title: The DPYSL2 gene connects mTOR and schizophrenia

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

summary: We report a transcriptome comparison of HEK293 cells modified at the DPYSL2 gene promoter dinucleotide repeat (chr8:26,435,510-26,435,534) by CRISPR/Cas9 to change from the common 11 repeats to the more rare 13 repeats

overall_design: 11/11 repeat HEK 293 cells were modified by CRISPR/Cas 9. Cell were flow sorted by the co-transfected GFP and single cells were expanded. From those we selected 4 modified and 8 unmodified clones for RNA seq. RNA was extracted at 80% confluency


title: LaminB1 DamID in HT1080 fibroblasts overexpressing NET29/TMEM120A, NET39/PPAPDC3 or NET47/TM7SF2

status: Public on Dec 31 2016

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Maps of genomic regions in proximity to the nuclear lamina were determined in untreated HT1080 fibroblasts and HT1080 stable cell lines expressing NET29/TMEM120A, NET39/PPAPDC3 or NET47/TM7SF2 as GFP fusions

overall_design: The nuclear transmembrane proteins (NETs) NET29/TMEM120A, NET39/PPAPDC3 and NET47/TM7SF2 are able to reposition chromosomes towards/away from the nuclear envelope when overexpressed or knocked down in HT1080 cells. In this study we wanted to investigate peripheral chromatin changes after overexpression of these NETs.

middle: I

first: Nikolaj

last: Zuleger

first: Eric

middle: C

last: Schirmer


title: Rev-erb alpha citrome in brown adipose tissue

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary: We have reported that cold temperature challenge results in a dramatic decrease in levels of the transcriptional repressor, Rev-erb alpha. Performing Rev-erb alpha ChIP-seq on brown adipose from wildtype animals kept at thermoneutrality or cold-challenged (and using Rev-erb alpha KO brown adipose as a control), we were able to globally determine the genomic regions undergoing Rev-erb alpha-dependent de-repression.

overall_design: Examination of Rev-erb alpha binding in brown adipose tissues under thermoneutral and cold-challenged conditions

first: Zach

last: Gerhart-Hines

first: Dan

last: Feng

first: Matthew

middle: J

last: Emmett

first: Logan

last: Everett

first: Kyoung-Jae

last: Won

first: Mitchell

middle: A

last: Lazar


title: Defining the regulon of a CzcRS-like two-component system in Burkholderia cenocepacia K56-2

status: Public on Jan 01 2017

city: Exeter

first: Alan

middle: Reid

last: Brown

state: Devon

address: Geoffrey Pope Building, Stocker Road

department: Biosciences

institute: University of Exeter

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Direct probing of germinal center responses reveals immunological features and bottlenecks for nAb responses to an engineered HIV trimer

city: La Jolla

first: Shane

last: Crotty

state: CA

address: 9420 Athena Cir

department: Division of Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

summary: Generation of Tier 2 HIV neutralizing antibody (nAb) responses by immunization remains a challenging problem, and the immunological barriers to induction of such responses by Env immunogens remain unclear. We explored these barriers by combining a suite of innovative techniques, including longitudinal lymph node fine needle aspirates, germinal center (GC) B cell lineage tracking, and a new method for detecting and quantifying GC T follicular helper (GC Tfh) cells, in non-human primates immunized with a native-like HIV-1 Env trimer protein (BG505 SOSIP.v5.2). A majority of immunized animals (9/12) developed Tier 2 neutralizing antibodies (nAb). Tier 2 nAb development best correlated with GC B cell magnitude in response to later booster immunizations and the quality of the Tfh help. Notably, these immunological factors distinguished between qualitatively successful and unsuccessful vaccine Ab responses, as they correlated with nAb development but did not correlate with simple Env Ab binding titers. Therefore, direct probing of germinal centers in future vaccine trials is key, as this suite of technically robust approaches provides quantitation of the proximal immune correlates of neutralizing antibody development and could allow redesign of optimal multi-stage vaccination schedules.

overall_design: RNA-sequencing of circulating HIV Env-specific CD4 cells isolated from a cohort of rhesus macaques immunized with BG505 SOSIP.v5.2 HIV Env trimer. Cells were directly isolated from blood by flow cytometry using the AIM assay. Total RNA was extracted, messenger RNA was selected and cDNA was amplified linearly with a PCR based method (Picelli et al. 2014). Libraries were prepared. using the NexteraXT Illumina sequencing platform.

first: Colin

last: Havenar-Daughton

first: Samantha

middle: M

last: Reiss

first: Sandy

last: Rosales

first: Grégory

last: Seumois


title: Temporal gene expression in Escherichia coli

city: Marburg

first: Patrick

last: Sobetzko

address: Hans-Meerwein-Straße

department: Department of Chromosome Biology

country: Germany

institute: Philipps-Universität Marburg LOEWE-Zentrum für Synthetische Mikrobiologie

summary: In Escherichia coli crosstalk between DNA supercoiling, nucleoid-associated proteins and major RNA polymerase σ initiation factors regulates growth phase-dependent gene transcription. We show that the highly conserved spatial ordering of relevant genes along the chromosomal replichores largely corresponds both to their temporal expression patterns during growth and to an inferred gradient of DNA superhelical density from the origin to the terminus. Genes implicated in similar functions are related mainly in trans across the chromosomal replichores, whereas DNA-binding transcriptional regulators interact predominantly with targets in cis along the replichores. We also demonstrate that macrodomains (the individual structural partitions of the chromosome) are regulated differently. We infer that spatial and temporal variation of DNA superhelicity during the growth cycle coordinates oxygen and nutrient availability with global chromosome structure, thus providing a mechanistic insight into how the organization of a complete bacterial chromosome encodes a spatiotemporal program integrating DNA replication and global gene expression.

overall_design: Temporal gene expression data taken at 60, 120, 180 300 (wt only) and 420 min under controlled growth conditions. See also methods of Sobetzko et al. 2012

first: Monika

last: Glinkowska

first: Georgi

last: Muskhelishvili


title: LSD1 mediates MYCN control of epithelial-mesenchymal transition through silencing of metastatic suppressor NDRG1 gene

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

summary: Neuroblastoma (NB) with MYCN amplification is a highly metastatic tumor in children, and unraveling the key players involved in MYCN-induced invasion may identify new targets for therapy. Epithelial-mesenchymal transition (EMT) plays a critical role in promoting metastasis and we have recently determined that MYCN interacts with LSD1, a histone de-methylase flavin oxidase, which has been found to promote EMT. We show here that LSD1 affects motility and invasiveness of NB cells through transcription modulation of the metastasis suppressor NDRG1, N-Myc Downstream-Regulated Gene 1. LSD1 co-localizes with MYCN at the promoter region of the NDRG1 gene and it inhibits its expression. LSD1-inhibition relieves NDRG1 repression induced by MYCN with concomitant block of motility and invasiveness of NB cells, and such effects were recapitulated by overexpressing NDRG1. Moreover, we found that low NRDG1 and high LSD1 levels in NB patients were associated with poor survival. These data suggest that LSD1 inhibition may knock down the ability of MYCN-amplified Neuroblastomas to metastasize. Our findings elucidate a mechanism of how MYCN/LSD1 control motility and invasiveness of NB cells through transcription regulation of NDRG1 expression and they suggest that pharmacological targeting of LSD1 could inhibit the NB metastatic process.

overall_design: Examination of mRNA levels in SHEP Tet-21/N cells treated with TCP (tranylcypromine) and siLSD1.

first: Susanna

last: Ambrosio

first: Carmen

middle: D

last: Saccà

first: Mario

last: Capasso

first: Raffaele

last: Calogero

first: Luigi

last: Lania

first: Barbara

last: Majello


title: Transcriptome analysis of Drosophila Kr-h1 mutants

city: Providence

first: Hua

last: Bai

state: RI

address: 34 Olive St, BMC502

department: EEB

institute: Brown University

summary: Transcriptome analysis (RNA-Seq) was performed to identify Kr-h1 target genes. Message RNAs were extracted from wildtype and kr-h1[7] homozygous 3rd instar larvae at 100 hr after egg laying (two biological replicates for each genotype).

overall_design: Examination of transcript levels between wildtype and kr-h1 mutant larvae at 100 hr after egg laying


title: The Nuclear Receptor Rev-erb alpha Regulates Adipose Tissue-Specific FGF21 Signaling (GRO-seq)

first: Hee-Woong

last: Lim

summary: Based upon integrated analysis of transcriptomes and cistromes in Rev-erb alpha knock-out mice, we found that beta-Klotho (KLB) mRNA and protein are markedly induced in white adipose tissue but not in brown adipose tissue or liver of mice lacking Rev-erb alpha. In order to address the mechanism of the tissue-specific regulation of Klb transcription by Rev-erb apha, we performed global run-on followed by high-throughput sequencing (GRO-seq) to measure nascent transcription in different tissues in wildtype mice and Rev-erb alpha knock-out mice.

overall_design: Nascent RNA transcripts in mouse adipose tissue depots (brown adipose tissue, epididymal white adipose tissue, and inguinal white adipose tissue) were profiled in wildtype mice and Rev-erb alpha knockout mice.

first: Jennifer

last: Jager

first: Fenfen

last: Wang

first: Bin

last: Fang

first: David

last: Steger

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: Effective Detection of Variation in Single Cell Transcriptome using MATQ-seq

city: HOUSTON

first: Kuanwei

last: Sheng

state: TX

address: ONE BAYLOR PALAZA

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: We report here a new single-cell RNA-seq assay, Multiple Annealing and dC-Tailing based Quantitative single-cell RNA-seq (MATQ-seq), which provides the accuracy and sensitivity that enable the detection of transcriptional variations existing in single cells of the same type. We performed a systematic characterization of the technical noise using pool-and-split averaged single-cell samples and showed that the biological variations in single cells were observed with statistical significance.

overall_design:
10 HEK293T single cells and 10 HEK293T pool-and-split averaged single cell samples were sequenced with MATQ-seq. We also sequenced 6 MCF10A single cells and 6MCF10A pool-and-split averaged single cell samples.
To characterize the capture efficiency, we also sequenced 6 averaged one-fifth MCF10A single-cell samples with ERCC spike-in.
Additional 38 HEK293T single cells (HEK293T_clone1_SC*) and 10 HEK293T pool-and-split averaged single cell samples (HEK293T_clone1_SC_average*) were sequenced with MATQ-seq.

