA extracted from quadriceps muscle of CD2F1 male mice exposed to either Folfiri (a combination of 5-FU, Leucovorin and CPT-11) or vehicle alone (n=4) for up to 5 weeks.


title: Characterizing the transcriptional adaptation of Staphylococcus aureus to stationary phase growth

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

country: USA

institute: University of South Florida

type: Expression profiling by high throughput sequencing

summary: Staphylococcus aureus is an important human pathogen that causes life-threatening infections, and is resistant to the majority of our antibiotic arsenal. This resistance is complicated by the observation that most antibacterial agents target actively growing cells, thus, proving ineffective against slow growing populations, such as cells within a biofilm or in stationary phase. Recently, our group generated updated genome annotation files for S. aureus that not only include protein-coding genes but also regulatory and small RNAs. As such, these annotation files were used to perform a transcriptomic analysis in order to understand the metabolic and physiological changes that occur during transition from active growth to stationary phase; with a focus on sRNAs. We observed ∼24% of protein-coding and 34% of sRNA genes displaying changes in expression by ≥3-fold. Collectively, this study adds to our understanding of S. aureus adaptation to nutrient-limiting conditions, and sheds new light onto the contribution of sRNAs to this process.

overall_design: Bacterial cells were grown in TSB medium at 37°C with shaking for 3h (exponential growth phase) or 16h (stationary growth phase).

first: William

middle: H

last: Broach

first: Lindsey

middle: N

last: Shaw


title: Type IV pili promote early biofilm formation by Clostridium difficile

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Transcriptional analysis of Clostridium difficile R20291 in biofilm formation, planktonic state and grown on blood agar

overall_design: RNA sequencing was performed on Clostridium difficile R20291 in three different conditions: Biofilm formation, plantonic state and grown on blood agar plates. Each condtion has 3 replicates.

first: Grace

middle: A

last: Maldarelli

first: Kurt

last: Piepenbrink

first: Alison

middle: J

last: Scott

first: Jeffrey

last: Freiberg

first: Yang

last: Song

first: Yvonne

last: Achermann

first: Robert

middle: K

last: Ernst

first: Mark

middle: E

last: Shirtliff

first: Eric

last: Sundberg

first: Michael

middle: S

last: Donnenberg

first: Erik

middle: C

last: von Rosenvinge


title: The Glioma-Infiltrating T Cell Receptor Repertoire

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: While immune signaling has emerged as a defining feature of the glioma microenvironment, local selection of responding T cells and their anti-tumor potential as a population are difficult to measure directly in patients. High-throughput sequencing of T cell receptor repertoires (TCRseq) provides a population-wide statistical description of how T cells respond to disease.  Here, we define new immunophenotypes in glioma based on TCRseq and RNA-Seq of tumor tissue, non-neoplastic brain tissue, and peripheral blood from patients. Using information theory, we characterize antigen-driven selection in glioma and its relationship with the expression of distinct immune-functional pathways in the tumor microenvironment. Finally, we identify a strong relationship between usage of certain TCR in peripheral blood and the divergence of the infiltrating T cell population from the peripheral repertoire. We anticipate that these immunophenotypes will be foundational to monitoring and predicting response to anti-glioma vaccines and immunotherapy.

overall_design: We characterized the T cell receptor (TCR) repertoires of 11 high-grade glioma patients, three low-grade glioma patients, and thee non-glioma patients by TCRseq of brain-infiltrating T cells and matching peripheral blood. In addition, we obtained gene expression profiles from brain tissue of each patient by RNA-Seq.  We additionally measured the TCR repertoires exclusively from peripheral blood of one additional non-glioma patient.


title: Memory CD8+ T cells require stress-levels of acetate for optimal function

city: Basel

first: Christoph

last: Hess

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University Basel

summary: How systemic metabolic alterations during acute infections impact immune-cell function remains poorly understood. Hess and colleagues demonstrate that acetate rapidly increases during infections, which drives acetylation of GAPDH in memory CD8+ T cells and thereby catalyzes the rapid recall response.

overall_design: Comparison of mRNA profile of control vs. 3d acetate exposed memory OT-I T cells

first: Maria

middle: L

last: Balmer

last: Ma

first: Glenn

middle: R

last: Bantug

first: Jasmin

last: Grählert

first: Simona

last: Pfister

first: Timo

last: Glatter

first: Annaise

last: Jauch

first: Sarah

last: Dimeloe

first: Emma

last: Slack

first: Philippe

last: Dehio

first: Magdalena

last: Krzyzaniak

first: Carolyn

middle: G

last: King

first: Anne-Valérie

last: Burgener

first: Marco

last: Fischer

first: Leyla

last: Develioglu

first: Réka

last: Belle

first: Mike

last: Recher

first: Weldy

middle: V

last: Bonilla

first: Daniel

middle: D

last: Pinschewer

first: Andrew

last: Macpherson

first: Siegfried

last: Hapfelmeier

first: Russell

last: Jones


title: A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus

status: Public on May 19 2016

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

summary: During vertebrate limb development, Hoxd genes are regulated following a bimodal strategy involving two topologically associating domains (TADs) located on either side of the gene cluster. These regulatory landscapes alternatively control different subsets of Hoxd targets, first into the arm and, subsequently, into the digits. We studied the transition between these two global regulations, a switch that correlates with the positioning of the wrist, which articulates these two main limb segments. We show that the HOX13 proteins themselves help switch off the telomeric TAD, likely through a global repressive mechanism. At the same time, they directly interact with distal enhancers to sustain the activity of the centromeric TAD, thus explaining both the sequential and exclusive operating processes of these two regulatory domains. We propose a model whereby the activation of Hox13 gene expression in distal limb cells both interrupts the proximal Hox gene regulation and re-enforces the distal regulation. In the absence of HOX13 proteins, a proximal limb structure grows without any sign of wrist articulation, likely related to an ancestral fish-like condition.

overall_design: RNA-seq analysis of proximal and distal forelimbs  from E12.5 wt or Hoxa13-/-;Hoxd13-/- mutant embryos

first: L

last: Beccari

first: J

last: Woltering

first: D

last: Duboule


title: Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts

city: Warsaw

first: Tomasz

middle: Wojciech

last: Turowski

address: Pawinskiego 5a

department: Laboratory of Transcription Mechanisms

country: Poland

institute: Insitute of Biochemistry and Biophysics PAS

summary: RNA polymerase III (RNAPIII) synthesizes a range of highly abundant small stable RNAs, principally pre-tRNAs. Here we report the genome-wide analysis of nascent transcripts attached to RNAPIII under permissive and restrictive growth conditions. This revealed strikingly uneven polymerase distributions across transcription units, generally with a predominant 5´ peak. This peak was higher for more heavily transcribed genes, suggesting that initiation site clearance is rate limiting during RNAPIII transcription. Down-regulation of RNAPIII transcription under stress conditions was found to be uneven; a subset of tRNA genes showed low response to nutrient shift or loss of the major transcription regulator Maf1, suggesting potential “housekeeping” roles. Many tRNA genes were found to generate long, 3´-extended forms due to read-through of the canonical poly(U) terminators. The degree of read-through was anti-correlated with the density of T-residues in the coding strand, and multiple, functional terminators can be located far downstream. The steady-state levels of 3´-extended pre-tRNA transcripts are low, apparently due to targeting by the nuclear surveillance machinery; especially the RNA-binding protein Nab2, cofactors for the nuclear exosome and the 5´-exonuclease Rat1.

overall_design: CRAC protocol performed on samples containing HTP-tagged proteins: Rpc160(Rpo31), Nab2, Rrp44(Dis3), Rrp6 and Mtr4. Rpc-160-bound RNAs were analyzed in wildtype and maf1 mutant cells and after a shift to medium containing glycerol.

middle: W

first: Ewa

last: Makała

first: Clementine

last: Delan-Forino

first: Camille

last: Sayou

last: Boguta

first: David

last: Tollervey


title: Gene expression alterations in Dnmt3aKO/FLT3-ITD leukemia

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

summary: We assessed global gene expression profiles in two mouse models of oncogenic FLT3-driven leukemia in the presence and absence of Dnmt3a.

overall_design: Mouse mRNA profiles of Dnmt3aKO/FLT3-ITD leukemias, FLT3-ITD leukemias, normal CD4+/CD8+ thymocytes, Dnmt3aKO thymocytes, heterozygous Dnmt3a/heterozygous Flt3-ITD knockin leukemia, and heterozygous Flt3-ITD knockin pre-leukemic bone marrow cells were obtained by sequencing on Illumina HiSeq 2000 or 2500.

first: Benjamin

last: Rodriguez

first: Wei

last: Li


title: Arabidopsis thaliana Col-0 inflorescence small RNAs

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA sequences from Arabidopsis thaliana Col-0 inflorescence tissues of three biological replicates. The data were analyzed to identify non-templated nucleotides in Arabidopsis small RNAs.

overall_design: Inflorescence samples are collected from three biological replicates of Col-0 wild-type Arabidopsis plants.

first: Feng

last: Wang


title: CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

summary: Capture Hi-C (CHi-C) is a state-of-the art method for profiling chromosomal interactions involving targeted regions of interest (such as gene promoters) globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model, and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments, in which many spatially dispersed regions are captured, such as in Promoter CHi-C. We implement these procedures in CHiCAGO (http://regulatorygenomicsgroup.org/chicago), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Three human CHi-C biological replicates were generated (comprising 1, 2and 3 technical replicates). Two mouse CHi-C biological replicates were generated (both comprising three technical replicates) and a mouse Hi-C dataset. The publicly available HiCUP pipeline (doi: 10.12688/f1000research.7334.1) was used to process the raw sequencing reads. This pipeline was used to map the read pairs against the mouse (mm9) and human (hg19) genomes, to filter experimental artefacts (such as circularized reads and re-ligations), and to remove duplicate reads. For the CHi-C data, the resulting BAM files were processed into CHiCAGO input files, retaining only those read pairs that mapped, at least on one end, to a captured bait. CHiCAGO then identified Hi-C restriction fragments interacting, with statistical significant, to captured baits.

