title: The ParS/ParR regulon in Pseudomonas aeruginosa PAO1

city: College station

first: Dongping

last: Wang

state: TX

address: Wellborn

institute: TAMU

summary: The ParS/ParR two component regulatory system plays important roles for multidrug resistance in Pseudomonas aeruginosa. In this study we report RNA-seq analyses of the transcriptomes of P. aeruginosa PAO1 wild type and par mutants growing in a minimal medium containing 2% casamino acids. This has allowed the quantification of PAO1 transcriptome, and further defines the regulon that is dependent on the ParS/ParR system for expression. Our RNA-seq analysis produced the first estimates of absolute transcript abundance for the 5570 coding genes in P. aeruginosa PAO1. Comparative transcriptomics of P. aeruginosa PAO1 and par mutants identified a total of 464 genes regulated by ParS and ParR. Results also showed that mutations in the parS/parR system abolished the expression of the mexEF-oprN operon by down-regulating the regulatory gene mexS. In addition to affecting drug resistance genes, transcripts of quorum sensing genes (rhlIR and pqsABCDE-phnAB), were significantly up-regulated in both parS and parR mutants. Consistent with these results, a significant portion of the ParS/ParR regulated genes belonged to the MexEF-OprN and quorum sensing regulons. Deletion of par genes also lead to overproduction of phenazines and increased swarming motility, consistent with the up-regulation of quorum sensing genes. Our results established a link among ParS/ParR, MexEF-OprN and quorum sensing in Pseudomonas aeruginosa. Based on these results, we propose a model to illustrate the relationship among these regulatory systems in P. aeruginosa.

overall_design: A total of 9 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas aeruginosa PAO1 wild type strain (3 replicates);  Pseudomonas aeruginosa parS mutant (3 replicates); Pseudomonas aeruginosa parR mutant (3 replicates).

first: Elizabeth

last: Pierson


title: Next Generation Sequencing Facilitates Small RNA Mediated Rice Resistance to Xoo

status: Public on Feb 25 2016

city: WUHAN

first: hanming

last: hong

address: SHIZHISHAN

country: China

institute: NCPGR

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goal of this study is to identify small non-conding RNAs which are involved in rice resistance to Xoo.
Methods: Rice leaves were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). And then, total RNA was extracted to be sequenced using Illumina GAIIx.
Results: Using an optimized data analysis workflow to count the expression level of small ncRNA, we found several differentially expressed small ncRNA which may be participated in the interaction between rice and Xoo.
Conclusions: Small ncRNA have be found to function in a variety of biological processes. Our study here has showed that several candidate miRNA or siRNA may play a significant role in rice immunity.

overall_design: Plants were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). Samples were collected before inoculation (ck) and at 2, 4, and 24 hours after PXO61 or mock inoculation from Rb49 and MDJ8. Leaf fragments approximately 2 cm in length that were immediately next to the inoculation site were collected.

first: Hanming

last: Hong

first: Yanyan

last: Liu

first: Haitao

last: Zhang

first: Jinghua

last: Xiao

first: Xianghua

last: Li

first: Shiping


title: BLUEPRINT methylome of the HapMap cell line GM18507 (Coriell cell line NA18507)

city: London

first: Emanuele

last: Libertini

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

type: Methylation profiling by high throughput sequencing

summary: Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line

overall_design: high resolution methylome of one cell type

first: Simon

last: Heath

first: Stephan

last: Beck

first: Agata

last: Czyz

first: Victor

last: Ruotti


title: Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer

status: Public on Feb 29 2016

city: Beijing

first: Jing

address: 1130 St Nicholas Ave ICRC, room403

country: USA

institute: Columbia University Medical Center

type: Expression profiling by high throughput sequencing

summary:
Aberrant DNA methylation is common in cancer.
To associate DNA methylation with gene function, we performed RNAseq upon tumor  tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients.
To quantify 5mC and 5hmC level in each CG site at genome-wide level, we performed BS-seq and TAB-seq upon tumor  tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients, respectively.