first: Chenghang

last: Zong


title: Zinc acquisition in Pseudomonas aeruginosa

city: Adelaide

first: Bart

last: Eijkelkamp

state: SA

address: North Tce

country: Australia

institute: University of Adelaide

summary: This study addresses the impact of zinc limitation on the opportunistic human pathogen, Pseudomonas aeruginosa. Zinc limitation was assessed in the P. aeruginosa PAO1 strain using an isogenic deletion mutant lacking the periplasmic, zinc solute-binding protein, znuA (PA5498). ZnuA delivers bound zinc to its cognate ABC transporter, ZnuBC, for import into the cytoplasm. Our transcriptional analyses revealed P. aeruginosa to possess a multitude of zinc acquisition mechanisms, each of which were highly up-regulated in the zinc-deficient znuA mutant strain. P. aeruginosa also utilized zinc-independent paralogues of zinc-dependent genes to maintain cellular function under zinc limitation. Together, these data reveal the complex transcriptional response and versatility of P. aeruginosa to zinc depletion.

overall_design: The WT (zinc replete) and znuA mutant strain (zinc limited) were grown in cation-defined media to mid-log phase prior to RNA isolation and analysis.

first: Victoria

middle: G

last: Pederick

first: Stephanie

middle: L

last: Begg

first: Lauren

last: McAllister

first: James

last: Paton

first: Christopher

last: McDevitt


title: Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to Nodal/Activin signaling

city: London

first: Caroline

middle: S

last: Hill

address: 1 Midland Road

department: Developmental Signalling

institute: Francis Crick Institute


title: Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF [ChIP-Seq]

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

summary: The homeotic genes (Hox genes) encode transcription factors (HOX-TFs) that are key regulators of animal development. Single and compound deletion of Hox genes in mice revealed that they act in a partially redundant manner to pattern the vertebrate limb. Biochemical screens probing the sequence specificity of the DNA-binding domains showed that HOX-TFs recognize largely similar DNA sequences, but also emphasized the important role of co-factors in HOX DNA-binding.  However, due to their high sequence homology and overlapping expression patterns, little is known about the genome-wide binding of these transcription factors  Here, we set out to systematically compare the effects of the nine limb-bud expressed HOX-TFs on cell differentiation and gene regulation, and compare their genome-wide binding characteristics. We find that HOX-TFs induce distinct regulatory programs in transduced cells. Through genome-wide DNA binding profiling we find that the posterior HOX-TFs can be separated into two groups with distinct binding motifs and association with co-factors. Through this unexpected grouping, we characterize the CCCTC-binding factor (CTCF) as a novel co-factor of HOX-TFs and show that one, but not the other group of HOX-TFs binds to thousands of CTCF-occupied sites in the chicken genome.

overall_design: Examination of the binding of 10 different transcription factors, a Cohesin subunit and an expression analysis (RNAseq analysis) in the chicken primary cell culture overexpression system.

first: Ivana

last: Jerković

first: Guillaume

last: Andrey

first: Jochen

last: Hecht

first: Stefan

last: Mundlos


title: Epigenetic therapy as a novel approach for GFI136N-associated AML

city: Essen

first: Cyrus

last: Khandanpour

address: Hufelandstr. 55

institute: Universitätsklinikum Essen

summary: Acute myeloid leukemia (AML) is characterized by accumulation of myeloid blast cells in the bone marrow. Despite all efforts, prognosis of AML patients remains poor, warranting new therapeutic approaches. A single nucleotide polymorphism of growth factor independence 1 (GFI1), a hematopoietic transcription factor, generates a protein with an asparagine (GFI136N) instead of a serine at position 36 (GFI136S), which we have previously reported to be associated with de novo AML in humans. Using knock-in mouse strains, in which the endogenous murine Gfi1 coding sequences are substituted by human GFI136N or GFI136S, we found that GFI136N shortened latency and increased incidence of AML in three different, well-established murine models of AML. On a molecular level, the presence of GFI136N was associated with increased acetylation of histone H3 at lysine 9 (H3K9) at Gfi1 target genes in both murine and human samples, contributing to AML development. Since in GFI136N containing leukemic cells Gfi1 target genes have hyperacetylated H3K9, the treatment strategy currently used with histone deacetylases inhibitors (HDACis) might not be beneficial. We show that treatment with an HDACi impeded growth of murine and human cells homozygous for GFI136S, but had a limited effect on cells expressing GFI136N. In contrast, treatment with a histone acetyltransferase inhibitor (HATi) specifically targeted GFI136N-expressing malignant cells while sparing non-malignant cells. These results establish, as a proof of principle, how epigenetic changes in GFI136N-induced AML can be exploited to treat AML and implicate HATi as a new, more effective potential therapeutic strategy for GFI136N AML patients.

overall_design: one sample per genotype has been sequenced

first: Lacramioara

last: Botezatu

first: Lars

last: Michel

first: Anne

last: Helness

first: Charles

last: Vadnais

first: Judith

last: Hönes

first: François

last: Robert

first: Damien

last: Grapton

first: Lothar

last: Vassen

first: Jan

last: Fleckhaus

last: Schütte

first: Bernd

last: Giebel

first: André

last: Görgens

first: Michael

last: Heuser

first: Hind

last: Medyouf

first: Ulrich

last: Dührsen

first: Jaroslaw

last: Maciejewski

first: Tarik

last: Möröy


title: Transcriptome comparison of LUBEL catalytic dead mutants to their parental line

city: Wien

first: Fumiyo

last: Ikeda

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

summary: Effect of LUBEL catalytic dead mutation in immune response

overall_design: Mutation was introduced in the LUBEL catalytic region by CRISPR/Cas9 techonology in Drosophila melanogaster and their transcriptome was compared in control (sample 23930 to 23941) and e.coli pricked samples (sample 28984 to 28995).

first: Sini

last: Junttila


title: Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF [RNA-Seq]

first: Daniel

last: Ibrahim

first: Ivana

last: Jerković

first: Guillaume

last: Andrey

first: Jochen

last: Hecht

first: Stefan

last: Mundlos


title: Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF


title: Genome-wide analysis of the circulating miRNome after cerebral ischemia reveals a reperfusion-induced microRNA cluster

city: Heidelberg

last: Uhlmann

address: INF 400

department: Department of Neurology

institute: University of Heidelberg

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background and Purpose - Circulating microRNAs (miRNAs) are emerging biomarkers for stroke due to their high stability in the bloodstream and association with pathophysiologic conditions. However, the circulating whole-genome miRNAs (miRNome) has not been characterized comprehensively in the acute phase of stroke.

Methods - We profiled the circulating miRNome in mouse models of acute ischemic and hemorrhagic stroke by next-generation sequencing (NGS). Stroke models were compared to sham-operated and naïve mice to identify deregulated circulating miRNAs. Top-ranked miRNAs were validated and further characterized by qRT-PCR.

Results - We discovered 24 circulating miRNAs with an altered abundance in the circulation 3 hours following ischemia, whereas the circulating miRNome was not altered after intracerebral hemorrhage compared to sham-operated mice. Among the upregulated miRNA in ischemia, the top-listed miR-1264/1298/448 cluster was strongly dependent on reperfusion in different ischemia models. A time course experiment revealed that the miR-1264/1298/448 cluster peaked in the circulation around 3 hours after reperfusion and gradually decreased thereafter.

Conclusions - Alteration of the miRNome in the circulation is associated with cerebral ischemia/reperfusion, but not hemorrhage, suggesting a potential to serve as biomarkers for reperfusion in the acute phase. The pathophysiological role of reperfusion-inducible miR-1264/1298/448 cluster, which is located on chromosome X within the introns of the serotonin receptor HTR2C, requires further investigation.

overall_design:
Profiling of the circulating miRNome in mouse models of acute ischemic and hemorrhagic stroke by next-generation sequencing (NGS)

MCAO: Filament-induced ischemia experiment, which led to a transient focal cerebral ischemia through the occlusion of the left-sided middle cerebral artery (MCAO). Afterwards mice were re-anesthetized and the filament was removed following 30 min of ischemia. Blood was collected after 150 min of reperfusion and subsequently the serum was isolated to measure the abundance of circulating miRNA.

MCAO-Sham: The preparation for the sham surgery was identical but the filament was not inserted into the vessel of the middle cerebral artery (MCO).

ICH: This blood infusion model was used to simulate ICH (intracerebral hemorrhage) in mice. Briefly, after placing the anesthetized animals in a stereotactic frame, a borehole was drilled at 2.2 mm left and 0.2 mm anterior to the bregma. Using an infusion system containing a 26 G needle connected to a 50 μl microsyringe, 20 μL of autologous blood was infused into the striatum at a depth of 3.7 mm.

ICH-Sham: Sham operation was conducted by the same procedure and duration including placement of the microneedle but without injection of fluid.

Naïve: Received no treatment.

first: Eva

last: Mracsko

first: Ehsan

last: Javidi

first: Sarah

last: Lamble

first: Ana

last: Teixeira

first: Agnes

last: Hotz-Wagenblatt

first: Karl-Heinz

last: Glatting

first: Roland

last: Veltkamp


title: Ebolavirus species associated with differential pathogenicity induce distinct host responses in human macrophages

city: New York

first: Angela

last: Rasmussen

state: NY

department: Center for Infection and Immunity

institute: Columbia University

summary: Highly pathogenic Zaire ebolavirus (EBOV) infection is associated with a dysregulated immune response and high levels of cytokines and chemokines are observed in fatal human cases. . In stark contrast Reston ebolavirus (RESTV) might be non-pathogenic for humans yet the underlying mechanisms determining pathogenicity for different Ebola viruses are not understood. In this study we investigate antiviral immune responses in EBOV- and RESTV- infected primary human monocyte-derived macrophages (MDM). We provide evidence that increased pathogenicity of the highly pathogenic EBOV is associated with a strong activation of host responses from infected MDM. The observed cytokine response after EBOV infection is strikingly similar to LPS-mediated immune signatures however EBOV caused significant induction of the interferon response in addition. In contrast we show that the low pathogenic RESTV fails to elicit significant immune responses in infected MDM. These results demonstrate a correlation of pathogenicity and excessive MDM activation for different Ebola virus species. Interaction of the viral glycoprotein (GP) with Toll-like receptor 4 (TLR4) leading to activation of NF_B signaling is responsible for this effect rather than differences in replication or blocking of immune signaling. We demonstrate that inhibition of TLR4 is able to abolish EBOV-GP mediated NF_B activation which might offer the possibility to develop targeted treatments for EBOV limiting the extreme immune response that seems to be detrimental to the host.