first: Jonathan

last: Cairns

first: Paula

last: Freire-Pritchett

first: Csilla

last: Várnai

first: Andrew

last: Dimond

first: Vincent

last: Plagnol

first: Daniel

last: Zerbino

first: Stefan

last: Schoenfelder

first: Biola-Maria

last: Javierre

first: Cameron

last: Osborne

first: Peter

last: Fraser

first: Mikhail

last: Spivakov


title: Molecular profiling of mouse Dnmt3a/FLT3-ITD leukemia models

first: Margaret

last: Goodell

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

city: Royal Parade

last: Keniry

state: Victoria

department: Molecular Medicine

country: Australia

institute: The Waler and Eliza Hall Institute of Medical Research

summary:
Purpose: The aim of this study was to determine the DNA methylation state of wildtype female mouse embryonic fibroblasts with nonsilencing shRNA mediated knockdown and Setdb1 geneTrap heterozygous cells with Setdb1 shRNA mediated knockdown.
Methods: Enhanced Reduced Representation Bisulfite Libraries (eRRBS) were produced as previously descirbed (Akalin et al. 2012). Libraries were pooled and sequenced on the Illumina HiSeq 2000 platform for 100 bp single-end reads with dark cycle parameters (Boyle et al. 2012). Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. Real-time base calling on the HiSeq instrument computer was performed with the RTA software. Illumina CASAVA1.8 pipeline was used to generate the sequence data.

overall_design:
Determine the DNA methylation state of mouse embryonic fibroblasts (MEFs) with wildtype MEFs and nonsilencing shRNA mediated knockdown or Setdb1 geneTrap heterozygous MEFs with Setdb1 shRNA mediated knockdown.
Single-end with dark cycle protocol (Boyle et al. 2012)


title: Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research


title: RNA-seq identifies novel lncRNAs involved in vascular smooth muscle cell proliferation

city: Glasgow

first: Rachel

last: Dakin

address: 126 University Place

department: ICAMS

institute: University of Glasgow

summary: Smooth muscle cell (SMC) phenotypic switching from a contractile to a synthetic state is implicated in diverse vascular pathologies, including neointimal formation. This study was designed to identify lncRNAs that may play a role in vascular pathologies. Primary smooth muscle cells cultured from surplus human saphenous vein tissue were treated with inflammatory and proliferative stimuli, IL1α and PDGF, for 72h and RNA extracted for RNA-sequencing. Using edgeR processed data we found expression of many lncRNAs was altered following treatment and could play a role in vascular disease.

overall_design: 4 groups of samples, n= 3/group each replicate using cells cultured from a different venous patient sample. Cells were quiesced in 0.2% serum for 48h followed by addition of 10ng/ml IL1α , 20ng/ml PDGF or both 10ng/ml IL1α and 20ng/ml PDGF together. Cells were collected after 72h and RNA extracted using Qiagen RNeasy kits. RNA-sequencing was carried out by Beckman Coulter Genomics on the r-RNA depleted fraction.

last: Baker

last: Ballantyne


title: Genome-wide maps in PDGFB-induced glioma

status: Public on May 17 2016

city: Cincinnati

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: We performed genome-wide profiling of oligodendrocyte lineage transcription factor 2 (Olig2) and other histone markers in platelet-derived growth factor subunit B (PDGFB)-induced glioma and genome-occupancy analyses coupled with transcriptome profiling to reveal gene regulatory network.

overall_design: Examination of Olig2, H327Ac, and H3K4me3 genome-wide occupancy in PDGFB-induced Ctrl-T and Olig2cKO brain tumors (gliomas).

first: F

first: C

last: Zhao

first: R


summary:
Purpose: The aim of this study was to profile the transcriptome of differentiating embryonic stem cells (ES) with nonsilencing shRNA mediated knockdown and Setdb1 geneTrap heterozygous cells with Setdb1 shRNA mediated knockdown.
Methods: Female Setdb1+/+ Xist∆A/+ ES cells were induced to differentiate and RNA sampled on day 0, day 3 and day 5 of differentiation. RNAseq libraries were prepared with TruSeq RNA sample preparation v2 kit. Libraries were pooled and sequenced on the Illumina HiSeq 2000 platform for 100 bp single-end reads. Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. Real-time base calling on the HiSeq instrument computer was performed with the RTA software. Illumina CASAVA1.8 pipeline was used to generate the sequence data.

overall_design: Total RNA was extracted and purified from each cell type and their transcriptomes analysed by RNA-Seq.


title: Gene expression profiling of retrovirus PDGFB-induced glioma

summary: We performed gene expression profilings of platelet-derived growth factor subunit B (PDGFB)-induced mouse glioma to compare the differential transcriptome profiles between Ctrl-T tumor cells and Olig2cKO tumor cells.

overall_design: Expression profiling of Ctrl-T and Olig2cKO brain tumor (glioma) cells, normal oligodendrocyte progenitor cells (OPCs), normal astrocytes, and normal brain cortex by high-throughput sequencing.


title: Gene expression profiling and genome-wide maps in PDGFB-induced glioma


title: Pervasive TTP binding but selective target mRNA destabilization in the macrophage transcriptome [RNA-Seq_2]

city: Vienna

first: Vitaly

last: Sedlyarov

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: Research Center for Molecular Medicine

summary: Precise control of mRNA decay is fundamental for robust yet not exaggerated inflammatory responses to pathogens. Parameters determining the specificity and extent of mRNA degradation within the entire inflammation-associated transcriptome remain incompletely understood. Using transcriptome-wide high resolution occupancy assessment of the mRNA-destabilizing protein TTP, a major inflammation-limiting factor, we qualitatively and quantitatively characterize TTP binding positions and functionally relate them to TTP-dependent mRNA decay in immunostimulated macrophages. We identify pervasive TTP binding with incompletely penetrant linkage to mRNA destabilization. A necessary but not sufficient feature of TTP-mediated mRNA destabilization is binding to 3’ untranslated regions (UTRs). Mapping of binding positions of the mRNA-stabilizing protein HuR in activated macrophages revealed that TTP and HuR binding sites in 3’ UTRs occur mostly in different transcripts implicating only a limited co-regulation of inflammatory mRNAs by these proteins. Remarkably, we identify robust and widespread TTP binding to introns of stable transcripts. Nuclear TTP is associated with spliced-out introns and maintained in the nucleus throughout the inflammatory response. Our study establishes a functional annotation of binding positions dictating TTP-dependent mRNA decay in immunostimulated macrophages. The findings allow navigating the transcriptome-wide landscape of RNA elements controlling inflammation.

overall_design: Experiment comparing RNA decay rates in WT and TTP-/- macrophages at LPS 3 h and 6 h. Transcription was blocked with actinomycin D for 0, 45 or 90 min. Decay rates was calculated using linear model.

first: Joerg

last: Fallmann

first: Florian

last: Ebner

first: Masa

last: Ivin

first: Kristina

last: Kreiner

first: Andrea

last: Tanzer

first: Ivo

last: Hofacker

first: Pavel

last: Kovarik


first: Andrew

summary:
Purpose: The aim of this study is (1) to identify the chromatin occupancy of the epigenetic regulator Setdb1 in mouse embryonic fibroblasts (MEF); (2) to profile key epigenetic marks H3K9me2, H3K9me3 and H3K27me3; utilizing wildtype cells with nonsilencing shRNA mediated knockdown and Setdb1 geneTrap heterozygous cells with Setdb1 shRNA mediated knockdown.
Methods: Chromatin immunoprecipitation for Setdb1, H3K9me2, H3K9me3 and H3K27me3 was performed essentially as in (Nelson et al. 2006). Briefly, nuclei were isolated from formaldehyde crosslinked MEFs and chromatin was fragmented by sonication. Chromatin immunoprecipitation was performed with corresponding antibodies for Setdb1, H3K9me2, H3K9me3 and H3K27me3. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking. Isolated DNA was used to generate sequencing libraries with Illumina's TruSeq DNA Sample Preparation Kit according to manufacturer's instruction. Libraries were pooled and sequenced on the Illumina HiSeq 2000 platform for 100 bp single-end reads. Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. Real-time base calling on the HiSeq instrument computer was performed with the RTA software. Illumina CASAVA1.8 pipeline was used to generate the sequence data.

overall_design: Chromatin occupancy of the epigenetic regulator Setdb1, H3K9me2, H3K9me3 and H3K27me3 in mouse embryonic fibroblasts (MEFs) with wildtype MEFs and nonsilencing shRNA mediated knockdown or Setdb1 geneTrap heterozygous MEFs with Setdb1 shRNA mediated knockdown was determined by Setdb1, H3K9me2, H3K9me3 and H3K27me3 ChIP-seq, respectively.


title: Single-cell RNA sequencing reveals non-canonical brain macrophage activation states in murine neurotrauma

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary:
Background: Macrophage polarization programs, commonly referred to as “classical” and “alternative” activation, are widely considered as distinct states that are exclusive of one another, and are associated with different functions such as inflammation and wound healing, respectively. In a number of disease contexts, such as traumatic brain injury (TBI), macrophage polarization influences the extent of pathogenesis, and efforts are underway to eliminate pathogenic subsets. However, previous studies have not distinguished whether the simultaneous presence of both classical and alternative activation signatures represents the admixture of differentially polarized macrophages, or if they have adopted a unique state characterized by components of both classical and alternative activation.
Results: We analyzed the polarization of individual macrophages responding to TBI using single-cell RNA sequencing. Analysis of signature polarization genes revealed diverse activation states, including M(IL4), M(IL10), and M(LPS, IFNγ). However, the expression of a given polarization marker was no more likely than at random to predict simultaneous expression or repression of markers of another polarization program within the same cell, suggesting a lack of exclusivity in macrophage polarization states in vivo in TBI. Also unexpectedly, individual TBI macrophages simultaneously expressed high levels of signature polarization genes across two or three different polarization states, and in several distinct and seemingly incompatible combinations.
Conclusions: Single-cell gene expression profiling demonstrated that monocytic macrophages in TBI are not comprised of distinctly polarized subsets, but are uniquely and broadly activated. TBI macrophage activation in vivo is deeply complex, with individual cells concurrently adopting both inflammatory and reparative features. These data provide physiologically relevant evidence that the early macrophage response to TBI is comprised of novel activation states that are discordant with the current paradigm of macrophage polarization—a key consideration for therapeutic modulation.

overall_design: Monocyte derived macrophages were isolated from the ipsilateral hemisphere of mouse brains one day following traumatic brain injury elicited by control cortical impact in C57BL/6 adult male mice.   Single-cells were isolated and processed for RNA sequencing using a Fluidigm C1 integrated fluidic circuit chip.  45 biological replicates were analyzed.