overall_design:
mRNA profiles of tumor and matched normal tissues from two ccRCC patients were generated by deep sequencing, using Hiseq 2000.
Single-nucleotide-resolution, whole-genome, 5mC and 5hmC profiles of tumor and matched normal tissues from two ccRCC (clear cell renal cell carcinoma) patients were generated by deep sequencing, using Hiseq 2000.

first: Ke

last: Chen


title: Transcriptome profiling in knock-in mouse models of Huntington's disease (cortex_mRNA).

status: Public on Feb 24 2016

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). Knock-in mouse models of HD with human exon 1 containing expanded CAG repeats inserted in the murine huntingtin gene (Hdh) provide a genetic reconstruction of the human causative mutation within the mouse model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in 6 and 10 month old knock-in mice with CAG lengths of 20, 50, 92,  140 along with littermate control wild-type animals

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on samples from the Cerebral Cortex tissue of 6 and 10  month old knock-in mice with CAG lengths of 20, 50, 92, 140 along with littermate control wild-type animals.

first: Jim

last: Rosinski


title: Transcriptome profiling in knock-in mouse models of Huntington's disease (striatum_mRNA).

summary: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). Knock-in mouse models of HD with human exon 1 containing expanded CAG repeats inserted in the murine huntingtin gene (Hdh) provide a genetic reconstruction of the human causative mutation within the mouse model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in 6  and 10 month old knock-in mice with CAG lengths of 20, 50, 92,  140 along with littermate control wild-type animals

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on samples from the Corpus Striatum tissue of 6 and 10  month old knock-in mice with CAG lengths of 20, 50, 92, 140 along with littermate control wild-type animals.


title: Transcriptome profiling in knock-in mouse models of Huntington's disease (liver_mRNA).

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on samples from the Liver tissue of 6 and 10  month old knock-in mice with CAG lengths of 20, 50, 92, 140 along with littermate control wild-type animals.


title: Reduced representation bisulfite sequencing data of mouse genome

status: Public on Feb 26 2016

city: Nanjing

first: Quan

last: Zhou

state: Jiangsu

address: NO. 140, Hanzhong Road

institute: Nanjing Medical University

summary: RRBS was used to analyse global imprinting gene methylation pattern of offspring from the in vitro derived spermatids like cells and normal control

overall_design: Global imprinting gene methylation pattern comparision of two offspring (one male and one female) from the in vitro derived spermatids like cells and two normal control mice (one male and one female)

first: Jiahao

last: Sha

first: Qi


title: Placental protein-1 (Plac1) modulates immune tolerance in mammary tumor cells

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

summary: Plac1 is an X-linked (Xq26) trophoblast gene expressed at high levels in the placenta, at low levels in the testis, but not in other normal somatic tissues. However, it is re-expressed in several malignancies, including breast, colon, lung, gastric, liver and endometrial cancers as well as in most human cancer cell lines. Plac1 contains HLA-A2-restricted epitopes capable of eliciting a cytotoxic T lymphocyte (CTL) response against human breast cancer cells, and colorectal cancer patients with a Plac1-specific CTL response demonstrate long-term survival. To explore the role of Plac1 in cancer, mouse mammary tumor E0771 cells expressing high levels of Plac1 were transduced with a lentivirus expressing a Plac1 shRNA (E0771/shPlac1).

overall_design: The RNeasy Mini Kit was used to purify total RNA from three independent cell culture samples for gene expression analysis. After isolation in parallel, 1 μg of each of the total RNA from E0771/Scram or E0771/Shplac1 was pooled prior to microarray gene expression analysis. E0771/Scram was considered as control group in this experiment.

first: Hongyan

last: Yuan


title: Transcriptome profiling in knock-in mouse models of Huntington's disease (cerebellum_mRNA).