overall_design: RNA was isolated from primary cultured human macrophages (n=3 donors) that were either mock-infected, infected with Ebola virus (Kikwit-95) or Reston virus (Pennsylvania), or treated with lipopolysaccharide (LPS).

first: Judith

last: Olejnik

first: Adriana

last: Forero

first: Elke

last: Mühlberger


title: Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to Nodal/Activin signaling [Epigenetic marks and RNA PolII ChIP]

first: Caroline

last: Hill

summary: During development, key processes are orchestrated by Nodal/Activin signaling via SMAD2. Interplay between the SMADs, co-factors and chromatin determines cell-type specific responses, but the sequence of events underpinning SMAD2-mediated transcription is unknown. We performed RNA-and ChIP-sequencing for SMAD2, RNA Polymerase II and various histone modifications in different signaling states. Integration of these data reveals a dynamic transcriptional network downstream of Nodal/Activin signaling regulated by SMAD2 acting via multiple mechanisms. Upon  ligand stimulation, SMAD2 can bind to pre-acetylated nucleosome-depleted sites, but also to unacetylated closed chromatin, where it induces nucleosome displacement and histone acetylation. Importantly, SMAD2 binding is highly dynamic and does not directly correlate with the transcriptional kinetics of target genes. Moreover, we show that SMAD2 initiates transcription by inducing RNA Polymerase II recruitment. We therefore define new paradigms for SMAD2-dependent transcription and provide a framework to understand how cells correctly execute gene expression programs in response to Nodal/Activin signaling.

overall_design: RNA-sequencing, SMAD2 ChIP-sequencing, H3K9Ac, H3K27Ac, H3K9Me3, H3K27Me3, RNA Polymerase II (ser5P), RNA Polymerase II (ser2P) CHIP-sequencing performed at various time points following Activin/Nodal signal stimulation or inhibition in p19 mouse embryonic teratoma cells: signal-ihibited, 1 hr Activin, 4 hr Activin, 8 hr Activin, Untreated (chronically Nodal-signalling cells).

first: Tessa

last: Gaarenstroom

first: Davide

last: Coda

first: Philip

last: East

first: Harshil

last: Patel

last: Miller

first: Anna

last: Lobley

first: Nik

last: Matthews

first: Aengus

last: Stewart


title: The venom gland and ovary transcriptome of the parasitoid wasp Nasonia vitripennis

city: Palmerston North

first: Andre

last: Sim

address: Tennent Dr

department: Institute of Fundamental Sciences

country: New Zealand

institute: Massey University

summary: Background  The generalist dipteran pupal parasitoid Nasonia vitripennis injects 79 venom peptides into the host before egg laying. This venom induces several important changes in the host, including developmental arrest, immunosuppression, and alterations to normal metabolism. It is hoped that diverse and potent bioactivities of N. vitripennis venom provide an opportunity for the design of novel acting drugs. However, currently very little is known about the individual functions of N. vitripennis venom peptides and less than half can be bioinformatically annotated. The paucity of annotation information complicates the design of studies that seek to better understand the potential mechanisms underlying the envenomation response. Although the RNA interference system of N. vitripennis provides an opportunity to functionally characterise venom encoding genes, with 79 candidates this represents a daunting task. For this reason we were interested in determining the expression levels of venom encoding genes in the venom gland, such that this information could be used to rank candidate venoms. To do this we carried out deep sequencing of the transcriptome of the venom gland and neighbouring ovary tissue and used RNA-seq to measure expression from the 79 venom encoding genes. The generation of a specific venom gland transcriptome dataset also provides further opportunities to investigate novel features of this highly specialised organ.     Results  High throughput sequencing and RNA-seq revealed that the highest expressed venom encoding gene in the venom gland was a serine protease called Nasvi2EG007167, which has previously been implicated in the apoptotic activity of N. vitripennis venom. As expected the RNA-seq confirmed that the N. vitripennis venom encoding genes are almost exclusively expressed in the venom gland relative to the neighbouring ovary tissue. Novel peptides appear to perform key roles in N. vitripennis venom function as only four of the highest 15 expressed venom encoding genes are bioinformatically annotationed. The high throughput sequencing data also provided evidence for the existence of an additional 471 novel genes in the Nasonia genome that are expressed in the venom gland and ovary. Finally, metagenomic analysis of venom gland transcripts identified viral transcripts that may play an important part in the N. vitripennis venom function.    Conclusions  The expression level information provided here for the 79 venom encoding genes provides an unbiased dataset that can be used by the N. vitripennis community to identify high value candidates for further functional characterisation. These candidates represent bioactive peptides that have value in drug development pipelines.

overall_design: Examination of the transcriptional profile of Nasonia vitripennis ovary and venom gland cells

first: David

last: Wheeler


title: Bladder tumor sequencing

city: Cambridge

first: Kelvin

last: Zhang

state: Massachusetts

address: 35 CambridgePark Drive, Suite 500

institute: Codiak Biosciences

summary: Prospective sequencing of a patient's bladder tumor

overall_design:
We obtained fresh tissue from a patient's bladder tumor and performed whole-exome sequencing and RNA-Seq
Only the RNA-Seq data is being made available through GEO. The whole exome data will be submitted to dbGaP for controlled access.

first: Kris

last: Prado

first: Arnold

last: Chin


title: RNA-seq analysis in Jurkat cells

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

summary: RNA-seq analysis was performed in Jurkat cells (T-cell lymphoblastic leukemia cell line).

overall_design: RNA-seq analysis was performed using total RNA extracted from Jurkat cells.

first: Shi

middle: H

last: Tan

first: C

middle: T

last: Phuong

first: Takaomi

last: Sanda


title: Comparative transcriptomic and epigenomic analyses reveal new regulators of murine brown adipogenesis

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

country: China

institute: Tsinghua University

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: RNA-seq of YB5 cells treated with epigenetic therapy

city: Philadelphia

first: Takahiro

last: Sato

state: PA

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

summary: RNA-seq was performed after YB5 cells were treated with S2101, UNC0638, GSK343, depsipeptide alone or in combination with decitabine

overall_design: Biological triplicates were performed for a total of 30 samples. Fold change of each gene was calculated by comparing change in expression after inhibitor treatment to expression in the control samples

first: Matteo

last: Cesaroni

first: Shoghag

last: Panjarian

first: Anthony

last: Tran

first: Jozef

last: Madzo

first: Yasuyuki

last: Okamoto

first: Hanghang

first: Xiaowei

last: Chen

first: Jaroslav

last: Jelinek

first: Jean-Pierre

last: Issa


title: Negative allosteric modulation of mGluR5 partially corrects pathophysiology in a mouse model of Rett Syndrome

city: Boston

first: Hao

last: Wu

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: Genetics

institute: Harvard Medical School/HHMI

summary: Rett syndrome is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MECP2), an epigenetic regulator of mRNA transcription. Here we report a test of the hypothesis of shared pathophysiology of Rett syndrome and fragile X, another monogenic cause of autism and intellectual disability. In fragile X, the loss of the mRNA translational repressor FMRP leads to exaggerated protein synthesis downstream of metabotropic glutamate receptor 5 (mGluR5). We found that mGluR5- and protein synthesis-dependent synaptic plasticity is similarly altered in area CA1 of Mecp2 KO mice. CA1 pyramidal cell-type-specific, genome-wide profiling of ribosome-bound mRNAs was performed in wild-type and Mecp2 KO hippocampal CA1 neurons to reveal the MeCP2-regulated ‘translatome’. We found significant overlap between ribosome-bound transcripts overexpressed in the Mecp2 KO and FMRP mRNA targets. These tended to encode long genes that are functionally related to either cytoskeleton organization or the development of neuronal connectivity. In the Fmr1 KO mouse, chronic treatment with mGluR5 negative allosteric modulators (NAMs) has been shown to ameliorate many mutant phenotypes by correcting excessive protein synthesis. In the Mecp2 KO mice we found that mGluR5 NAM treatment significantly reduces the level of overexpressed ribosome-associated transcripts, particularly those that are also FMRP targets. Some Rett phenotypes were also ameliorated by treatment, most notably hippocampal cell size and life span. Together, these results suggest a potential mechanistic link between MeCP2-mediated transcription regulation and mGluR5/FMRP-mediated protein translation regulation through co-regulation of a subset of genes relevant to synaptic functions.

overall_design: TRAP-seq analysis of the effect of negative modulator of mGluR5 on the CA1 neurons (marked by Cck-EGFP-L10a) of a mouse model of Rett syndrome

first: Jifang

last: Tao

first: Mark

last: Bear


title: RNA-seq of MCF7 cells treated with epigenetic therapy

summary: RNA-seq was performed after MCF7 cells were treated with S2101, UNC0638, GSK343, depsipeptide alone or in combination with decitabine

last: Zhang


title: Comparative transcriptomic and epigenomic analyses reveal new regulators of murine brown adipogenesis [Seq]

summary: Increasing energy expenditure by promoting the thermogenic program in brown adipocytes is a promising approach to combat human obesity. To fully exploit the potential of this approach a comprehensive understanding of the gene regulatory network that controls both lineage commitment and differentiation of brown cells is necessary. Here, we systematically examine the transcriptomic and epigenomic transitions from mesenchymal stem cells to brown adipocytes (BA) and we perform a comparative analysis with differentiating white adipocytes (WA). We identify coding genes, lncRNA genes, and microRNA genes that are differentially regulated upon BA differentiation. In addition, we generate genome wide reference maps for several chromatin marks throughout brown adipogenesis. We identify putative (super-)enhancers, super-enhancers controlled genes in brown and white adipocytes, as well as target genes of the brown lineage-committing factor BMP7. Finally we show that overexpression and knockdown of four putative novel adipogenic regulators (the kinase Pim1, and the transcription factors Six1, Rreb1, and Sox13), indeed affects BA differentiation, suggesting an important role in brown adipogenesis.

overall_design: The murine mesenchymal stem cell line C3H10T1/2 was differentiatied into brown adipocytes and ChIP-seq (Input, H3K27ac, H3K4me3, H3K4me1, H3K9ac, PPARG, SIX1; samples 1-32), and RNA-seq (samples 33-42) were generated at different timepoints. Samples 43-48 contain RNA-seq data from the murine white preadipcyte cell line 3T3-L1 at different timopints of differentiation and samples 49-53 contain RNA-seq data from  C3H10T1/2 cells differentiated without addition of BMP7.