first: Charles

first: Christine

last: Hsieh

first: Mary

last: Nakamura


title: RNA-sequencing analysis of gilt blood gene expression during Porcine Reproductive and Respiratory Syndrom Virus infection

city: Edmonton

first: James

middle: Michael

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

country: Canada

institute: University of Alberta

summary: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection of pregnant females causes fetal death and increased piglet mortality, but there is substantial variation in the extent of reproductive pathology between individual dams. This study used RNA-sequencing to characterize the whole blood transcriptional response to PRRSV in pregnant gilts during the first week of infection, and attempted to identify gene expression signatures associated with a low or high level of fetal mortality at necropsy, 21 days post-inoculation.

overall_design: RNA-sequencing experiment compared whole blood gene expression in two groups of gilts: a low fetal mortality group (LFM) and a high fetal mortality (HFM) group (n=8 per group). Two sets of contrasts were perfromed. First, a time-course experiment in which gene expression at day 2 (D2) post-inoculation was compared to day 0 (D0-just prior to inoculation) and expression at day 6 post-inoculation was compared to D2. Second, a comparison of gene expression between LFM and HFM groups at each of the three time-points (D0, D2, and D6).

first: Jamie

middle: M

last: Ladinig

first: Hua

last: Bao

first: Arun

last: Kommadath

first: Paul

last: Stothard

first: Joan

last: Lunney

first: Graham

last: Plastow

first: John

last: Harding


title: Transcriptome analysis reveals global regulation in response to CO2 supplementation in oleaginous microalga Coccomyxa subellipsoidea C-169

city: Guangzhou

first: Huifeng

last: Peng

address: Wushan Road No.381, Tianhe District

country: China

institute: South China University of Technology

summary: The microalga Coccomyxa subellipsoidea C-169 possesses some features that may be valuable for lipid production, and, as demonstrated in this study, can be greatly induced to produce a high amount of fatty acid by CO2 supplementation. Here we have compared the transcriptome of air group (AG, cells cultured under 0.04% CO2) and CO2-supplemented group (CG, cells cultured under 2% CO2), and found that dramatic and collaborative regulation in central metabolic pathways as well as biochemical processes occured in response to CO2 supplementation. This study gains a broad understanding of how CO2 stress regulates gene expression and eventually reveals a fine-tuned strategy adopted by C-169 to sustain rapid cell growth and lipid production, which will be helpful for the implementation of biofuels production from oleaginous microalgae.

overall_design: Transcriptomic profiles of Coccomyxa subellipsoidea C-169 cultured for 4 days under two CO2 levels (0.04% and 2%, v/v) were generated by digital gene expression (DGE) analysis, in triplicate, using Illumina Hiseq2000.

first: Gu

last: Chen

first: Dong

last: Wei

first: Feng


title: Transcriptome profiling of hnRNP A2/B1 and A1 depleted cells

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

summary: We used NEBNext Ultra Directional RNA Library Prep Kits to prepare RNA-seq libraries of total RNA from hnRNP A2/B1 and A1 depleted A549 cells. Pro-seq libraries were prepared from A549 cells using Illumina adapters

overall_design: hnRNP A2/B1 and A1 depleted A549 cells were generated by lentiviral infections of shRNA constructs. RNAs were isolated using Trizol.

first: Rene

last: Geissler

first: Alfred

last: Simkin

first: Doreen

last: Floss

first: Ravi

last: Patel

first: Elizabeth

last: Fogarty

first: Jürgen

last: Scheller


title: The dynamic interactome and genomic targets of Polycomb complexes during stem cell differentiation

city: Nijmegen

first: Susan

last: Kloet

address: Geert Grooteplein 26, Route 274

department: Proteomics and Chromatin Biology

country: Netherlands

institute: RIMLS-Radboud Universiteit

summary: While the core members of the Polycomb family of proteins (PRC2, PRC1, PR-DUB) are well-characterized, little is known about the specific composition of and protein-protein interactions within these complexes in different cell types.  We performed quantitative interaction proteomics and cross-linking mass spectrometry on core Polycomb complex members to identify novel interactors, the relative abundance (stoichiometry) of subunits, and the architecture of these complexes in mouse embryonic stem cells (mESCs) and neural progenitor cells (NPCs). Differentiation to NPCs resulted in dramatic binding changes for several substoichiometric interactors of PRC2 and PRC1.  ChIP-seq of core PRC2 and PRC1 subunits in mESCs and NPCs also identified dynamic changes in the genomic localization of these complexes.  We observed a loss of PRC2 from most H3K27me3 sites during differentiation, whereas PRC1 is retained at these sites.  Additionally, we found PRC1 at enhancers and promoters of active genes independent of PRC2 binding.  Overexpression studies using NPC-specific PRC1 interactors demonstrated that the subunit switching observed during differentiation can change PRC1 target site binding.  Altogether, these findings extend our understanding of Polycomb family composition, architecture, and genome-wide localization.

overall_design: ChIP-seq samples for Suz12, Ezh2, Ring1b, Pcgf2, and inputs from mouse embryonic stems cells (mES) and neural progenitor cells (NPC) as well as NPC histone H3K4me1 ChIP-seq.


title: Gene expression profiling of retrovirus PDGFB induced Glioma in control and Olig2cKO tumor

first: Richard

last: Lu

summary: We performed gene expression pofiling of of Olig2cKO and control glioma tumor and identified significantly changed genes

overall_design: RNA-seq of  control tumor tissues and Olig2cKO tumor tissues

first: Fanghui

first: Q


title: Transcription Profile of Aging and Cognition-Related Genes in the Medial Prefrontal Cortex.

city: Gainesville

first: Thomas

last: Foster

address: 1149 Newell Drive Bldg 59

department: Neuroscience

institute: University of Florida-McKnight Brain Institute

summary:
This study focused on transcription in the medial PFC (mPFC) as a function of age and cognition. Young and aged F344 rats were characterized on tasks, attentional set shift and spatial memory, which depend on the mPFC and hippocampus, respectively. Differences in transcription associated with age and cognitive function were examined using RNA sequencing to construct transcriptomic profiles for the mPFC, white matter, and region CA1 of the hippocampus.
The results indicate regional differences in vulnerability to aging associated with increased expression of immune and defense response genes and a decline in synaptic and neural activity genes. Importantly, we provide evidence for region specific transcription related to behavior. In particular, expression of transcriptional regulators and neural activity-related immediate-early genes (IEGs) are increased in the mPFC of aged animals that exhibit delayed set shift behavior; relative to age-matched animals that exhibit set shift behavior similar to younger animals.

overall_design: The study contains 11 young and 20 aged rats for the mPFC and CA1 samples, which were used to investigate expression patterns associated with aging and behavior. White matter samples were used to investigate an age-related effect with 8 young and 9 aged rats.

first: Lara

last: Ianov

first: Blanca

last: Beas

first: Asha

last: Rani

first: Ashok

last: Kumar


title: H3K27ac ChIP-Seq in LOUCY

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

summary: H3K27ac ChIP-Seq data of the T-ALL cell line LOUCY was obtained to find active regions in the genome and to correlate that with expression profiling of lncRNAs in the LOUCY cell line.

overall_design: ChIP-sequencing data was generated for H3K27ac in the T-ALL cell line LOUCY.

first: Filip

last: Matthijssens

first: Kaat

last: Durinck

first: Wouter

last: Van Loocke

first: Frank

last: Speleman

first: Pieter

last: Van Vlierberghe


title: Deep sequencing identifies PD0325901 modulated microRNAs in the J1 mESCs

city: xi'an

first: Zhiying

last: Ai

state: shannxi

address: No.3 Taicheng Road, Yangling

institute: Northwest A&F University (NWAFU)

summary: PD0325901 is involved in improving reprogramming efficiency during inducing pluripotent stem cells (iPSC) or maintain a blastocyst-like state in embryonic stem cells (ESC). However, the knowledge about this small molecule regulating miRNAs in ESC was limited. To understand the role of miRNAs during PD03-induced ESC maintenance and gain an insight how PD0325901 regulates miRNAs expression; we performed small RNA sequencing using Illumina HiSeq 2000 under the compounds treatment. The data show the miRNAs regulated by PD0325901.

overall_design: J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented with PD0325901 for 24 hours, J1 treated with DMSO was set as control. Then total RNA was extracted for analysis.

first: Yongyan

last: Wu

first: Zekun

last: Guo


title: TTP binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution

first: Vitaly

last: Sedlyarov

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

overall_design: Refer to individual Series


title: Pervasive TTP binding but selective target mRNA destabilization in the macrophage transcriptome [PAR-iCLIP]

overall_design: PAR-iCLIP for TTP (3 replicates) and for HuR (2 replicates)

first: Joerg

last: Fallmann

first: Florian

last: Ebner

first: Masa

last: Ivin

first: Kristina

last: Kreiner

first: Andrea

last: Tanzer

first: Ivo

last: Hofacker

first: Pavel

last: Kovarik


title: Marker gene/pathway discovery for polystyrene particle toxicity in zebrafish larvae

status: Public on May 16 2016

city: Leiden

last: Veneman

state: Zuid-Holland

address: Einsteinweg 55

department: Institute Biology Leiden

institute: Leiden University

summary: We use the zebrafish embryo model to study the innate immune response against polystyrene particles. Therefore, we injected 700nm polystyrene into the yolk at 2 dpf and took samples at 1 and 3 days post injection.