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on samples from the Cerebellum tissue of 6 and 10  month old knock-in mice with CAG lengths of 20, 50, 92, 140 along with littermate control wild-type animals.


title: TGF-β Tumor Suppression Through A Lethal EMT

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TGF-β is a major tumor suppressor in gastrointestinal (GI) and squamous carcinomas, which exhibit frequent genetic inactivation of Smad4, a key TGF-β signaling component. Apoptosis is implicated as an important mediator of the tumor suppressive function of TGF-β, although this process remains poorly understood. To address this long-standing question, we dissected the tumor suppressive action of TGF-β in naïve pancreatic ductal adenocarcinoma (PDA) cells. Here we show that TGF-β/Smad4 signaling triggers an EMT in Kras-mutant pancreatic progenitor cells but turns this process into a trigger of apoptosis by converting the progenitor cell transcription factor Sox4 from an enforcer of epithelial progenitor identity into an activator of apoptosis. This occurs as a result of the EMT-linked repression of the endodermal master regulator Klf5, which cooperates with Sox4 to promote epithelial progenitor identity, and loss of which unmasks a latent apoptotic transcriptional program driven by Sox4. By losing Smad4, Kras-mutant PDA cells avoid this fate and instead use Sox4 as a TGF-β-dependent enforcer of the epithelial progenitor cell state.

overall_design: In this study, 16 RNA-Seq samples and 6 ChIP-Seq samples are included.

first: Charles

last: David

first: Yun-Han

last: Huang

first: Joan

last: Massagué


title: MicroRNA and gene expression changes in human cerebral aneurysms [RNA-seq]

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

summary: Cerebral Aneurysm tissues and superficial temporal arteries were compared through RNA-Seq to identify differentially expressed genes, and through microRNA microarray to identify differentially expressed microRNAs. Significant miR:gene pairs were identified for potential microRNA silencing regualtory effects.

overall_design: To study differentially expressed genes and microRNAs in cerebral aneurysms, we collected 7 cerebral aneurysm tisses and 10 superficial temporal artery (STA) tisses from 17 individuals. We performed RNA-Seq and microRNA microarray analysis on these samples, and compared them using STA as a control.

first: Kimon

last: Bekelis

middle: A


title: Macrophages Mediate the Repair of Brain Vascular Rupture through Direct Physical Adhesion and Mechanical Traction

status: Public on Feb 23 2016

city: ChongQing

first: Chi

last: Liu

address: TianShen road

institute: SouthWest university Of China

summary: transcriptional profile of both macrophages and endothelial end cells between three different lesion stages (uninjured control , upon macrophage arrival , and during macrophage traction).

overall_design: Examination of gene expression different in 2 cell types.

first: Chuan

last: Wu

first: Ling

middle: F

last: Luo


title: Transcriptome sequencing of three yeast strains

city: Jinan

first: Chunlei

last: JIAO

state: Shandong

address: 27 Shanda nan Road

department: School of Life Science

institute: Shandong University

summary: The aim of transcriptome sequencing was to find out the genes differentially expressed among three strains

overall_design:
Three strains were analyzed in duplicate:
ASK10WT
ask10Δ
ASK10M475R

first: Bo

last: Peng


title: Grainyhead-like 2 (GRHL2) maintains the epithelial status of ovarian cancer through miR-200-ZEB1 regulatory networks

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

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

overall_design: Refer to individual Series


title: Histone modification and transcription factor ChIPseq of Xenopus laevis epithelial progenitors

city: La Jolla

first: Ian

middle: K

last: Quigley

state: CA

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

summary: To determine the positions of promoters and enhancers in developing Xenopus laevis epithelial progenitors, we performed ChIPseq on the histone modifications H3K4me3 and H3K27ac. We also performed ChIPseq on the transcription factors foxj1 (in the presence or absence of rfx2), myb (in the presence or absence of multicilin), and rad21.

overall_design: Some embryos were harvested as wild-types; in other experiments, we injected  embryos with mRNAs encoding FLAG-foxj1 (with and without rfx2 morpholino) or GFP-myb (with and without an inducible form of multicilin (mcidas-HGR)).  We then isolated epithelial progenitors surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested chromatin at 9 hours after induction (roughly stage 18) and performed ChIPseq using antibodies against endogenous targets (H3K4me3, H3K27ac, rad21) or protein tags (FLAG, GFP). We then sequenced these libraries, aligned the reads to the X. laevis genome (version 9.1) with bwa mem and called peaks with HOMER, using input as background.

first: Chris

last: Kintner


title: MicroRNA and gene expression changes in human cerebral aneurysms

platform_organism:
Homo sapiens
synthetic construct


title: MLL1 is essential for the senescence-associated secretory phenotype [ChIP-Seq]