first: Reinhard

last: Brunmeir

first: Jingyi

first: Xu

last: Peng

first: Feng

last: Xu


title: Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to Nodal/Activin signaling [SMAD2 ChIP & RNA-seq]

first: Caroline

last: Hill

overall_design: RNA-sequencing, SMAD2 ChIP-sequencing, H3K9Ac, H3K27Ac, H3K9Me3, H3K27Me3, RNA Polymerase II (ser5P), RNA Polymerase II (ser2P) CHIP-sequencing performed at various time points following Activin/Nodal signal stimulation or inhibition in p19 mouse embryonic teratoma cells: signal-ihibited, 1 hr Activin, 4 hr Activin, 8 hr Activin, Untreated (chronically Nodal-signalling cells)

first: Tessa

last: Gaarenstroom

first: Davide

last: Coda

first: Philip

last: East

first: Harshil

last: Patel

first: Daniel

last: Miller

first: Anna

last: Lobley

first: Nik

last: Matthews

first: Aengus

last: Stewart


title: Identification of genes cooperating with PML/RAR in leukemogenesis

city: Milan

first: Chiara

last: Ronchini

address: Via Adamello, 16

department: Center for Genomic Science of IIT@SEMM

institute: Istituto Italiano di Tecnologia

summary: The oncogenic fusion protein PML/RAR is expressed in most cases of acute promyelocytic leukemia (APL). In transgenic models, PML/RAR is able to induce a preleukemic state. However, it is not sufficient to induce leukemia, which develops with low frequency (~50%) and long latency (about 1 year). These data indicate that secondary genetic cooperating alterations are required in order to induce leukemia. In an effort to identify the genes that cooperate in the leukemogenesis PML/RAR-dependent, we performed an insertional mutagenesis screening infecting the PML/RAR KI mice with Moloney Murine Leukemia Virus (MLV). The infection of the PML/RAR KI mice significantly accelerated the onset (~6 months) and increased the penetrance (~75% of infected animals) of the leukemia. To identify genes mutated by the proviral integrations, flanking sequences of the retrovirus insertions were cloned by IPCR and analysed by parallel sequencing. We sequenced DNAs from the spleen of 48 independent leukemic mice. After filtering, ~133,000 reads were univocally mapped onto the mouse genome. Of them, ~131,000 were present more than once in the DNA from the same mouse and produced a total of 1,707 independent genomic insertions (retroviral insertion sites - RISs). To identify chromosomal regions that are frequently mutated by retrovirus insertions (common insertion sites; CISs), we evaluated the density of RISs distribution over the mouse genome, using statistical approaches that calculate the significance of RISs occurrence (p<0.05) within specific genomic regions (Monte Carlo simulation or Kernel Convolution). The two different approaches identified the same set of 221 CISs. Finally, we identified 271 genes putatively targeted by retroviral insertions in the 221 CISs. These putative targets appeared to be enriched in genes identified as relevant cancer-genes in different tumor types. Moreover, from a biological point of view, our screening was performed in saturating conditions. Therefore, to our knowledge, our is the first report of an exhaustive list of virtually all the mouse genes that functionally cooperate with PML/RAR in the induction of APL.

overall_design:
Insertional mutagenesis screen by infection with MLV of PML/RAR KI transgenic mice (analysis of 48 independent leukemias).
PML/RAR KI newborn mice were injected i.p. with viral supernatant containing high titer MLV. At signs of disease mice were sacrificed and underwent necropsy. Infiltrated organs were collected and frozen.

first: Alessandro

last: Brozzi

first: Lucilla

last: Luzi

first: Laura

last: Riva

first: PierGiuseppe

last: Pelicci


title: The transcriptome of central nervous system myelin

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

summary: Rapid nerve conduction in the CNS is facilitated by the insulation of axons with myelin, a specialized oligodendroglial compartment distant from the cell body. Myelin is turned over and adapted throughout life; however, the molecular and cellular basis of myelin dynamics is not well understood. Hypothesizing that only a fraction of all myelin-related mRNAs has been identified so far, we subjected myelin biochemically purified from mouse brains at various ages to RNA sequencing. We find a surprisingly large pool of transcripts abundant and/or enriched in myelin. By bioinformatic comparison, the myelin transcriptome is closely related to the myelin proteome but clearly distinct from the transcriptomes of oligodendrocytes and brain tissues, suggesting that the incorporation of mRNAs into the myelin compartment is highly selective. The mRNA-pool in myelin displays maturation-dependent dynamic changes of composition, abundance, and functional associations; however ageing-dependent changes after 6 months of age were minor. We suggest that this transcript pool provides a basis for the local modulation of myelin turnover and adaptation, i.e. in the individual internode.

overall_design: RNA-seq of different stages of myelin

first: Angela

last: Garding

first: Ramona

middle: B

last: Jung

first: Christina

last: Müller

first: Sandra

last: Goebbels

first: Robin

last: White

first: Hauke

last: Werner

first: Vijay

last: Tiwari


title: Biallelic mutations in the 3’ exonuclease TOE1 cause Pontocerebellar Hypoplasia Type 7 and result in snRNA processing defects

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Processing of RNA polymerase II-transcribed spliceosomal small nuclear RNAs (snRNAs) initiates with cleavage by the Integrator complex, but the factors that subsequently remove 3’ end extensions from metazoan snRNAs have remained unknown. We studied human families with a unique recessive syndromic constellation of pontocerebellar atrophy with ambiguous genitalia, uncovering biallelic inactivating mutations in TOE1, which encodes a conserved unconventional deadenylase. TOE1 demonstrated tight association with snRNA-protein (snRNP) complexes with specificity for incompletely processed pre-snRNAs containing 3’ end extensions that often included post-transcriptionally added tails. Human cells deficient for TOE1 catalytic activity showed accumulation of 3’-end extended U1, U2, U4 and U5 pre-snRNAs, and TOE1 immuno-isolated from human cells was capable of processing 3’-end extended snRNPs in vitro. The missense mutations identified in patients impaired TOE1 stability and snRNA processing in patient cells, which was associated with defects in splicing. Our findings reveal the cause of a unique brain malformation and uncover a long-sought 3’ exonuclease required for snRNA processing.

overall_design: We performed 154 experiments to profile snRNA tails for U1, U2, U4, and U5 snRNAs. Samples profiled include HEK 293, primary patient fibroblasts, and NPCs derived from primary patient fibroblasts, which were subjected to various treatments to study TOE1/cap1Z function (including siRNA of TOE1 compared to control siRNA, and over-expression of various TOE1 mutants compared to wild-type TOE1 and a FLAG-only control). For some indicated samples total RNA was used; for others in which FLAG-tagged TOE1 was over-expressed, profiling was performed on RNA isolated by RIP (RNA immunoprecipitation) using an anti-FLAG antibody.

first: Rea

last: Markmiller

first: Ashleigh

middle: E

last: Shaffer

first: Veerle

middle: R

last: Eggans

first: Maha

last: Zaki

first: Stephanie

last: Grainger

first: Shashank

last: Sathe

first: Eric

last: VanNostrand

first: Zinayida

last: Schlachetzki

first: Basak

last: Rosti

first: Naiara

last: Akizu

last: Scott

last: Heckman

first: Rasim

middle: O

first: Esra

last: Dikoglu

first: Anne

last: Gregor

first: Alicia

last: Guemez-Gamboa

first: Damir

last: Musaev

first: Rohit

last: Mande

first: Ari

last: Widjaja

first: Tim

last: Shaw

first: Sebastian

first: Isaac

last: Marin-Valencia

first: Nicola

last: Foulds

first: William

last: Dobyns

first: Neil

last: Chi

first: David

last: Traver

first: Luigina

last: Spaccini

first: Stefania

last: Bova

first: Stacey

last: Gabriel

first: Murat

last: Gunel

first: Enza

last: Valente

last: Bennett

middle: W

first: Frank

last: Baas

first: Jens

last: Lykke-Andersen

first: Joseph

last: Gleeson


title: Mapping the Landscape of a Eukaryotic Degronome

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

department: School of Engineering

country: Israel

institute: The Hebrew University of Jerusalem

summary: Maintenance of cellular protein homeostasis requires controlled temporal and spatial protein degradation as well as the continuous removal of damaged proteins. Despite our detailed knowledge of the cellular proteolytic network, little is known about sequence and structural determinants that target proteins for elimination (termed “degrons”). Here we introduce a systematic approach to map degrons, either native or out-of-frame. We use a reporter-based high throughput degron competition assay, followed by deep sequencing analysis, to quantitatively evaluate the degradation potency of thousands of polypeptides originating from the yeast genome (degronome). We show that our assay is quantitative and recapitulates relative degradation rates in vivo. By applying our assay in cells with deletion of the E3 ligase Doa10p, we identify specific targets in a principal branch of the ubiquitin-mediated protein quality control (PQC) pathway. We further compare nuclear and cytosolic specific degrons and identify substantial variations between the degradation signals in these respective cellular compartments. Our results provide the first comprehensive map of the yeast degronome and identify hundreds of degradation signals that reside within open reading frames of native proteins. Based on the versatility and robustness of the system described herein we anticipate that it can be utilized in more complex in vivo studies in eukaryotic cells aimed at better understanding how proteolysis regulates various cellular functions.

overall_design: Mid-log yeast mRNA was purified, reverse transcribed to cDNA and cleaved using a 4-cutter (Sau3AI). The resulting fragments were cloned into the c-terminus of a URA3-HA-GFP reporter. Each of the resulting fragments was randomly inserted into one of the three possible translation frames, followed immediately by a stop codon. Plasmids from this library were transformed into ~5x106 yeast colonies (Leu selection). These were harvested into a single flask and kept in plasmid-selective conditions with 5FOA for the duration of the experiment. Yeast samples were drawn at indicated time points and plasmid DNA was amplified using specific primers followed by high-throughput sequencing.

first: Tommer

last: Ravid


title: Next Generation Sequencing Facilitates Quantitative Analysis of HCC cells transfected with NCsiRNA or ODC1siRNA

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

summary: We investigated if targeting of ODC1 with siRNA could inhibit HCC progression. To accomplish this, Huh1 and Huh7 human HCC cells were transfected with ODC1 siRNA and tested for growth inhibition and apoptotic induction using MTS, FACS and microscopic analysis. To obtain insights into the molecular changes in response to ODC1 knockdown, global changes in gene expression were examined using RNA sequencing. Our results show that ODC1 silencing caused inhibition of HCC cell growth through blockade of cell cycle progression and a strong induction of apoptosis. Subsequent Western blotting revealed that ODC1 silencing decreased the levels of cell cycle regulator cyclin E1, PARP-1, and pro-caspase 3 accelerating apoptotic signaling in HCC cells. In addition, ODC1 silencing resulted in a strong inhibition in the expressions of important regulators of glycolysis and lipogenesis, GLUT4 and ChREBP, and caused a marked decrease in fat accumulation. These findings suggest that ODC1 can be a promising target for systemic therapy of HCC by modulating tumor metabolism.

overall_design: Examination of 2 different siRNA transfected cells in 2 cell lines.

first: Sang

last: Oh

first: Yun-Han

last: Lee


title: Genome-wide maps of transcription factor and co-factor binding and nucleosome density during B-cell to Macrophage lineage switching

city: Barcelona

first: Chris

last: van Oevelen

state: Catalunya

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: Using homogenous populations of cells undergoing cell switching we observed an interplay between lymphoid and myeloid transcription factors during lineage switching

overall_design: Examination of transcription factor binding and nucleosome density several time points after induction of transdifferentiation

first: Thomas

last: Graf


title: A Genome-Wide Identification of the miRNAome in Response to Salinity Stress in the Date palm tree (Phoenix dactylifera L.)