overall_design: This deep sequence study was designed to determine the gene expression profile by  polystyrene particle toxicity. RNA was isolated from embryos at 1 and 3 days post injection. Wildtypes zebrafish embryos were micro-injected into the yolk (2dpf) with 1nl of  5mg/ml of 700nm red fluorescent polystyrene particles suspended in PVP (Polyvinylpyrrolidone) (n=3), mock injected with pvp (n=2), or Non-injected as a control (n=3). After injections embryos were transferred into fresh egg water and incubated at 28°C. At 1 and 3 days post injection 10 embryos per group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

first: W

first: H

middle: P

last: Spaink

first: M

last: Vijver


title: The Mot1 ATPase and Spt16 Histone Chaperone Co-Regulate Transcription Through Preinitiation Complex Assembly and Nucleosome Organization

city: Charlottesville

first: David

last: Auble

state: VA

address: Box 800733 Jordan Hall University of Virginia Health System

department: Biochemistry and Molecular Genetics

institute: University of Virginia

type: Expression profiling by genome tiling array


title: Genome-wide Localization of Mot1, Spt16, and Nucleosomes in mot1, spt16, and mot1 spt16 cells

summary: Mot1 is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis, and in so doing exerts global effects on transcription.  Spt16 is also essential and functions globally in transcriptional regulation as a component of the FACT histone chaperone complex.  Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae.  As expected, Mot1 was found to control TBP levels at co-regulated promoters.  In contrast, Spt16 did not affect TBP recruitment.  On a global scale, Spt16 was required for Mot1 promoter localization, and Mot1 also affected Spt16 localization to genes.  Interestingly, we find that Mot1 has an unanticipated role in establishing or maintaining the occupancy and positioning of nucleosomes at the 5’ ends of genes.  Spt16 has a broad role in regulating chromatin organization in gene bodies, including those nucleosomes affected by Mot1. These results suggest that the large-scale overlap in Mot1 and Spt16 function arises from a combination of both their unique and shared functions in transcription complex assembly and chromatin structure regulation.

overall_design: ChIP was performed for Spt16-myc in WT cells and mot1-42 cells in duplicate with input DNA from WT as control.  ChIP was performed for Mot1-myc in WT cells and spt16-197 cells in dublicate with input DNA from WT as control.  Micrococcal nuclease digested chromatin from WT, mot1-42, spt16-197, and mot1-42 spt16-197 cells were immunoprecipitated with H3 antibody in duplicate.  All samples were sequenced by Illumina MiSeq.

first: Jason

last: True

first: Joseph

last: Muldoon

first: Melissa

middle: N

last: Carver

first: Savera

last: Shetty

first: Kunal

last: Poorey

first: Stefan

last: Bekiranov

middle: T


title: Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming [ChIP-seq]

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

summary: Differentiated cell can be reprogrammed into totipotent embryo through somatic cell nuclear transfer (SCNT). However, this process is highly inefficient and most cloned embryos arrest at certain developmental stages. Through single cell sequencing combined with embryo biopsy, here we generate a global map of DNA methylome and RNA transcriptome for SCNT embryos with distinct developmental fates. We subsequently demonstrate that the unfaithful reactivation of two histone demethylases, Kdm4b and Kdm5b, accounts for the arrest of cloned embryos at 2-cell and 4-cell stage, respectively. Ectopic expression of Kdm4b and Kdm5b in SCNT can remove H3K9me3 barrier, restore the transcription profile and facilitate the blastocyst developmental efficiency over 95%. Moreover, these cloned embryos can further support full-term development and the derivation of SCNT-embryonic stem cells with greater efficiency. Our study reveals that histone methylation reset is crucial for the development of SCNT embryos, which provides a clue to further improve therapeutic cloning.

overall_design: Examination of histone H3K9me3 modifications in 2-cell embryos and cumulus cells.

first: Xiaoyu

last: Liu

first: Chenfei

last: Wang

first: Yawei

first: Wenqiang

last: liu

first: Wei

first: Tao

last: Cai

first: Yong

last: Zhang


title: Determination of RNA Secondary Structure By RNA-Sequencing of HEK293T Cells

city: Philadelphia,

first: Nathan

middle: Daniel

last: Berkowitz

state: Pennsylvania

address: 433 S University Ave.

institute: University of Pennsylvania

summary: RNA molecule fold into three dimensional structures in order to fill important roles in the cell such as translation and post-transcriptional regulation. These three dimensional structures, in turn, depend on the pattern of hydrogen bonds between ribonucleotides. We employ a technique based on high throughput RNA Sequencing (RNA-Seq) to uncover this patter on a transcriptome wide scale.

overall_design: We take advantage of two ribonucleases that have structure specific activity. RNAse S1 specifically digests single stranded RNA while RNAse V1 is specific to double stranded RNA. We aliquot each of our sample into to reactions. One is thoroughly treated with RNAse S1, digesting away single stranded RNA and leaving behind dsRNA. The other is treated with RNAse V1, which has the inverse effect. The surviving dsRNA and ssRNA molecules are then subject to high throughput sequencing. The resulting reads are used to generate a structure score, revelaing which regions of each transcript are involved in base pairing and which are unpaired.

last: Berkowtiz

first: Ian

last: Silverman

first: Brian

last: Gregory


title: RNA-seq expression data from FL-HSPCs after HOXA7 knockdown

city: Los Angeles

first: Hanna

middle: Katri Annikki

last: Mikkola

address: 621 Charles E Young Drive South, 2204, Mailbox 160606

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: HOXA7 regulates FL-HSPC self-renewal in vitro and in vivo. We profiled  FL-HSPCs after HOXA7 knockdown, to assess the gene expression programs regulated by HOXA7.

overall_design: CD34+CD38-CD43+CD90+ HSPCs were infected with lentiviral shRNA vector targeting HOXA7 (sh-HOXA7). The emtpy lentiviral vector (LKO) was used as a control. Cells were expanded on op9 for 5 days and selected for puromicin resistance for 3 days, than sorted for HSPC immunophenotype.

first: Diana

last: Dou

first: Vincenzo

last: Calvanese

first: Maria

middle: I

last: Sierra

first: Andrew

last: Nguyen

first: Arazin

last: Minasian

first: Pamela

last: Saarikoski

first: Rajkumar

last: Sasidharan

first: Christina

last: Ramirez

first: Jerome

middle: A

last: Zack

first: Gay

last: Crooks

first: Zoran

last: Galic

middle: K


title: RNA-seq expression data from EB-HSPCs after HOXA7 overexpression

summary: HOXA7 regulates FL-HSPC self-renewal in vitro and in vivo. We profiled  EB-HSPCs after HOXA7 overexpression (EB-HOXA7), or with a control vector (EB-CTR), to assess the gene expression programs regulated by HOXA7.

overall_design: CD34+CD38-CD43+CD90+ HSPCs were infected with lentiviral FUGW vector either empty (FUGW-GFP) or encoding HOXA7(FUGW-GFP-HOXA7) protein. Cells were expanded on op9 for 15 days and than sorted for GFP HSPC immunophenotype.

middle: R


title: ATAC-seq data from EB-HSPC after AM580 treatment compared to DMSO-treated EB

summary: RA signalling regulated endothelial to hematopoietic transition and HSC generation.

overall_design: EB-derived HSPC were profiled after 6 days of treatment with 0.2uM AM580 on OP9


title: Pervasive TTP binding but selective target mRNA destabilization in the macrophage transcriptome [RNA-Seq]

first: Vitaly

last: Sedlyarov

summary: Precise control of mRNA decay is fundamental for robust yet not exaggerated inflammatory responses to pathogens. Parameters determining the specificity and extent of mRNA degradation within the entire inflammation-associated transcriptome remain incompletely understood. Using transcriptome-wide high resolution occupancy assessment of the mRNA-destabilizing protein TTP, a major inflammation-limiting factor, we qualitatively and quantitatively characterize TTP binding positions and functionally relate them to TTP-dependent mRNA decay in immunostimulated macrophages. We identify pervasive TTP binding with incompletely penetrant linkage to mRNA destabilization. A necessary but not sufficient feature of TTP-mediated mRNA destabilization is binding to 3’ untranslated regions (UTRs). Mapping of binding positions of the mRNA-stabilizing protein HuR in activated macrophages revealed that TTP and HuR binding sites in 3’ UTRs occur mostly in different transcripts implicating only a limited co-regulation of inflammatory mRNAs by these proteins. Remarkably, we identify robust and widespread TTP binding to introns of stable transcripts. Nuclear TTP is associated with spliced-out introns and maintained in the nucleus throughout the inflammatory response. Our study establishes a functional annotation of binding positions dictating TTP-dependent mRNA decay in immunostimulated macrophages. The findings allow navigating the transcriptome-wide landscape of RNA elements controlling inflammation.

overall_design: RNA-Seq of RNA isolated from murine bone marrow derived macrophages (WT or TTP-deficient) stimulated for 6 h with LPS

first: Joerg

last: Fallmann

first: Florian

last: Ebner

first: Masa

last: Ivin

first: Kristina

last: Kreiner

first: Andrea

last: Tanzer

first: Ivo

last: Hofacker

first: Pavel

last: Kovarik


title: Medial HOXA gene expression is a landmark for the definitive haematopoietic fate and a prerequisite for human HSC function

first: Hanna

last: Mikkola


title: Modeling genome-wide transcriptional cis-regulation in n LNCaP-abl cell line after siRNA knock down of a series of gene factors [RNA-seq]

first: Chongzhi

last: Zang

summary: We describe, MARGE, Model-based Analysis of the Regulation of Gene Expression, a robust methodology that leverages a large library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse. MARGE adopts a gene centric approach to define a regulatory potential that summarizes the aggregate activity of multiple cis-regulatory elements on each gene. This model is effective in describing cis-regulatory activity and, unlike the super-enhancer based approach, is highly predictive of gene expression changes in response to BET-bromodomain inhibitors. We show that linear combinations of H3K27ac defined regulatory potentials, selected from an extensive database of published H3K27ac profiles, can accurately model diverse gene sets derived from differential gene expression experiments. In addition, we demonstrate a novel semi-supervised learning approach for identifying transcription factor binding sites associated with the set of transcription factors that regulate the gene set. MARGE leverages published H3K27ac ChIP-seq data to enhance the interpretation of newly generated H3K27ac ChIP-seq profiles. MARGE can also be used to analyze gene expression studies, without the production of matched H3K27ac ChIP-seq data.

overall_design: Transcriptome profiling in LNCaP-abl cell line after siRNA knock down of a series of gene factors.

first: Housheng

middle: H

last: He

first: Tengfei

last: Xiao

first: Myles

last: Brown

first: X

middle: S

last: Liu


title: Genome-wide mapping of MYCN binding in neuroblastoma cells

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: To identify the MYCN transcription factor binding sites across the genome, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using anti-MYCN and anti-IgG antibodies on a MYCN-amplified NB cell line, SK-N-BE(2)-C.

overall_design: Identification of MYCN binding in neuroblastoma cells.