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Oncogene-induced senescence (OIS) and therapy-induced senescence (TIS), while tumor-suppressive, also promote procarcinogenic effects by activating the DNA damage response (DDR), which in turn induces inflammation. This inflammatory response prominently includes an array of cytokines known as the senescence-associated secretory phenotype (SASP). Previous observations link the transcription-associated methyltransferase and oncoprotein MLL1 to the DDR, leading us to investigate the role of MLL1 in SASP expression. Our findings reveal direct MLL1 epigenetic control over proproliferative cell cycle genes: MLL1 inhibition represses expression of proproliferative cell cycle regulators required for DNA replication and DDR activation, thus disabling SASP expression. Strikingly, however, these effects of MLL1 inhibition on SASP gene expression do not impair OIS and, furthermore, abolish the ability of the SASP to enhance cancer cell proliferation. More broadly, MLL1 inhibition also reduces “SASP-like” inflammatory gene expression from cancer cells in vitro and in vivo independently of senescence. Taken together, these data demonstrate that MLL1 inhibition may be a powerful and effective strategy for inducing cancerous growth arrest through the direct epigenetic regulation of proliferation-promoting genes and the avoidance of deleterious OIS- or TIS-related tumor secretomes, which can promote both drug resistance and tumor progression.

overall_design: This study examines the genome-wide distribution of gH2A.x and H3K4me3 by chIP-seq, using input and whole histone subunit H3 (respectively) as controls for local sonication efficiency bias. Each of the four chIPs has a single replicate each in (i) IMR90 fibroblasts transfected with a scramble control vector, (ii) the same cells subject to oncogene-induced senescence by stimulation of H-Ras V12, and (iii) in OIS cells with a shRNA targeting MLL1. Additionally, gH2A.x and input were sequenced with another replicate in control and OIS cells (both scramble control).

first: Brian

middle: C

last: Capell

first: Adam

middle: M

last: Drake

first: Jiajun

last: Zhu

first: Parisha

middle: P

last: Shah

first: Zhixun

last: Dou

first: Jean

last: Dorsey

first: Daniel

last: Simola

first: Greg

first: Morgan

last: Sammons

first: Taranjit

middle: S

last: Rai

first: Christopher

last: Natale

first: Todd

middle: W

last: Ridky

first: Peter

middle: D

last: Adams

first: Shelley

middle: L

last: Berger


title: Trimming of sequence reads alters RNA-Seq gene expression estimates

city: Seattle

first: Jay

last: Parrish

state: Washington

department: Department of Biology

institute: University of Washington

summary:
Background
High-throughput RNA-Sequencing (RNA-Seq) has become the preferred technique for studying gene expression differences between biological samples and for discovering novel isoforms, though the techniques to analyze the resulting data are still immature. One pre-processing step that is widely but heterogeneously applied is trimming, in which low quality bases, identified by the probability that they are called incorrectly, are removed. However, the impact of trimming on subsequent alignment to a genome could influence downstream analyses including gene expression estimation; we hypothesized that this might occur in an inconsistent manner across different genes, resulting in differential bias.

Results
To assess the effects of trimming on gene expression, we generated RNA-Seq data sets from four samples of larval Drosophila melanogaster sensory neurons, and used three trimming algorithms—SolexaQA, Trimmomatic, and ConDeTri—to perform quality-based trimming across a wide range of stringencies. After aligning the reads to the D. melanogaster genome with TopHat2, we used Cuffdiff2 to compare the original, untrimmed gene expression estimates to those following trimming. With the most aggressive trimming parameters, over ten percent of genes had significant changes in their estimated expression levels. This trend was seen with two additional RNA-Seq data sets and with alternative differential expression analysis pipelines. We found that the majority of the expression changes could be mitigated by imposing a minimum length filter following trimming, suggesting that the differential gene expression was primarily being driven by spurious mapping of short reads. Slight differences with the untrimmed data set remained after length filtering, which were associated with genes with low exon numbers and high GC content. Finally, an analysis of paired RNA-seq/microarray data sets suggests that no or modest trimming results in the most biologically accurate gene expression estimates.