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary:
Purpose: To identify conserved and novel miRNAs in date palm and, most importantly, to identify miRNAs that could play a role in salt tolerance
Methods: we generated sRNA libraries from the leaves and roots of NaCl-treated and untreated seedlings of date palm,then Deep sequencing of these four sRNA libraries,last The bioinformatics analysis,further validated using semi-quantitative PCR (qPCR).
Results: Deep sequencing of these four sRNA libraries yielded approximately 251 million reads. The bioinformatics analysis has identified 153 homologs of conserved miRNAs, 89 miRNA variants, and 180 putative novel miRNAs in date palm. Expression profiles under salinity revealed differential regulation of most miRNAs in date palm. In leaves, all of the identified miRNAs were affected by the salinity treatment, and the majority (75%) of them were upregulated, whereas in roots, only 33% of the miRNAs were upregulated, but 44% of them were downregulated, while the remaining miRNAs (22%) were unaffected by the treatment. The salt responsiveness of some of these miRNAs was further validated using semi-quantitative PCR (qPCR). Some of the predicted targets for the identified miRNA include genes with known functions in plant salt tolerance, such as potassium channel AKT2-like proteins, vacuolar protein sorting-associated protein, and calcium-dependent and mitogen-activated proteins. As one of the first cultivated trees in the world with a wide range of abiotic stress tolerance, date palm contains a large population of conserved and nonconserved miRNAs that function at the posttranscriptional level.
Conclusions: This study provided insights into miRNA-mediated gene expression that are important for adaptation to salinity in date palms.

overall_design: Deep sequencing of four small RNA libraries from the leaves and roots of NaCl-treated and untreated seedlings of date palm

first: Mahmoud

last: Yaish


title: Small RNAs in rice cultivar Kasalath (Oryza sativa L.) induced by high temperatures during germination

city: Bandar Sunway

first: Huan You

last: Gan

state: Selangor

address: Jalan Lagoon Selatan

country: Malaysia

institute: Monash University Malaysia

summary: The impact of global warming on weather patterns raises concerns for agriculture management. Using NGS technologies, we identified the miRNA profile that is expressed in rice cultivar grown at two different temperatures. We observed 118 and 100 miRNAs uniquely expressed at 35°C and 25°C respectively. Potential targets of these miRNAs have been identified. An interesting example, would be mir1863b which targets Os07g46670.3; a homologue of the ERD15 gene in Arabidopsis which is involved in dehydration stress response.

overall_design: miRNA profiles were generated using the Illumina Miseq sequencer for rice cultivar biological triplicate samples grown under temperature conditions of 35°C and 25°C respectively.

first: Huan

middle: Y

first: Mohana

last: Ragu

first: Sadequr

last: Rahman


title: microRNA study of rectal tissue collected from super-shedders vs cattle negative for E. coli O157:H7

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

summary: Total microRNA from rectal tissues of E. coli O157 super-shedders and non-shedders were sequenced using Illumina Hiseq 2000 system. For comparative analysis, differentially expressed microRNAs were identified with edgeR. Two of differentially expressed genes were identified, and one of up-regulated microRNA in super-shedders potentially targets genes related to innate and adaptive immune functions.  The findings indicated that microRNA could play a role in super-shedding phenomenon.

overall_design: We performed a differential analysis of microRNA expression of rectal tissues collected from E. coli O157 super-shedders and non-shedders, targets prediction for interested microRNAs, and functional analysis for interested microRNAs, to study molecular mechanisms of super-shedding phenomenon.

first: Leluo

last: Guan

first: Ou

last: Wang


title: BT474 tumors grown in the brain and mammary fat pad

city: Charlestown

first: Kamila

last: Naxerova

state: MA

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

summary: Comparison of gene expression in tumors grown in the brains and mammary fat pads of immunodeficient mice.

overall_design: Tumors grown in the brain and mamary fat pad, 4 replicates per condition

first: Gino

last: Ferraro


title: Small RNA sequencing of WT, ∆EZL1 and ∆DCL1 cells in conjugation 3, 6 and 10 (C3, C6 anc C10) hours of Tetrahymena thermophila

city: Ann Arbor

first: Yifan

last: lIU

state: Michigan

address: 1301 Cathrine street

institute: University of Michigan

summary: The goals of this study to find the switching between ncRNA and mRNA production underlies transcription silencing and reactivation of TE-related sequences inTetrahymena thermophila.

overall_design: Small RNA sequencing data generated in WT, EZL1KO, DCL1KO cells at C3, C6 anc C10. Small RNA expression were analyzed in IES and the EZL1KO and DCL1KO induced non-MDS loci.

last: Liu


title: HNRNPL and its RNA Targets in Prostate Cancer

city: Houston

first: Yiwen

last: Chen

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center


title: Transcriptome profiling of peripheral blood mononuclear cells from Bos indicus Malnad Gidda breed

city: Bangalore

first: Ramesha

middle: P.

last: Kerekoppa

state: Karnataka

address: Adugodi

country: India

institute: ICAR-NDRI

summary:
Background:   The Malnad Gidda are unique dwarf Bos indicus cattle native to heavy rainfall Malnad and coastal areas of Karnataka in India. These cattle are highly adapted to harsh climatic conditions and are more resistant to Foot and Mouth disease as compared to other breeds of B.indicus. Since the first genome reference became available from B.taurus Hereford breed, only a few other breeds have been genotyped using high-throughput platforms. Also despite the known reports on high diversity within indicine breeds as compared to taurine breeds, only one draft genome of Nellore and horn transcriptome of Kankrej breed were sequenced at base level resolution. Because of the special characteristics Malnad Gidda possess, it becomes the choice of breed among many indicine cows to study at molecular level and genotyping.
Results:  Sequencing mRNA from the PBMCs isolated from blood of one selected Malnad Gidda bull resulted in generation of 55 million paired-end reads of 100bp length. Raw sequencing data is processed to trim the adaptor and low quality bases, and are aligned against the whole genome and transcript assemblies of Bos taurus UMD 3.1 and Bos indicus (Nellore breed) respectively. About 72% of the sequenced reads from our study could be mapped against the B.taurus genome where as only 41% of reads could be mapped against the Bos indicus transcript assembly. Transcript assembly from the alignment carried out against the annotated B.taurus UMD 3.1 genome resulted in identification of ~10,000 genes with significant expression (FPKM>1). In a similar analysis against the B.indicus Kankrej assembled transcripts we could identify only ~6,000 transcripts. From the variant analysis of the sequencing data we found ~10,000 SNPs in coding regions among which ~9,000 are novel and ~6,400 are amino acid changing.
Conclusions:  For the first time we have genotyped and explored the transcriptome of B.indicus Malnad Gidda breed. A comparative analysis of mapping the RNA-Seq data against the available reference genome and transcript sequences is demonstrated. An enhanced utility of transcript sequencing could be achieved by improving or completing the sequence assembly of any B.indicus breed to better characterize the indicine breeds for productivity features and selective breeding.

overall_design: Total RNA was isolated using RNeasy Mini kit (Qiagen, Venlo, The Netherlands).  RNA was quantitated by 260 nm absorbance with a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies Inc, DE, USA) as well as by measuring fluorescence using Qubit 2.0 (Life Technologies, NY, USA). The quality of RNA was further determined using capillary electrophoresis with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA sample was rRNA depleted using Epicentre Ribo-Zero™ kit to enrich the sample for mRNA and non-coding RNA. Enriched RNA samples is further  processed to generate RNA library using the TruSeq RNA Sample Preparation v2 kit following the manufactures guide. Paired-end 100bp read sequencing of RNA library was carried out on Illumina HiSeq 2000 platform.

first: K

middle: P

last: Ramesha

first: TS

middle: K

last: Prasad


title: Transcriptome analysis of Jurkat T-ALL clones from control and CBAP-knockdown/knockout sets

city: Taipei

first: Yun-Jung

last: Chiang

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: We sequenced whole-genome mRNA from 8 different single stable clones of Jurkat cells modified with CBAP gene expression usng shRNA knockdown or CRISPR/Cas9-mediated knockout and their controls.

overall_design: Examination of mRNA levels from individual cell line using high throughput sequencing

first: Jeffrey

middle: J

last: Yen


title: Transcriptome Analysis of gastric epithelial cells isolated from high fat diet (HFD)-fed mice by using Next Generation Sequencing

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

country: Japan

institute: Axiohelix Co. Ltd.

summary: We obtained transcriptome profiling (RNA-seq) of H+/K+ ATPase negative epithelial cells purified from gastric corpus of mice fed with HFD or control diet by using next generation sequencing.

overall_design: Comparison of expression pfofiles between HFD-fed and control mice.

first: Yuki

last: Hirata

first: Taeko

last: Dohi

middle: I

last: Kawamura


title: Short Read Sequencing Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture or Placebo [tissue 1]

city: Shanghai

first: Christine

last: Nardini

address: 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology

summary: We report the application of Illumina HiSeq 2000 sequencing technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis rat model induced by collegen with acupuncture and placebo treatments, at time points before, 1 hour and 34 days after.