first: Hsueh-Fen

last: Juan


title: Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming [RRBS]

first: Shaorong

last: Gao

overall_design: For SCNT embryos 4-8 replicates were performed for each stage . As the control, 3 replicates were performed for each stage of wild type samples

first: Rui

first: Chenfei

last: Wang

first: Xiaoyu

first: Yawei

first: Wenqiang

last: liu

first: Wei

first: Tao

last: Cai

first: Yong

last: Zhang


title: Long noncoding RNA signatures define oncogenic subtypes in T-cell acute lymphoblastic leukemia

first: Annelynn

last: Wallaert


title: Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming.


title: Identification of Beef Heifers with Superior Uterine Capacity for Pregnancy

status: Public on May 15 2016

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: Infertility and subfertility represent major problems in domestic animals and humans, and the majority of embryonic loss occurs during the first month of gestation that involves pregnancy recognition and conceptus implantation. The critical genes and physiological pathways in the endometrium that mediate pregnancy establishment and success are not well understood. In Study One, 270 predominantly Angus heifers were classified based on fertility using four rounds of serial embryo transfer (ET) to select animals with intrinsic differences in pregnancy loss. In each round, a single in vitro-produced high-quality embryo was transferred into heifers on day 7 post-estrus and pregnancy was determined on days 28 and 42 by ultrasound and then terminated. Heifers were classified based on pregnancy success as high fertile (HF), subfertile (SF), or infertile (IF). In Study Two, fertility-classified heifers were resynchronized and bred with semen from a single high fertility bull. Blood samples were collected every other day from days 0 to 36 post-mating. Pregnancy rate was determined on day 28 by ultrasound and tended to be higher in HF (70.4%) and SF (46.7%) than IF (0%) heifers. Progesterone concentrations in serum during the first 20 days post-estrus were not different in non-pregnant heifers and also not different in pregnant heifers among fertility groups. In Study Three, a single in vivo-produced embryo was transferred into fertility-classified heifers on day 7 post-estrus. The uteri were flushed on day 14 to recover embryos, and endometrial biopsies were obtained from the ipsilateral uterine horn. Embryo recovery rate and conceptus length and area were not different among the heifer groups. RNA was sequenced from the day 14 endometrial biopsies of pregnant HF, SF and IF heifers (n=5 per group) and analyzed by edgeR robust analysis. There were 26 differentially expressed genes (DEG) in the HF compared to SF endometrium, 12 DEG for SF compared to IF endometrium, and 3 DEG between the HF and IF endometrium. Many of the DEG encoded proteins involved in immune responses and are expressed in B cells. Results indicate that pre-implantation conceptus survival and growth to day 14 is not compromised in SF and IF heifers. Thus, the observed difference in capacity for pregnancy success in these fertility-classified heifers is manifest between days 14 and 28 when pregnancy recognition signaling and conceptus implantation must occur for the establishment of pregnancy.

overall_design: Endometrial biopsies were subjected to RNA sequencing from high fertile (HF; n=5), subfertile (SF; n=5) and infertile (IF; n=5) classified heifers on day 14 of pregnancy.

last: Geary

first: Gregory

last: Burns

first: Joao

last: Moraes

first: James

last: Moss

first: Anna

middle: C

last: Denicol

first: Kyle

middle: B

last: Dobbs

first: M

last: Ortega

first: Peter

middle: J

last: Hansen

first: Michael

middle: E

last: Wehrman

first: Holly

middle: L

last: Neibergs

first: Eleanore

middle: V

last: O'Neil

first: Sustanta

last: Behura


title: Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming [RNA-seq]

first: Shaorong

last: Gao

overall_design: For SCNT embryos or injected SCNT embryos 3-8 replicates were performed for each stage . As the control, 3-6 replicates were performed for each stage of wild type samples

first: Xiaoyu

last: Liu

first: Yawei

first: Chenfei

last: Wang

first: Wenqiang

last: liu

first: Jingyi

last: Li


title: Modeling transcriptional cis-regulation with a library of genome-wide histone H3K27ac profiles

first: Chongzhi

last: Zang

overall_design: Identifying genomic profiles of histone modification H3K27ac in LNCaP-abl cell line after siRNA knock down of a series of gene factors.

first: Tengfei

last: Xiao

first: Su

first: Clifford

last: Meyer

first: Myles

last: Brown

first: Xiaole


title: Nucleosome positioning changes during human embryonic stem cell differentiation.

city: Athens

first: wenjuan

last: zhang

state: GA

address: 120 Green street, Life Science Building, Room B304B

institute: University of Georgia

summary: Nucleosomes are the basic unit of chromatin. Nucleosome positioning (NP) plays a key role in transcriptional regulation and other biological processes. To better understand NP we used MNase-seq to investigate changes that occur as human embryonic stem cells (hESCs) transition to nascent mesoderm and then to smooth muscle cells (SMCs). Compared to differentiated cell derivatives, nucleosome occupancy at promoters and other notable genic sites, such as exon/intron junctions and adjacent regions, in hESCs shows a stronger correlation with transcript abundance and is less influenced by sequence content. Upon hESC differentiation, genes being silenced, but not genes being activated, display a substantial change in nucleosome occupancy at their promoters. Genome-wide, we detected a shift of NP to regions of higher G+C content as hESCs differentiate to SMCs. Notably, genomic regions with higher nucleosome occupancy harbor twice as many G↔C changes but fewer than half A↔T changes, compared to regions with lower nucleosome occupancy. Finally, our analysis indicates that the hESC genome is not rearranged and has a sequence mutation rate resembling normal human genomes. Our study reveals another unique feature of hESC chromatin, and sheds light on the relationship between nucleosome occupancy and sequence G+C content.

overall_design: We determined genome-wide nucleosome positioning in hESCs (WA09) and two derivatives (WA09-INM and WA09-SMC) from these WA09-hESCs.

first: Wenjuan

last: Zhang

first: Yaping

last: Kulik

first: Rochelle

last: Tiedemann

first: Keith

last: Robertson

first: Stephen

last: Dalton

first: Shaying

last: Zhao


title: Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil

city: Aberdeen

first: Sophie

last: Shaw

state: Aberdeen City

address: 23 St. Machar Drive

department: Centre for Genome Enabled Biology and Medicine

institute: University of Aberdeen

summary: The free-living soil fungus Trichoderma hamatum GD12 is notable amongst other Trichoderma strains in exhibiting both biocontrol and plant growth promotion (PGP) activities, which are coincident with a markedly expanded genome when compared to other characterised biocontrol and PGP isolates. Here, we make direct comparisons of T. hamatum GD12 transcription during PGP, and during antagonism of the root-infecting pathogen Sclerotinia sclerotiorum, in peat-based microcosms. An extensive mRNA-seq analysis sampling six time-points, 1, 2, 4, 7, 10 and 15 days after microcosm establishment revealed dynamic and biphasic signatures in the transcriptional responses of T. hamatum GD12 during Sclerotinia biocontrol and lettuce growth promotion. Functional analysis of differentially expressed genes demonstrated up-regulation of transportation and oxidation-reduction genes during both processes. Sclerotinia biocontrol is most likely mediated by the synthesis and secretion of antifungal compounds. Notably, the biphasic response during biocontrol was further characterised by the expression of a number of uncharacterised GD12 genes, small-secreted cysteine rich proteins and secondary metabolite producing gene clusters. This work demonstrates that T. hamatum GD12 harnesses a reservoir of uncharacterised genes that are actively engaged during effective biological control of a plurivorous plant pathogen.

sample_organism:
Sclerotinia sclerotiorum
Trichoderma hamatum GD12

overall_design: RNA extracted directly from soil containing lettuce seedlings with either Trichoderma hamatum GD12 alone, T.hamatum GD12 and Sclerotinia sclerotiorum, or S. sclerotiorum alone. RNA was extracted in triplicate at days one, two, four, seven, ten and fifteen and then sequenced using an Illumina HiSeq2500. Two samples were taken in duplicate due to issues with RNA extraction.

first: Kate

last: Le Cocq

first: Konrad

last: Paszkiewicz

first: Karen

last: Moore

first: Rebecca

last: Winsbury

first: Deborah

last: Salmon

first: Chris

last: Thornton

first: Murray

last: Grant

first: David

last: Studholme

first: Marta

last: de Torres Zabala


title: Gene expression changes in the retina following human neural progenitor cell injection into a rodent model for retinal degeneration

first: Melissa

middle: Kaye

last: Jones

address: 8700 Beverly Blvd.

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

summary: The goal of this study is to compare gene expression changes in retinal degenerate Royal College of Surgeons (RCS) rats following an injection of human neural progenitor cells (hNPCs) using RNA-seq, as compared to RCS rats receiving a sham surgery and wild-type Long Evans rats. These changes may lead to understanding of the therapeutic potential of hNPCs in inducing photoreceptor survival and visual function preservation.

overall_design: RNA-seq from wild-type Long Evans rats, retinal degenerate Royal College of Surgeons (RCS) rats, and RCS rats following transplantation of human neural progenitor cells (hNPCs)

first: M

last: Saghizadeh

first: B

last: Lu

first: C

last: Svendsen

first: S

last: Wang


title: CHIP-seq analysis for chemical-induced neural stem cells from defined fibroblasts

city: SAN FRANCISCO

first: Sheng

last: Ding

state: California

address: 1650 Owens Street

department: Gladstone Institute of Cardiovascular Disease

institute: THE J DAVID GLADSTONE INSTITUTES

overall_design: Refer to individual Series


title: Genome-wide chromatin landscape of chemical-induced neural stem cell reprogramming from defined fibroblasts

summary: Cellular reprogramming using chemically defined conditions, without genetic manipulation, is a promising approach for generating clinically relevant cell types for regenerative medicine and drug discovery. However, small molecule-driven approaches for inducing lineage-specific stem cells from somatic cells across lineage boundaries have been challenging to develop. Here, we report highly efficient reprogramming of mouse fibroblasts into induced neural stem cell-like cells (ciNSLCs) using a cocktail of nine small molecules (M9). The resulting ciNSLCs closely resemble primary neural stem cells molecularly and functionally. Transcriptome analysis revealed that M9 induces a gradual and specific conversion of fibroblasts towards a neural fate. During reprogramming specific transcription factors such as Elk1 and Gli2 that are downstream of M9-induced signaling pathways bind and activate endogenous master neural genes to specify neural identity. Our study therefore provides an effective chemical approach for generating neural stem cells from mouse fibroblasts, and reveals mechanistic insights into underlying reprogramming process.