Conclusions
We find that aggressive quality-based trimming has a large impact on the apparent makeup of RNA-Seq-based gene expression estimates, and that short reads can have a particularly strong impact. We conclude that implementation of trimming in RNA-Seq analysis workflows warrants caution, and if used, should be used in conjunction with a minimum read length filter to minimize the introduction of unpredictable changes in expression estimates.

overall_design: Four biological replicates of 100 Drosophila melanogaster larval multi-dendritic sensory neurons were profiled by mRNA-Seq

first: Claire

middle: R

last: Williams

first: Alyssa

last: Baccarella

middle: Z

first: Charles

last: Kim


title: MLL1 is essential for the senescence-associated secretory phenotype

status: Public on Feb 22 2016

first: Gregory

last: Donahue

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

Oncogene-induced senescence (OIS) and therapy-induced senescence (TIS), while tumor-suppressive, also promote procarcinogenic effects by activating the DNA damage response (DDR), which in turn induces inflammation. This inflammatory response prominently includes an array of cytokines known as the senescence-associated secretory phenotype (SASP). Previous observations link the transcription-associated methyltransferase and oncoprotein MLL1 to the DDR, leading us to investigate the role of MLL1 in SASP expression. Our findings reveal direct MLL1 epigenetic control over proproliferative cell cycle genes: MLL1 inhibition represses expression of proproliferative cell cycle regulators required for DNA replication and DDR activation, thus disabling SASP expression. Strikingly, however, these effects of MLL1 inhibition on SASP gene expression do not impair OIS and, furthermore, abolish the ability of the SASP to enhance cancer cell proliferation. More broadly, MLL1 inhibition also reduces “SASP-like” inflammatory gene expression from cancer cells in vitro and in vivo independently of senescence. Taken together, these data demonstrate that MLL1 inhibition may be a powerful and effective strategy for inducing cancerous growth arrest through the direct epigenetic regulation of proliferation-promoting genes and the avoidance of deleterious OIS- or TIS-related tumor secretomes, which can promote both drug resistance and tumor progression.

Previously published samples GSM1135046, GSM1135044, GSM1135047, and GSM1135045 were also studied in this investigation and appear in GSE36641. This did not involve re-sequencing or re-alignment, nor any other deviation from the data protocols in that series.


title: MLL1 is essential for the senescence-associated secretory phenotype [RNA-Seq]

overall_design: This study consists of a single replicate of RNA-seq from oncogene-induced senescent (or control) IMR90 cells in a MLL1 knockdown (or WT) background, for a total of four samples

first: Brian

last: Capell

first: Adam

last: Drake

first: Jiajun


title: Injury-dependent hydrogen peroxide oxidation of IKK-alpha regulates keratinocyte migration through induction of EGF

city: Orono

first: Benjamin

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

summary: Hydrogen peroxide is known to promote skin keratinocyte migration, although the mechanism of action is unclear. In an attempt to identify signaling pathways regulated by hydrogen peroxide in the skin, 3 day post fertilized (dpf) zebrafish larvae (nacre strain) were treated with 3mM hydrogen peroxide for 2 hours and subjected to RNA-seq analyses.  Pools of about 1000 embryos for each of three biological replicates were derived from 5 independent mating pairs and raised to larval stages until 3 dpf. All larvae were subsequently homogenized in Trizol and total RNA was extracted using a chloroform extraction protocol treated with DNAse. Messenger RNA (mRNA) was subsequently purified from total RNA using biotin-tagged poly dT oligonucleotides and streptavidin-coated magnetic beads, followed by quality control using an Agilent Technologies 2100 Bioanalyzer (values >7 were used for sequencing). The poly(A)-tailed mRNA samples were fragmented and double-stranded cDNA generated by random priming for deep sequencing studies.

overall_design: 6 samples total were analyzed. 3 untreated, and 3 hydrogen peroxide treated (3mM, 2hr)

first: Thomas

last: Lisse

first: Sandra

last: Rieger


title: ChIPseq analysis of MYST5 (cg1894) in Drosophila S2 cells

city: Berlin

first: Ann

middle: E.