overall_design: 10 rats in total: 2 replicates before treatments (RA_0); 2 replicates receiving acpuncture at 1 hour (AP_1h); 2 replicates receiving placebo at 1 hour (PLA_1h); 2 replicates receiving acpuncture at 34 days (AP_34d); 2 replicates receiving placebo at 34 days (PLA_34d).

first: Valentina

last: Devescovi

first: Yuanhua


title: Differential gene expression in developing grains of two tropical indica rice genotypes differing in grain iron concentration through RNA-seq

city: Kolkata

first: Avijit

last: Das

state: West Bengal

address: 12 Regent Park

department: Quality Evaluation and Improvement

institute: NIRJAFT

summary: Rice (Oryza sativa L.) is the main staple food for nearly half of the world’s population. Cereals, especially rice is deficient in micronutrients such as Fe. However, rice genotypes differ in grain Fe concentration (Panda B, et.al. Am J Plant Sci. 2014;5:2829-41. doi: 10.4236/ajps.2014.518299). The present study is focused on identification of gene(s) involved in Fe accumulation in developing rice grain through high throughput RNA-seq technology and to understand the basis of differential Fe accumulation in developing rice grain. Two cultivars of rice viz. Sharbati (high Fe) and Lalat (low Fe) differing in grain iron concentration were used in the study. Root and grain transcriptome sequences of these two cultivars (at mid-grain filling stage) were generated using RNA-Seq (Illumina Hiseq 2000 platform). For each genotype, on an average 9.7 and 7 Gb data was generated for grain and root samples, respectively. The short reads were aligned against the Nipponbare reference genome (IRGSP build 5.0), thereby successfully mapping 95% and 67% of the reads from grain and root samples, respectively.  Genes known to be involved in Fe metabolism were analyzed for expression. Among the genes coding for phytosiderophore synthesizing enzymes, OsNAS1 and OsNAAT2 showed higher expression in the grains of Sharbati while OsDMAS1 had higher expression in its root. Of the 18 yellow-stripe like (YSL) genes in rice, only 11 were found to be expressed in the two cultivars. Out of these, 2 (OsYSL2 and OsYSL 8) were up-regulated in the grains of Sharbati highlighting their importance in the uptake of Fe from soil and its accumulation in the developing grain. Two other genes (OsFRO1 and OsIRT1) known to be involved in Fe uptake by the root were also found to be highly expressed in the root of Sharbati.  Our findings suggest that higher grain iron concentration of cv. Sharbati might be due to higher expression of key Fe transporters (viz. OsYSL2, OsYSL8 and OsITR1) and root membrane bound OsFRO1, which give an advantage in terms of absorption, transport and assimilation of Fe by this cultivar as compared to the low iron containing cultivar, Lalat.

overall_design: CRD was used to grow rice plants in the net house under ambient condition. Plants Sharbati and Lalat having contarsting grain Fe concentration (24.88 ppm and 7.80 ppm of Fe in the brown rice samples of Sharbati and Lalat, respectively) [Panda et. al., 2014] were grown in the net house. One week old seedlings were transferred to plastic pots filled soil and farm yard manure in 3:1 ratio and grown in the net house under ambient conditions till maturity. Fifteen days after  panicle emergence (mid-grain-filling stage) roots and developing grains were collected, washed in sterile nanopure water, blotted, dipped in RNA stabilizer solution in a falcon tube and stored in refrigerator for 24h. The tubes were sifted to -80oC ultra freezer for until future use. Differences in gene expression between different samples were tested with Cuffdiff package of Cufflinks using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) from reference-guided mapping. Genes expressed at very low levels (read counts < 10 across all six libraries) were not used in analysis of differential gene expression. Significance tests for differential expression were based on a modified exact test. A false discovery rate (FDR) of 0.05 and p-value ≤0.05 was used for identifying differentially expressed genes.

first: Trilochan

last: Mohapatra


title: RNA-seq expression profiling of hair-cells in zebrafish

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

institute: Tel Aviv University

summary: Sensorineural hearing loss affects the majority of the elderly population.  Mammalian hair cells (HC) do not regenerate and current stem cell and gene delivery protocols result only in immature hair cells like-cells.  For this reason, characterization of the transcriptional cascades that lead to development and survival of inner ear HC is essential for designing molecular-based treatments for deafness.  We employed a cell type-specific approach to analyze the transcriptomes of the mouse early postnatal auditory and vestibular sensory epithelia and of hair cells derived from zebrafish model.

overall_design: We utilized the ppv3b:GFP transgenic zebrafish, which express GFP predominantly in HC. We sorted GFP-positive and negative cells from 5 day post fertilization (dpf) larvae using flow cytometry, and profiled their transcriptomes using RNA-seq

first: R

last: Hertzano


title: Arabidopsis thaliana cao mutant alternative splicing exploration by RNAseq

city: Alicante

first: Angel

last: Barco

address: Ramon y Cajal

department: Neuro Plasticity

institute: NeuroSciences Institute of Alicante CSIC

summary: The early flowering Arabidopsis cäö mutant is defective in the BRR2a helicase involved in splicing. In order to get some explanation about the phenotype, we compared the expression profiles of wt and mutant with RNA-seq. In addtion, the same RNA-seq data was used to measure the extent of intron retention in the cäö mutant

overall_design: Comparison of gene expression and alternative splicing between the cao mutant and the wt

first: Lars

last: Hennig

first: Walid

last: Mahrez

first: Rafael

middle: M

last: Viana


title: The GYF domain protein CD2BP2 plays a crucial role in alternative splicing, embryonic development and podocyte integrity

city: Berlin

first: Sebastian

last: Schafer

state: Deutschland

address: Robert-Roessle-Str. 10

department: Experimental Genetics

institute: MDC Berlin

summary: The spliceosome is a multimolecular ribonucleoprotein complex, which catalyzes the removal of introns from pre-mRNA and extends the complexity of genetic information by defining alternative transcripts. Here we analyzed the in vivo function of CD2BP2, which is a marker of early spliceosomal complexes.   Using gene targeting in mice, we show that constitutive or mesoderm- specific ablation of the CD2BP2 gene causes embryonic lethality by E10.5 associated with delayed development, growth retardation and pericard effusion.   Transcriptome analysis in CD2BP2 deficient bone-marrow-derived macrophages (BMM) and podocytes revealed dramatic alterations in the alternative splicing pattern of several mRNAs including VEGFA. Consistent with a previously described critical role of specific VEGFA isoforms for podocyte integrity, mice, which specifically lack CD2BP2flox/flox in this cell type, develop progressive albuminuria followed by lethal kidney failure. We further identified the phosphatase PP1 as a GYF domain independent CD2BP2 interaction partner, suggesting that CD2BP2 acts as an important modulator for spliceosome dephosphorylation, thereby affecting alternative splicing of  physiologically highly relevant transcripts.

overall_design: 3x KO vs 3x WT mus m.

first: Gesa

last: Albert

first: Christopher

last: Schell

first: Johanna

last: Zierow

first: Mathias

last: Girbig

first: Tobias

last: Huber

first: Karin

last: Kirschner

first: Sebasatian

first: Norbert

last: Hubner

first: Benno

last: Kuropka

first: Eberhard

last: Krause

first: Holger

last: Scholz

first: Ronald

last: Naumann

first: Klaus-Peter

last: Knobeloch

first: Christian

last: Freund


title: A mechanistic linkage between low CO2 and evolution of C4 photosynthesis

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

institute: Shanghai Institutes for Biological Sciences, CAS

summary: Physiological and molecular evidences have shown earlier that low CO2 might have been a major driving force during the evolution of C4 photosynthesis, not only being a selection pressure but also as a signaling agent. However, a mechanistic linkage between low CO2 and C4 emergence is missing. In this study, using transcriptomics study in model plant Arabidopsis thaliana, we demonstrated that under long-term low CO2 treatments, the up-regulation of C4 related genes were linked to the up-regulation of genes involved in photorespiration, nitrogen assimilation and glycolysis. Plants under low CO2 also showed altered d13C. The carbonic anhydrase (CA), phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), glutamine oxoglutarate aminotransferase (GS-GOGAT), which are required to reassimilate ammonia, were up-regulated under low CO2. Furthermore, under low CO2, genes involved in PEP regeneration from glycolysis were up-regulated while pyruvate orthophosphate dikinase (PPDK) was down-regulated, suggesting a route of PEP regeneration from glycolysis. All these results suggested that under long-term low CO2 treatment, the selection pressure to recapture the released ammonia from the increased photorespiration might have promoted the evolution of mechanisms for generation PEP from glycolysis and enhancement of enzymes catalyzing formation of oxaloacetate, one intermediate which can accept ammonia residue. These adjustments in metabolism provide a mechanistic linkage between low CO2 and evolution of C4 photosynthesis.

overall_design: Examination of six different samples from two kinds of treated leaf samples

first: Noor

last: Ul Haq

first: Ming-Ju

middle: A

last: Lyu

first: Xin-Guang

last: Zhu


title: Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions.

city: Heidelberg

first: Jan-Philipp

last: Mallm

address: Im Neuenheimer Feld 267

institute: DKFZ

summary: Robust comparison of deep-sequencing data sets is often hampered by differences in their pattern structure or signal-to-noise ratio. Here, we established multi-scale correlation evaluation (MCORE), a method to dissect and compare the genome-wide topology of chromatin features. We applied MCORE to Hi-C, ChIA-PET, ChIP-seq, RNA-seq and Bisulfite-seq data from mouse embryonic stem cells and neural cells to track the extension, transformation and spatial repositioning of chromatin domains during differentiation.

overall_design: ChIP-seq of histone modifications and RNA-seq of total RNA in mouse ESCs and retinoic acid derived NPCs

first: J

last: Molitor

first: K

last: Rippe

first: F

last: Erdel


title: Post-Translational Dosage Compensation Buffers Genetic Perturbations to Stoichiometry of Protein Complexes

status: Public on Dec 30 2016

city: Okayama

first: Hisao

last: Moriya

address: Tsushima-naka 3-1-1, Kita-Ku

department: Research Core for Interdisciplinary Sciences

institute: Okayama University

summary: Understanding buffering mechanisms for various perturbations is essential for understanding robustness in cellular systems. Protein-level dosage compensation, which arises when changes in gene copy number do not translate linearly into protein level, is one mechanism for buffering against genetic perturbations. Here, we present an approach to identify genes with dosage compensation by increasing the copy number of individual genes using the genetic tug-of-war technique. Our screen of chromosome I suggests that dosage-compensated genes constitute approximately 10% of the genome and consist predominantly of subunits of multi-protein complexes. Importantly, because subunit levels are regulated in a stoichiometry-dependent manner, dosage compensation plays a crucial role in maintaining subunit stoichiometries. Indeed, we observed changes in the levels of a complex when its subunit stoichiometries were perturbed. We further analyzed compensation mechanisms using a proteasome-defective mutant as well as ribosome profiling, which provided strong evidence for compensation by ubiquitin-dependent degradation but not reduced translational efficiency. Thus, our study provides a systematic understanding of dosage compensation and highlights that this post-translational regulation is a critical aspect of robustness in cellular systems.