overall_design: Genome-wide epigenetic changes of H3K4me1, H3K4me3, H3K27me3, and H3K27ac were analyzed by CHIP-seq for tdMEFs from day 0 (ciNSLC), day 4 (D4), day 8 (D8) of M9-induced neural reprogramming, and ciNSLCs and pri-NPC.

first: Mingliang

last: Zhang

first: Jiashun

last: Zheng


title: Genome-wide chromatin binding of Elk1 and Gli2 in chemical induced neural reprogramming

overall_design: Genome-wide binding of Elk1 and Gli2 was analyzed by CHIP-seq for tdMEFs from day 0 (ciNSLC), day 4 (D4), day 8 (D8) of M9-induced neural reprogramming, and ciNSLCs and pri-NPC.


title: Profling of the Drosophila melanogaster neuronal microRNA transcriptome by small RNA deep sequencing

city: Denver

first: Scott

last: Barbee

state: CO

address: 2190 E. ILIFF Ave.

department: Biological Sciences

institute: University of Denver

summary: microRNAs (miRNAs) are a class of small non-coding RNAs involved in the coordination and/or fine-tuning of gene expression. As such, miRNAs are thought to be critical cis-acting regulatory factors that control a wide range of physiological processes in the brain. The datasets presented here represent the miRNA transcriptome of the adult and larval Drosophila melanogaster CNS as determined by small RNA deep sequencing (RNA-Seq). They were derived from adult and larval samples explanted from the animal that contain minimal extraneous (non-neuronal) tissues. Here we present a concise summary of our profiling results as well as the original sequencing data. We identify many miRNAs that are expressed at equal levels in both tissues and several that are significantly enriched in the larval and adult brain. Some of these belong to miRNA families with conserved members in mammals. These datasets should provide a good starting point for others interested in characterizing miRNAs with putative functions in Drosophila neurons.


title: Plasma cell mitochondrial pyruvate import controls the duration of humoral immunity.

status: Public on May 14 2016

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

summary: RNA-sequencing was performed on human CD19- CD138+ bone marrow plasma cells.

overall_design: 4 biological replicates of human CD19- CD138+ bone marrow plasma cells and 1 replicate each of naïve, IgM memory, IgG memory, and plasmablasts from peripheral blood.

first: Amy

last: Becker


title: The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally

city: Valencia

first: Susana

last: Rodríguez-Navarro

address: Eduardo Primo Yúfera 3

country: Spain

institute: Centro de Investigación Príncipe Felipe (CIPF)

summary: Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of nearly all transcripts and are recruited genome-wide in yeast. However, how this broad recruitment confers selectivity under specific conditions remains an open question. Here we find that the SAGA DUBm subunit Sus1 associates upstream regulatory regions of many yeast genes and that heat shock drastically changes Sus1 binding pattern. While Sus1 binding to TFIID-dominated genes is not affected by temperature, its recruitment to SAGA-dominated genes and RP genes is significantly disturbed under heat shock, being Sus1 relocated to environmental stress responsive genes in these conditions. Moreover, in contrast to recent results showing that SAGA deubiquitinating enzyme Ubp8 is dispensable for RNA synthesis, genomic run-on experiments demonstrate that Sus1 contributes to synthesis and stability for a wide range of transcripts. Our study provides support for a model in which SAGA acts as a global transcriptional regulator in yeast but acquires differential binding affinities under thermal stress conditions.

overall_design: Genome wide analysis of Sus1 in wild type and Spt7 and Spt8 deletion mutants using ChIP-exo and genomic run-on experiments

first: Varinia

last: García-Molinero

first: José

last: García-Martinez

first: Rohit

last: Reja

first: Pedro

last: Furió-Tarí

first: Oreto

last: Antúnez

first: Vinesh

last: Vinayachandran

first: Ana

last: Conesa

first: Benjamin

middle: F

last: Pugh

last: Pérez-Ortín


title: Increased Acid Resistance of the Archaeon, Metallosphaera sedula by Adaptive Laboratory Evolution

city: Lincoln

first: Paul

last: Blum

state: NE

address: 1901 Vine St.

department: School of Biological Sciences

institute: University of Nebraska-Lincoln

summary: Extremely thermoacidophilic members of the Archaea such as the lithoautotroph, Metallosphaera sedula, are among the most acid resistant forms of life and are of great relevance in bioleaching. Here, adaptive laboratory evolution was used to enhance the acid resistance of this organism while genomics and transcriptomics were used in an effort to understand the molecular basis for this trait. Unlike the parental strain, the evolved derivative, M. sedula SARC-M1, grew well at pH of 0.90. Enargite (Cu3AsS4) bioleaching conducted at pH 1.20 demonstrated SARC-M1 leached 23.78% more copper relative to the parental strain. Genome re-sequencing identified two mutations in SARC-M1 including a nonsynonymous mutation in Msed_0408 (an amino acid permease) and a deletion in pseudogene Msed_1517. Transcriptomic studies by RNA-seq of wild type and evolved strains at various low pH values demonstrated there was enhanced expression of genes in M. sedula SARC-M1 encoding membrane complexes and enzymes that extrude protons or that catalyze proton-consuming reactions. In addition, M. sedula SARC-M1 exhibited reduced expression of genes encoding enzymes that catalyze proton-generating reactions.  These unique genomic and transcriptomic features of M. sedula SARC-M1 support a model for increased acid resistance arising from enhanced control over cytoplasmic pH.

overall_design: 3 samples were analyzed: 1 control and 2 experimental samples

first: Chenbing

last: Ai

first: Samuel

last: McCarthy

first: Valerie

last: Eckrich

first: Deepak

last: Rudrappa

first: Guanzhou

last: Qiu


title: iCLIP-Seq analyses of DDX46-bound RNAs

status: Public on May 13 2016

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

summary: DDX46 is identified to be required at the early step of pre-spliceosome assembly,but the potential roles of DDX46 in RNA editing and whether DDX46 could regulate antiviral innate immunity by editing antiviral transcripts in the nucleus remain elusive.

overall_design: iCLIP-Seq analyses of DDX46-bound RNAs from uninfected and VSV-infected RAW264.7 cells

first: Qingliang

last: Zheng

first: Jin

last: Hou


title: small RNA-Seq showing transfer of bacterial outer membrane vesicle (OMV) sRNA to host airway epithelial cells

city: Hanover

first: Katja

last: Koeppen

state: NH

address: 504 Remsen

institute: Geisel School of Medicine at Dartmouth

summary: This study is the first to show transfer of regulatory bacterial sRNAs from bacterial OMVs to host cells.

sample_organism:
Pseudomonas aeruginosa
Homo sapiens

platform_organism:
Pseudomonas aeruginosa
Homo sapiens

overall_design: Demonstration of transfer of bacterial sRNA from Pseudomonas aeruginosa OMVs to host cells in two cell types. RNA isolated from PA14 OMV exposed primary human bronchial epithelial cells or CFBE41o- bronchial epithelial cells as well as unexposed control cells was analyzed by small RNA-Seq. Primary cell exposures were performed on two donors and exposures of CFBE41o- cells were done in triplicate.


title: RNA-seq analysis of transcriptomes at 1 day after sexual induction in Fusarium graminearum strains

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

country: South Korea

institute: Seoul National University

summary: Fusarium graminearum (teleomorph Gibberella zeae) is a prominent pathogen that infects major cereal crops, such as wheat, barley, and maize. To dissect molecular mechanisms for initial stage of perithecia development, we compared transcriptomes of fungal cultures harvested from F. graminearum wild-type strain Z-3639, abaA, and fpo1 at 1 day after sexual induction.

overall_design: 9 samples examined: Fungal cultures harvested from Fusarium graminearum wild-type strain Z-3639, abaA, and fpo1 at 1 day after sexual induction.

first: Jae-Yun

last: Lim

first: Yin-Won

last: Lee


title: RNA-seq analysis of Fusarium graminearum Z-3639 in heat stress

summary: Fusarium graminearum (teleomorph Gibberella zeae) is a prominent pathogen that infects major cereal crops, such as wheat, barley, and maize. To dissect cellular responses toward heat stress in the plant pathogenic fungus F. graminearum, we compared transcriptomes of the fungal cultures incubated in normal temperature condition (25 ºC) and in high temperature condition (37 ºC) for 15 min.

overall_design: 6 samples examined: 24 h-old mycelia from complete medium (CM) of Fusarium graminearum wild-type Z-3639 were incubated in normal temperature condition (25 ºC) and in high temperature condition (37 ºC) for 15 min.

first: Jae Yun


title: Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective. doi: 10.1038/nm.4109

first: Gary

last: Owens

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

summary: The multiple claims about reactivation of the embryonic stem cell (ESC) pluripotency factor OCT4 in somatic cells are highly controversial due to the fact that there is no direct evidence that OCT4 has a functional role in cells other than ESCs. Herein we demonstrate that smooth muscle cell (SMC)-specific knockout of Oct4 within atherosclerotic mice resulted in increased lesion size and multiple changes consistent with decreased plaque stability. SMC-lineage tracing studies showed that lesions from SMC-specific conditional Oct4 KO mice had a reduced number of SMCs likely due to impaired SMC migration. RNA-seq analysis of lesion specimens showed that loss of Oct4 in SMCs was associated with marked activation of genes associated with inflammation and suppression of genes associated with cell migration, a number of which were shown to be activated in cultured SMCs by the combination of hypoxia and oxidized phospholipids in an OCT4-dependent manner. Activation of Oct4 within SMCs was associated with hydroxymethylation of the Oct4 promoter and was HIF1α- and KLF4-dependent. Results provide the first genetic evidence that OCT4 plays a functional role in somatic cells and highlight the importance of further investigation of possible OCT4 functions in somatic cells.

overall_design: In vivo: mRNA profiles of 18 week fed Western diet wild type (WT) and Oct4-/- mice were generated by deep sequencing, four animals per group, using Illumina HiSeq 2000. In vitro: a smooth muscle cell wild type (WT) and Oct4-/- (KO) primary aortic cell line was generated and used. mRNA profiles were generated by deep sequencing, in triplicates, using Illumina HiSeq 2000, for the following groups: WT-normoxia-vehicle; WT-normoxia-POVPC; KO-normoxia-vehicle; KO-normoxia-POVP; WT-hypoxia-vehicle; WT-hypoxia-POVPC; KO-hypoxia-vehicle; and KO-hypoxia-POVPC.

first: Olga

last: Cherepanova

first: Delphine

last: Gomez

first: Laura

last: Shankman

first: Pamela

last: Swiatlowska

first: Jason

last: Williams

last: Sarmento

first: Gabriel

last: Alencar

first: Melissa

last: Bevard

first: Elizabeth

last: Greene

first: Meera

last: Murgai

first: Stephen

middle: D

last: Turner

first: Yong-Jian

last: Geng

first: Stefan

last: Bekiranov

first: Jessica

last: Connely

first: Alexey

last: Tomilin


title: H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [HA-H33-H31_ChIP]

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

summary: The goal of this study is to understand the genome-wide alterations in chromatin landscape induced by a histone mutation (H3.3K36M) derived from chondroblastomas

overall_design: Examination of genome-wide distribution of HA-tagged histone H3.1/H3.3 in cells expressing HA-tagged H3.3WT, H3.3K36M, H3.1WT and H3.3K36M.

first: Chao

last: Lu

first: Siddhant

middle: U

last: Jain


title: H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [H31_ChIP-Rx]

summary: The goal of this study is to understand the genome-wide alterations in chromatin landscapy induced by a histone mutation (H3.3 K36M) derived from chondroblastomas

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Examination of 3 different histone post-translational modifications in 2 cell types using drosophila chromatin as normalization control


title: Transcriptomes of individual substantia nigra pars reticulata neurons

city: Boston

first: Andrew

last: Lutas

state: MA

address: 200 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: Certain neuron types fire spontaneously at high rates, an ability that is crucial for their function in brain circuits. The spontaneously active GABAergic neurons of the substantia nigra pars reticulata (SNr), a major output of the basal ganglia, provide tonic inhibition of downstream brain areas. A depolarizing "leak" current supports this firing pattern, but its molecular basis remains poorly understood. To understand how SNr neurons maintain tonic activity, we used single-cell RNA sequencing to determine the transcriptome of individual SNr neurons. We discovered that SNr neurons express the sodium leak current, NaLCN and that SNr neurons lacking NaLCN have impaired spontaneous firing.

overall_design: RNA sequencing profiles from 87 GFP-positive GABAergic SNr neurons and 9 GFP-negative SNr cells were carried out. However only 80 samples that passed initial quality control and that were included in the data processing are represented in this record.

first: Carolina

last: Lahmann

first: Magali

last: Soumillon

first: Gary

last: Yellen


title: Distinct Gene Regulatory Pathways for Human Innate Versus Adaptive Lymphoid Cells

city: Saint Louis

first: Eugene

middle: M

last: Oltz

state: Missouri

address: 660 Euclid Ave, Campus Box 8118

department: Pathology & Immumonolgy

institute: Washington University in St Louis

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


title: H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [Cbx2_ChIP]

overall_design: Examination of genome-wide Cbx2 distribution in cells expressing H3.3WT and H3.3K36M.


title: H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [Ring1a-1b_RNASeq]

overall_design: Examination of the transcriptome changes of Ring1a and Ring1b knockdown in mouse mesenchymal progenitor cells


title: H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [RNA_Chondroblastoma_H3K36M_H3WT]

overall_design: Examination of H3K36M mutations to H3WT Chondroblastomas.


title: Transcriptional response to the HSP70 inhibitor MAL3-101 in parental rhabdomyosarcoma cells and isogenic acquired-resistance lines.

city: San Francisco

first: Amit

last: Sabnis

state: CA

address: 1550 4th Street

institute: University of California, San Francisco

summary: We demonstrate that inhibition of HSP70 with MAL3-101 induces activation of the unfolded protein response, and that cells with acquired resistance upregulate a cytosolic HSP70 at the level of mRNA.

overall_design: Whole transcriptome sequencing was undertaken of parental or acquired-resistance RMS13 cells treated with either DMSO or 10 micromolar MAL3-101.

first: Trever

middle: G

last: Bivona


title: RNA-seq expression data from EB-HSPC after AM580 treatment compated to DMSO-trated and FL-HSPCs

city: Los Angeles

first: Hanna

middle: Katri Annikki

last: Mikkola

address: 621 Charles E Young Drive South, 2204, Mailbox 160606

institute: University of California, Los Angeles

summary: RA signalling regulated endothelial to hematopoietic transition and HSC generation.

overall_design: EB- or FL-derived HSPC were profiled before (d0) or after (d6) 6 days of treatment with 0.2uM AM580 on OP9, and after 6 additional days of expandion of OP9 (d12) without treatment.

first: Diana

last: Dou

first: Vincenzo

last: Calvanese

first: Maria

middle: I

last: Sierra

middle: T

last: Nguyen

first: Arazin

last: Minasian

first: Pamela

last: Saarikoski

first: Rajkumar

last: Sasidharan

first: Christina

last: Ramirez

first: Jerome

middle: A

last: Zack

first: Gay

last: Crooks

first: Zoran

last: Galic

middle: K


title: Distinct Gene Regulatory Pathways for Human Innate Versus Adaptive Lymphoid Cells [ChIP-seq & ATAC-seq]

summary: Innate lymphoid cells (ILCs) serve as sentinels in mucosal tissues, sensing release of soluble inflammatory mediators, rapidly communicating danger via cytokine secretion, and functioning as guardians of tissue homeostasis. Although ILCs have been studied extensively in model organisms, little is known about these “first responders” in humans, especially their lineage and functional kinships to cytokine-secreting T helper cell (Th) counterparts. Here, we report gene regulatory circuitries for four human ILC–Th counterparts derived from mucosal environments, revealing that each ILC subset diverges as a distinct lineage from Th and circulating natural killer cells, but shares circuitry devoted to functional polarization with their Th counterparts. Super-enhancers demarcate cohorts of cell identity genes in each lineage, uncovering new modes of regulation for signature cytokines, novel molecules that likely impart important functions to ILCs, and potential mechanisms for autoimmune disease SNP associations within ILC–Th subsets.

overall_design: Molecular profiling of innate lymphoid and T helper cells subsets purified from tonsils and NK cells purified from peripheral blood using Assay for Transposase-Accessible Chromatin (ATAC) and chromatin immunoprecipitation (H3K4me3 and H3K27ac).

first: Marco

last: Colonna

first: Olivia

last: Koues

first: Marina

last: Cella


title: miR396-OsGRF6 module controls rice inflorescence architecture

city: Wuhan

first: Wang

last: Kun

state: Hubei

address: Ba-yi Road

institute: wuhan university

summary: Developing strategies to increase rice productivity to meet global demand is one of the main challenges for breeders around the world. Here, we report a novel microRNA mediated process that increases rice grain yield in field trials. Expression of target mimicry of microRNA396 (MIM396) significantly increases rice yield by modulating the development of the auxiliary branches and spikelets through promoting the expression of Growth Regulation Factor 6 (OsGRF6). OsGRF6 coordinately induces the expression of several key factors involved in branch and spikelet development, auxin (IAA) biosynthesis, and auxin signaling pathway. Our results demonstrate that the miR396b-GRF6 module acts as a key player in shaping the inflorescence architecture of rice, which could be engineered to generate high-yield rice. This dataset records the profile of the binding peaks of OsGRF6 with GFP antibody in 35S:GRF6-GFP overexpression lines and the differential expressed genes between MIM396 and WT plants.

overall_design: Examination of OsGRF6 regulated genes.

first: Kun

last: Wang

first: Feng

last: Gao


title: Dynamic changes in E protein activity orchestrate germinal center and plasma cell development [RNA-Seq]

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: Humoral immunity requires the generation of high-affinity antibodies, which involves the generation of germinal centres (GC) promoting class switch and affinity maturation of antigen-specific B cells, and the differentiation of long-lived plasma cells. This multi-layered process is tightly controlled by the activity of a transcriptional network including Bcl6, essential for the development of GC, and Blimp1, required for the differentiation of plasma cells. Here, we reveal an additional layer of complexity by demonstrating that dynamic changes in E-protein activity mediated by Id3 govern both GC and plasma cell differentiation. We show that down-regulation of Id3 expression in B cells in essential for releasing E2A and E2-2, the combined activity of which is required for both GC B cell and plasma cell differentiation. We demonstrate that this pathway controls the expression of multiple key factors required for antigen-induced B cell differentiation, including Blimp1, Xbp1, Mef2b and CXCR4 and is therefore critical for establishing the transcriptional network that controls GC B cell and plasma cell differentiation.

overall_design: Transcriptional profiling of wild type, Id3 knockout and E2A/E22 double knockout B cells using RNA sequencing

first: Renee

last: Gloury

first: Yang

last: Liao

first: Axel

last: Kallies


title: Nucleosome positioning changes during human embryonic stem cell differentiation

city: Athens

first: wenjuan

last: zhang

address: 120 Green street, Life Science Building, Room B304B

institute: University of Georgia

overall_design: Refer to individual Series


title: Dynamic changes in E protein activity orchestrate germinal center and plasma cell development [ChIP-Seq]

overall_design: Genome binding of transcription factor E2A


title: Sequencing Universal Human Reference RNA by Smart-seq and early barcoding library preparation methods

city: Martinsried

first: Swati

last: Parekh

address: Grosshaderner Str. 2

department: Biology II

country: Germany

institute: Ludwig Maximillians University Munich

summary: Many library preparation methods are available for gene expression quantification. Here, we sequenced and analysed Universal Human Reference RNA (UHRR) prepared using Smart-Seq2, TruSeq (public data) and a protocol using unique molecular identifiers (UMIs) that all include the ERCC spike-in mRNAs to investigate the effects of amplification bias on expression quantification.

overall_design: UHRR 10 and 12 replicates for Smart-seq2 and UMI-seq library preparation methods, respectively.