overall_design: Ribosome profiling for Sample1-4. RNA-seq for Sample 5-8. Ribosome profiling and RNA-seq were performed upon the experimental condition where cells carry a high copy of Pop5 gene cloned into a multicopy plasmid and the control condition where they carry empty vector. For ribosome profiling, Sample 1, 2 (experimental condition) and Sample 3, 4 (control condition) are biological replicates of each condition. For RNA-seq, Sample 5, 6  (experimental condition) and Sample 7, 8  (control condition) are biological replicates of each condition.

first: Koji

last: Ishikawa

last: Makanae

first: Shintaro

last: Iwasaki

first: Nicholas

last: Ingolia


title: An RNAi-dependent Polycomb Repression Pathway Is Required for Co-transcriptional Silencing of Transposable Elements

first: Yifan

last: lIU

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

overall_design: Refer to individual Series


title: Schizophrenia: postmortem dorsal lateral prefrontal cortex (DLPFC)

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

institute: UNSW

summary: RNA-Seq analysis of post-mortem tissue from DLPFC of 19 schizophrenia patients and 19 controls.

overall_design: mRNA sequencing of post-mortem brain tissue from the  dorsal lateral prefrontal cortex (DLPFC)  from 19 male controls and 19 male schizophrenia patients generated by deep sequening using the Applied Biosystems SOLiD platform. Raw reads were mapped with Tophat2 to create the associated bam files. Feature counting was performed with HTSeq-count. This mapping and analysis protocol differs from the mapping and analysis reported previously in Fillman et al. Molecular Psychiatry (2012) 1-9.

first: Marc

last: Wilkins

first: Cyndi

last: Shannon-Weickert


title: Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinoma [SNP]

city: Innsbruck

first: Mirjana

last: Efremova

address: Innrain 80-82

institute: Medical University of Innsbruck

summary: We designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.

overall_design: MC38 cells were subcutaneously injected into wild-type C57Bl/6 and immunodeficient Rag1-/- mice. Samples were taken at predefined time points and subjected to detailed analysis, including FACS, exome sequencing, RNA sequencing and SNP arrays.

first: Zlatko

last: Trajanoski


title: mRNA sequencing  of WT, ∆EZL1 and ∆DCL1 cells in conjugation 3, 6 and 10 (C3, C6 anc C10) hours of Tetrahymena thermophila

summary: The goals of this study to find the locus which induced in EZL1KO and DCL1KO cells, especially in the non-MDS regions of the MIC genome of Tetrahymena thermophila.

overall_design: Compare the expression of non-MDS amnong WT, EZL1KO, DCL1KO cells in C3, C6 anc C10.

last: Liu


title: Circulating microRNAs and life expectancy among identical twins

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary:
Objective: To characterize miRNAs in 41-year archived plasma in relation to life expectancy independent of genes.
Method: Plasma miRNAs from nine identical male twins were profiled using next-generation sequencing.
Results: The average absolute difference in the minimum life expectancy was 9.68 years. Intra-class correlation coefficients were above 0.4 for 50% of miRNAs. Comparing deceased twins with their alive co-twin brothers, the concentrations were increased for 34 but decreased for 30 miRNAs.
Conclusion: Identical twins discordant in life expectancy were unlike in the majority of miRNAs, suggesting that environmental factors are pivotal in miRNAs related to life expectancy.

first: Shenghui

last: Wu

first: Jun

last: Dai


title: Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Time-course RNAseq]

city: Pretoria

first: Stanford

last: Kwenda

state: Gauteng

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

summary: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression, both in mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of lncRNAs in plant defense responses are yet to be fully explored. Here, we used strand-specific RNA sequencing to identify 1649 lncRNAs in potato (Solanum tuberosum) from stem tissues. The lncRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lncRNAs (86%) are transcribed from intergenic regions and possess single exons. A time-course RNA-seq analysis between a tolerant and susceptible potato cultivar challenged with Pectobacterium carotovorum subsp. brasilience revealed that 227 of these lncRNAs could be associated with response to this pathogen. These results suggest that lncRNAs have potential functional roles in potato defense responses. This work provides the foundation for further functional studies in understanding potato defense mechanisms.

overall_design: Time-course RNAseq to identify differentially expressed lncRNAs using 3 biological replicates per time-point (0, 6, 12, 24 and 72 hours post inoculation with Pectobacterium carotovorum subsp brasiliense 1692)

first: Paul

last: Birch

first: Lucy

middle: N

last: Moleleki


title: Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR


title: Deep Sequencing Analysis of the MicroRNAs in the Serum of Chronic Hepatitis B with Persistently Normal Alanine Aminotransferase

city: Zhenjiang

first: youwen

last: tan

address: Danjianmen 300

institute: the third hospital of zhenjiang affiliated Jiangsu University

summary:
Background: Circulating miRNAs, a new family of miRNAs presentin plasma and serum, have shown great potential as novel body fluid biomarkers for non-invasive diagnosis and prognosis of several diseases.

Methods: In the present study, we employed next-generation sequencing technology to analyze the expression profiles of circulating miRNAs in the serum of chronic hepatitis B (CHB) patients presenting persistently normal alanine aminotransferase with significant histological features (SPNALT),PNALT patients with no significant histological features (NSPNALT),and healthy control patients.

Results: MiRNAs were found to be the major constituents of small RNA-annotated reads by comparing the annotate draw sequence reads with miRNA databases and genome and other small RNA libraries. Our results point to a total of 2767 unique reads that can be mapped to human miRNAs or pre-miRNAs in miRbase, and the pre-miRNAs can be further mapped to the human genome. Thirty novel miRNA genes were identified in three groups. The differential expression levels of 143 miRNAs showed significant variation when the SPNALT and control group were compared. Among these, 22 miRNAs were >4-fold up-regulated (P<0.01) in SPNALT group and 4 were >2-fold down-regulated (P<0.01).When the SPNALT and NSPNALT group were compared, the differential expression levels of 84 miRNAs showed significant variation. Among these, 13 miRNAs showed a >4-fold up-regulation (P<0.01) in the SPNALT group and 21 showed a >2-fold down-regulation (P<0.01).

Conclusions: Our results show that circulating miRNAs in the serum of SPNALT patients could be more comprehensively detected by the next-generation sequencing technology. Newly identified miRNAs might be used as biomarkers for diagnosis of chronic hepatitis B patients presenting persistently normal alanine aminotransferase with significant histological features.

overall_design: Serum samples were pooled from 6 healthy control donors (control group), 6 NSPNALT patients (NSPNALT group),and 6 SPNALT patients (SPNALT group). Sample sets were obtained fromThe First Affiliated Hospital of Soochow University.


title: Short Read Sequencing Data of the Transcriptome of the Rheumatoid Arthritis and Treated with Acupuncture or not

last: Nardini

summary: We report the application of Illumina Hiseq2000 sequencing technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA) and treated with acupuncture or not.

overall_design: 2 rats in total, i.e., 2 replicates RA rat model before treatment (RA1, 2) for 3 in vitro culture conditions (standard serum FBS, blood serum from animals acupuncture treated AP+, blood serum from animals acupuncture untreated AP-).

first: Valentina

last: Devescovi

first: Yuanhua


title: RNAseq analysis of the global retinal transcriptome of rhodopsin knockout mice

city: Cleveland

first: Xiaodong

last: Bai

address: 10900 Euclid Avenue

department: Center for RNA Molecular Biology

institute: Case Western Reserve University

summary: We report RNAseq analysis of the transcriptome of retinas from mature rhodopsin knockout mice

overall_design: Examine retinal transcriptome of 3 biological replicates for each genotype from 4-week-old animals with tissue collected between 8:00 - 10:00AM

first: Debarshi

last: Mustafi

first: Krzysztof

last: Palczewski


title: WDR5 high expression and its effect on tumorigenesis in leukemia

city: Hershey

first: chunhua

last: song

state: PA

address: 500 University Drive

department: Pediatrics

institute: Pennsyvania  State University College of Medicine

summary: WD repeat domain 5 (WDR5) plays an important role in various biological functions through the epigenetic regulation of gene transcription. However, the oncogenic effect of WDR5 in leukemia remains largely unknown. Here, we found WDR5 expression is increased in leukemia patients. High expression of WDR5 is associated with high risk leukemia; Patients with WDR5 and MLL1 high expression have poor complete remission rate. We further identified the global genomic binding of WDR5 in leukemic cells and found the genomic co-localization of WDR5 binding with H3K4me3 enrichment. Moreover, WDR5 knockdown by shRNA suppresses cell proliferation, induces apoptosis, inhibits the expression of WDR5 targets, and blocks the H3K4me3 enrichment on the promoter of its targets. We also observed the positive correlation of WDR5 expression with these targets in the cohort study of leukemia patients. Our data reveal that WDR5 may have oncogenic effect and WDR5-mediated H3K4 methylation plays an important role in leukemogenesis.

overall_design: Examine the genome-wide binding of WDR5 and H3K4me3 in RS4;11 and THP-1 leukemic cells.

first: Chunhua

last: Song

first: Zheng

last: Ge


title: Foxa2 and Cdx2 cooperate with Nkx2-1 to inhibit lung adenocarcinoma metastasis

city: Cambridge

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

summary: Despite the fact that the majority of lung cancer deaths are due to metastasis, the molecular mechanisms driving metastat    ic progression are poorly understood. Here, we present evidence that loss of Foxa2 and Cdx2 synergizes with loss of Nkx2-    1 to fully activate the metastatic program. These three lineage-specific transcription factors are consistently downregul    ated in metastatic cells compared to non-metastatic cells. Knockdown of these three factors acts synergistically and is s    ufficient to promote the metastatic potential of non-metastatic cells to that of naturally arising metastatic cells in vi    vo. Furthermore, silencing of these three transcription factors is sufficient to account for a significant fraction of th    e genes expression differences between the non-metastatic and metastatic states in lung adenocarcinoma, including upregul    ated expression of the invadopodia component Tks5long, the embryonal proto-oncogene Hmga2, and the epithelial-to-mesenchy    mal mediator Snail. Finally, analyses of tumors from a genetically-engineered mouse model and patients show that low expr    ession of Nkx2-1, Foxa2, and Cdx2 strongly correlates with more advanced tumors and worse survival. Our findings reveal t    hat a large part of the complex transcriptional network in metastasis can be controlled by a small number of regulatory n    odes that function redundantly, and loss of multiple nodes is required to fully activate the metastatic program.