first: Ines

last: Hellmann


title: Reconstructing gene regulatory networks of tumorigenesis [ChIP-Seq]

city: Illkirch; Strasbourg

first: Valeriya

last: Malysheva

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: The mechanistic links between transcription factors and the epigenetic landscape, which coordinate the deregulation of gene networks during cell transformation are largely unknown. We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. By combining transcriptome and epigenome data for each step during transformation and by integrating transcription factor (TF) - target gene associations, we identified 142 TFs and 24 chromatin remodelers/modifiers (CRMs), which are preferentially associated with specific co-expression paths that originate from deregulated gene programming during tumorigenesis. These TFs are involved in the regulation of divers processes, including cell differentiation, immune response and establishment/modification of the epigenome. Unexpectedly, the analysis of chromatin state dynamics revealed patterns that distinguish groups of genes, which are not only co-regulated but also functionally related. Further decortication of TF targets enabled us to define potential key regulators of cell transformation, which are engaged in RNA metabolism and chromatin remodelling. Our study suggests a direct implication of CRMs in oncogene-induced tumorigenesis and identifies new CRMs involved in this process. This is the first comprehensive view of gene regulatory networks that are altered during the process of stepwise human cellular tumorigenesis in a virtually isogenic system.

overall_design: Examination of 4 different histone modifications marks and RNA PolII in all 3 cell lines of stepwise tumorigenesis model with biological replicates

last: Mendoza-Parra

first: Mohamed

last: Ashick

last: Saleem

first: Hinrich

last: Gronemeyer


title: Tracing the expression of circular RNAs in human preimplantation embryos

city: beijing

first: yujiao

last: dang

address: Yihe road

institute: BIOPIC

summary: We systematically analyzed transcriptome in individual human oocytes and preimplantation embryos with a new single-cell RNA seq method we recently developed.

overall_design: We sequenced individual single cells or embryos at seven consecutive stages (mature oocytes, zygotes, 2-cell, 4-cell, 8-cell embryos, morulae, and blastocysts) and single hESC using single-cell RNA seq.

first: Yujiao

last: Dang

first: Liying

last: Yan

first: Boqiang

last: Hu


title: short RNA-Seq of Pseudomonas aeruginosa outer membrane vesicles (OMVs) and whole cells

first: Katja

last: Koeppen

summary: Characterization of the sRNA content of P. aeruginosa OMVs compared to whole cells. Result: OMVs contain differentially packaged sRNAs.

overall_design: Whole cell PA14 and OMVs from 3 separate preparations.

first: Thomas

middle: H

last: Hampton

first: Michael

last: Jarek

first: Maren

last: Scharfe

first: Scott

last: Gerber

first: Emily

last: Dolben

first: John

last: Hammond

first: Deborah

last: Hogan

first: Bruce

last: Stanton


title: Genome-wide analysis of Estrogen Receptor-mediated response to acute Estradiol treatment in liver

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

institute: CNRS UMR 6290


title: Genome-wide analysis of Estrogen Receptor-mediated response to acute Estradiol treatment in liver (ChIP-seq)

summary: Estrogen-based treatments have numerous extra-reproductive effects. On the one hand, they have protective metabolic actions against abdominal fat accumulation, type 2 diabetes, liver steatosis,… But, on the other hand, the oral route of administration, presumably due to a hepatic impact on liver-derived coagulation factors, appears to increase risks of venous thrombosis and pulmonary embolism. The characterization of liver genes expression regulations by these hormones thereby appears of utmost interest, but the estrogen-sensitive transcriptome of liver and ER cistrome was so far explored under chronic hormonal treatment. To explore the early steps of these mechanisms, we determined here the short-term changes in liver transcriptional responses to acute E2 administration, and aimed to characterize the mechanisms allowing these programs to be engaged. Collectively, through the comparison of mice expressing or not ER, our data demonstrate that acute administration of E2 provokes genes expression variations which fit with a crucial role of ER in the prevention of liver steatosis in mice fed with a high fat diet by E2. They also evidenced higher proportion of ER binding sites (BSs) located at the direct vicinity (distance <3kb) of regulated genes than what is determined in human cancer cell models. Besides this specific aspect of ER cistrome in vivo, we unexpectedly found that 40 % of the BSs of the pioneer factor Foxa2 were dependent upon the expression of ER that indirectly influences the distribution of the nucleosomes harbouring a dimethylated H3K4 around these Foxa2 sites.

overall_design: Whole-genome analysis of estrogen receptor (ER) and FOXA2 binding events associated with the cartography of two histone marks (H3K4me2 and H3K27ac) in livers from wild-type or ERKO mice.

first: Gaëlle

last: Palierne

first: Aurélie

last: Fabre

first: Romain

last: Solinhac

first: Christine

last: Le Péron

first: Stéphane

last: Avner

first: Francoise

last: Lenfant

first: Coralie

last: Fontaine

first: Gilles

last: Salbert

last: Flouriot

first: Jean

last: Arnal


title: H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [Ring1b_ChIP]

first: Peter

last: Lewis

overall_design: Examination of genome-wide Ring1b distribution in cells expressing H3.3WT and H3.3K36M.

first: Chao

last: Lu

first: Siddhant

last: Jain


title: H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [ChIP-Rx]

overall_design: Examination of 3 different histone post-translational modifications in 2 cell types.


title: Histone H3K36M mutation impairs mesenchymal differentiation and drives sarcoma development [RNA_H33_K36M_HMT]

summary: The goal of this study is to understand the alterations in transcriptome induced by histone H3K36M mutations

overall_design: Transcritome profiling of 3 cell lines cultured in vitro and 6 murine tumors


title: H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [RNA_H31K36M_H33LAIMR]

overall_design: Transcritome profiling of C3H101/2 cells cultured in vitro and expressing 8 difference transgenes


title: Genome-wide analysis of DNA methylation in the sexual stage of the insect pathogenic fungus Cordyceps militaris

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

summary:
Genome-wide analysis of DNA methylation for asexual and sexual stages of  Cordyceps militaris
DNA methylation is a basic epigenetic mechanism found in eukaryotes, but its patterns and roles vary significantly among diverse taxa. In fungi, DNA methylation has various effects on diverse biological processes; however, its function underlying the sexual development of fungi remains unclear. Cordyceps militaris, readily performing sexual reproduction, provides a remarkably rich model for understanding epigenetic processes in sexual development. The methylome was surveyed to assess DNA methylation patterns of the nascent fruiting body in C. militaris at single-base resolution by genomic bisulfite sequencing (BS-Seq). The results showed that around 0.4 % of cytosines are methylated, and that there is no difference compared with the DNA methylation level (0.39 %) during asexual development. However, 225 differentially methylated regions (DMRs) were identified between the stages. Moreover, RNA-Seq analysis indicated that the DMRs have no direct relation with the genes for fungal sexual development in C. militaris. DNA methylation regions from the BS-Seq show a striking correspondence to regions predicted to be repetitive and repeat-induced point mutation (RIP) mutated, suggesting that DNA methylation functions as a genome defense mechanism in sexual development. These results provide a comprehensive characterization of DNA methylation in the sexual development of C. militaris, which will contribute to future investigations of epigenetics in fungi.

overall_design: Bisulphite converted genomic DNA from the mycelium and fruitingbody of Cordyceps militaris

first: Yu-long

first: Bo

last: Huang


title: Regulation of cuticle formation during fruit development and ripening in 'Newhall' navel orange (Citrus sinensis Osbeck) revealed by transcriptomic and metabolomic profiling

city: wuhan

first: jinqiu

last: wang

state: hubei

address: Shizishan Street

institute: College of Horticulture and Forestry, Huazhong Agricultural University

summary: To investigate global genome expression changes during fruit developmemt, We then performed genome-wide expression analyses on the fruit peel at 120 and 150 DAF with RNA-seq approach.A total of 865 genes were identified as differentially expressed, among which 494 genes were up-regulated and 371 genes were down-regulated in the fruits harvested at 150 DAF compared with in those harvested at 120 DAF.In general, data obtained from RNA-seq showed that the genes involved in photosynthesis and tetrapyrrole synthesis were significantly repressed at 150 DAF; in contrast, the genes involved in secondary metabolism including the biosynthesis of wax, terpenoids and phenylpropanoid were significantly induced at 150 DAF.

overall_design: Total four sample pools (two independent biological replicates of fruits peel from 120 DAF and 150 DAF)

first: Jinqiu

first: Yunjiang

last: Cheng


title: Control of Neuronal Synapse Specification by a Highly Dedicated Alternative Splicing program

status: Public on May 12 2016

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: The RNA binding protein SLM2 represents a major functional determinant of neuronal function by directing the splice isoform identity of synaptic recognition receptors.

overall_design: Examination of overall gene expression and alternative splicing events in hippocampi of wild-type and SLM2KO animals.

last: Scheiffele

first: Lisa

last: Traunmüller


title: Opposing Effects of Cyclooxygenase-2 (COX-2) on Estrogen Receptor β (ERβ) Response to 5α-reductase Inhibition in Prostate Epithelial Cells

city: Pittsburgh

first: Donald

middle: B

last: DeFranco

state: PA

address: 3501 Fifth Ave

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: Current pharmacotherapies for symptomatic benign prostatic hyperplasia (BPH), an androgen receptor (AR) driven, inflammatory disorder affecting elderly men, include 5α-reductase (5AR) inhibitors (i.e. dutasteride and finasteride) to block the conversion of testosterone to the more potent AR ligand dihydrotestosterone (DHT). Since DHT is the precursor for estrogen receptor β (ERβ) ligands, 5AR inhibitors could potentially limit ERβ activation, which maintains prostate tissue homeostasis. We have uncovered signaling pathways in BPH-derived prostate epithelial cells (BPH-1) that are impacted by 5AR inhibition. The induction of apoptosis and repression of the cell-adhesion protein E-cadherin by the 5AR inhibitor, dutasteride, requires both ERβ and TGFβ. Dutasteride also induces cyclooxygenase type 2 (COX-2), which functions in a negative-feedback loop in TGFβ and ERβ signaling pathways as evidenced by the potentiation of apoptosis induced by dutasteride or finasteride upon pharmacological inhibition or shRNA-mediated ablation of COX-2. Concurrently, COX-2 positively impacts ERβ action through its effect on the expression of a number of steroidogenic enzymes in the ERβ-ligand metabolic pathway. Therefore, effective combination pharmacotherapies, which have included non-steroidal anti-inflammatory drugs, must take into account biochemical pathways affected by 5AR inhibition and opposing effects of COX-2 on the tissue protective action of ERβ.

overall_design: Next-generation sequencing (n=3) of shRNA mediated knockdown of COX-2 or scrambled control in BPH-1 prostate epithelial cell line

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