overall_design: Cell lines derived from metastatic primrary tumor, and from non-metastatic primary tumors with and without subsequent knockdown of Nkx2-1, Foxa2 and Cdx2. All cell lines are in duplicate.

first: Carman

last: Li

first: Vasilena

last: Gocheva

first: Madeleine

last: Oudin

first: Arjun

first: Shi

first: Saya

last: Date

first: Sheng

last: Ng

first: Charles

last: Whittaker

first: Roderick

last: Bronson

first: Eric

middle: L

last: Snyder

first: Frank

last: Gertler

first: Tyler

last: Jacks


title: Context-specific regulation of BMAL1 target genes during the circadian cycle in mammals

city: Lausanne

first: Jonathan

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

summary: While the circadian rhythm is a highly conserved phenomenon, it has highly specific functions, which differ from one cell type to another. Hence, although the master regulators BMAL1-CLOCK are conserved, the input and output conveying the tissue specificity vary. Through comparative analyses of ChIP-seq data in mouse liver and NIH3T3 fibroblasts, we reveal that only a fraction of BMAL1 binding sites are shared between different cell types and that many sites are bound, active and accessible in a cell-type-specific way. While we found a large fraction of the overall active liver transcriptome to be rhythmically expressed, rhythmic genes among BMAL1 targets are more enriched compared to the overall cyclic transcriptome in NIH3T3 than in liver. Thus, BMAL1 may launch and reinforce oscillations of a number of genes that propagate timing information rather than globally drive rhythmic gene expression.

overall_design:
We conducted a comparative functional genomics study based on ChIP Seq and RNA Seq time courses in dexamethasone synchronized NIH3T3 cells and mouse liver. We assessed rhythmic gene expression in NIH3T3 cells through RNA Seq time courses that contained RNA samples taken for 48 every 4 hours starting at 16h after Dex.
The raw data of BMAL1 ChIP-seq in mouse liver is deposited under GSE26602 (Rey et al., 2011). The reprocessed data file for the liver BMAL1_ZT06_ChIP-Seq Samples (GSM654882, GSM654883), BMAL1_ZT06_Liver_Stringent_peaks_all_withannotation.bed, is linked below as a supplementary file.

first: Julia

last: Cajan

first: Cédric

last: Gobet

first: Guillaume

last: Rey

first: Félix

last: Naef


title: mRNA expression in human DAOY cells

city: La Jolla

first: Bruce

last: Hamilton

state: CA

address: 9500 Gilman Dr.

department: Medicine

country: USA

institute: UC San Diego

summary: We generate ZNF423 knockdown and control DAOY cells with lentivirus that co-expressed the fluorescent protein mCherry. We performed whole genome RNA sequencing (RNA-seq) of three batched of cultured ZNF423 KD or control KD cells. The sequence reads were analyzed by Homer followed by edgeR. The analyzed RNA-seq results showed  differential expression profile including 12 known cilia genes, and 3 of these were validated with qRT-PCR on mouse granule cell precursors. This study proved data how ZNF423 linked to cilia complexes.

overall_design: RNA-seq in three batched of control and ZNF423 KD cells(generated by lentivirus delivered shRNA targeting ZNF423 sequence).

first: Chen-Jei

last: Hong


title: Ralstonia solanacearum UY031 base modification detection and motif analysis

status: Public on Dec 29 2016

city: Sao Paulo

first: Joao

middle: C

last: Setubal

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of Sao Paulo

type: Methylation profiling by high throughput sequencing

summary: Examination of modified bases on the genome of Ralstonia solanacearum UY031

overall_design: Motif detection was performed using RS_Modification_and_Motif_analysis.1 protocol from SMRT Analysis using QV threshold of 30

first: Rodrigo

last: Guarischi-Sousa


title: TALEN-mediated MeCP2 Gene Mutagenesis in Rhesus and Cynomolgus Monkeys

first: hygine

last: lin

address: siping road 1239

institute: tongji unversity

summary: We report Transcription Activator-like Effector Nucleases (TALEN)-mediated mutagenesis of the Rett Syndrome gene, methyl-CpG binding protein 2 (Mecp2), in nonhuman primates (NHPs). Microinjection of Mecp2-targeting TALEN plasmids into rhesus and cynomolgus zygotes caused 40-50% of the embryos harboring mutations when examined beyond 8-cell stage. The surrogate pregnancy rates were 28.6% (2/7) and 16.7% (1/6) for rhesus and cynomolgus, respectively. The 2 rhesus surrogates went through miscarriage at 30- and 63/64-days of gestation. Analyses of two 63/64-day-old liter-mate embryos indicated both were male and carried MeCP2 mutations, yet chimeric. Mutation rate was higher in one embryonic brain than the other. RNA sequencing and anatomical analyses indicated that the brain with higher-degree mutations was underdeveloped, which, together with mid-gestation-stage male lethality likely recapitulate the disease. One live delivery of a female cynomolgus monkey occurred after 162 days of gestation, with abundant mutagenesis in peripheral tissues examined. We conclude that TALEN-mediated mutagenesis greatly facilitates disease modeling in NHPs.

overall_design: Examination of 25 different tissues transcriptome from the two aborted male rhesus monkeys

first: Hailiang

last: Liu


title: The Beagle Dog MicroRNA Tissue Atlas: Identifying Translatable Biomarkers of Organ Toxicity

first: Hugues

last: Bernard

address: 35 Landsdowne St.

department: Molecular Pathology

institute: Millennium: The Takeda Oncology company

summary: Purpose : Identification of novel microRNA biomarkers specific of organ toxicity

overall_design: micoRNA-SEQ and Q-RT-PCR were used to analyze changes in miRNA profiles of 16 tissues from beagle dogs

first: Erik

last: Koenig


title: Epigenetic profiling of prostate cells

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College street

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: Characterize the chromatin states of prostate cells based on histone modifications

overall_design: ChIP-seq assays conducted in duplicates

first: Kenneth

last: Kron


title: Comparative transcriptomic and proteomic analysis provides insight into the key genes involved in high-altitude adaptation in Tibetan pig (RNA-seq)

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

summary: In this study, RNA-seq technique was used to identify differentially expressed genes (DEGs) in cardiac muscle of the Tibetan pigs raised at highland (TH), Tibetan pigs raised at lowland (TL), Yorkshire pigs raised at highland (YH) and Yorkshire raised at lowland (YL). We obtained 551M clean reads and detected 18585 genes that were expressed in the eight heart samples. According to a standard of fold-change (FC>2 or FC <0.5) and difference significant (P<0.05), obtained 299, 169, 242 and 368 of significantly differentially expressed genes (DEGs) respectively in TH vs.YH, TH vs.TL, TL vs.YL and YH vs.YL. GO and pathways analysis for DEGs results showed enrichment in HIF-1 signaling pathway, and hypertrophic cardiomyopathy (Hypertrophic cardiomyopathy (HCM), cardiovascular development, immunity, DNA damage and other biological functions. Eight DEGs were randomly selected to validate the veracity of RNA-seq and using real-time PCR. The results showed that the expression corresponds to the trend in RNA-seq, hence the deep-sequencing methods were feasible and efficient. This study expanded the number of hypoxic-adaptation-related genes in pig and indicated that the expression patterns of hypoxia-related genes are significantly altered in the Tibetan pig. DEGs may play important roles in hypoxic adaptation after migration to hypoxic environments.

overall_design: mRNA profiles of 6-month old Tibetan pigs raised at highland (TH), Tibetan pigs raised at lowland (TL), Yorkshire pigs raised at highland (YH) and Yorkshire raised at lowland (YL) were generated by deep sequencing, every pig breed has two replicates, using Hiseq 2000.

first: Hao


title: Comparative transcriptomic profile of Wild Type and ∆halI::kanR/∆halR::kanR Mutant Transcriptomes

city: Kuala Lumpur

first: Jia-Yi

last: Tan

address: University of Malaya

institute: University of Malaya

summary: Comparative transcriptomic profile of quorum sensing regulated genes in Hafnia alvei FB1

overall_design:
mRNA profiles of two quorum sensing mutants vs. wild type, grown in LBB at 30°C to OD600 1.5.
mRNA profiles of two quorum sensing mutants vs. wild type, grown in LBB at 30°C to OD600 0.5.

first: Kok-Gan

last: Chan


title: Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinoma

first: Mirjana

last: Efremova

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

overall_design: Refer to individual Series


title: Immunoediting of the cancer genome during tumor progression and activation of PD-1/PD-L1 axis in a mouse model of carcinoma [RNA-seq]

summary:
We designed a study to investigate immunoediting of an epithelial cancer genome using wildtype and immunodeficient mice, NGS, and analytical pipelines to process and analyze the data. We carried out experiments with wildtype and immunodeficient RAG1-/- mice with transplanted tumors and analyzed longitudinal samples with respect to the genomic landscape and the immunophenotypes of the tumors. Finally, we performed also experiments with anti-PD-L1 antibodies and show how the activation of the PD1-PD-L1 axis modulates immunoediting.
MC38 cells were subcutaneously injected into wild-type C57Bl/6 and immunodeficient Rag1-/- mice. Samples were taken at predefined time points and subjected to detailed analysis, including FACS, exome sequencing, RNA sequencing and SNP arrays.

overall_design: Samples were taken at predifined time points, in triplicates and subjected to RNA sequencing using Ion Torrent Proton

first: Zlatko

last: Trajanoski


title: Whole genome bisulfite sequencing of hdp1-1 and hdp2-1and other relative mutants (Col-0 background)

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in 35S-SUC WT, hdp1-1 and hdp2-1, mbd7, idm1, and hdp2mbd7 double mutants

overall_design: 6 samples examined: WT, hdp1-1, hdp2-1 and idm1

first: Cheng-Guo

last: Duan

first: Xingang

last: Wang

first: Kai

last: Tang

first: Shaojun

last: Xie