last: Ehrenhofer-Murray

address: Philippstr. 13

department: Institut für Biologie

country: Germany

institute: Humboldt-Universität zu Berlin

summary: We report here the genome-wide localization of the histone acetyltransferase MYST5 (cg1984) in Drosophila. ChIP-seq analysis was performed with two anti-MYST5 antibodies in S2 cells. We found MYST5 to bind to the promoters of actively transcribed genes. MYST5 furthermore showed extensive colocalization with boundary/ insulator factors, including Chriz/ Chromator, CP190, dCTCF and BEAF-32, which mediate the organization of the genome into functionally distinct topological domains. Altogether, our data suggest a broad role for MYST5 both in gene-specific transcriptional regulation and in the organization of the genome into chromatin domains.

overall_design: Examination of genome-wide MYST5 localization in S2 cells


title: RNA-Seq analysis of the WEHI-231-derived stable cell lines WEHI-control and WEHI-miR-148a

first: Changchun

last: Xiao

state: California

address: 10550 North Torrey Pines Road

department: Immunology & Microbial Science

institute: The Scripps Research Institute

summary: miRNAs regulate the expression of its targets genes by promoting mRNA degradation and translational repression. The goal of this study is to perform RNA-Seq in control or miR-148a-expressing WEHI-231 cell lines for the identification of miR-148a target genes.

overall_design: WEHI-control and WEHI-miR-148a cells were stimulated with anti-IgM (2 ug/ml) for 14 h. Total RNA was extracted, enriched for polyA-containing RNAs and submitted to RNA-Seq.

first: Alicia

last: Gonzalez-Martin


title: O-linked β-N-acetylglucosamine (O-GlcNAc) acts as a glucose sensor to epigenetically regulate the insulin gene in pancreatic beta cells

city: Athens

first: Lance

last: Wells

state: Georgia

address: 315 Riverbend Road

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: We compare global gene expression changes in the Min6 cell line in response to altered glucose flux and pharmacological manipulation of the O-GlcNAc postranslational protein modification.

overall_design: Min6 cells were treated for 1hr in the following conditions: Low glucose (LG), high glucose (HG) and LG+GlcNAcstatin (LG+GNS). After treatment, total RNA was extracted and used for sequencing.

first: Sean

last: Durning


title: Genome-wide map of 4 histone modifications and PolII in iPSC-derived human cardiomyocytes

city: Chicago

first: Noboru

middle: Jo

last: Sakabe

state: IL

address: 920 E 58th st

department: Human Genetics

institute: University of Chicago

summary: We generated maps of H3K4me1, H3K27ac (enhancers), H3K4me3, Pol II (promoters) and H3K27me3 (repressed chromatin) in the genome of human iPSC-derived cardiomyocytes

overall_design: Differentiation of cardiomyocytes from iPSC followed by ChIP-seq of H3K27ac, H34me1, H327me3, H3K4me3 and PolII

first: Marcelo

last: Nobrega

first: Ivy

last: Aneas

first: Lindsey

last: Montefiori

first: Courtney

last: Burrows


title: RNA-seq analysis of FHS1-dependent genes in Fusarium graminearum Z-3639

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

country: South Korea

institute: Seoul National University

summary: Fusarium graminearum (teleomorph Gibberella zeae) is a prominent pathogen that infects major cereal crops, such as wheat, barley, and maize. Fhs1 contains a Zn(II)2Cys6 fungal-type DNA-binding domain and localized to nuclei , suggesting that Fhs1 is a transcription factor required for hydroxiurea.

overall_design: 6 samples examined: 24 h after inoculation of Fusarium graminearum wild-type Z-3639 and fhs1 (Δfhs1::GEN) strains in complete media

first: Jae

middle: Y

last: Lim

first: Yin-Won

last: Lee


title: Role of the histone demethylase KDM2B in hematopoietic homeostasis and malignancies [RNA-seq]

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

summary: Development of the hematopoietic system is dynamically controlled by the interplay of transcriptional and epigenetic networks to determine cellular identity. Those networks are critical for homeostasis and frequently dysregulated in leukemias. We identified histone demethylase Kdm2b as a critical regulator of definitive hematopoiesis and lineage specification of hematopoietic stem and progenitor cells (HSPCs). RNA sequencing in murine HSPCs and genome-wide chromatin immunoprecipitation studies in human leukemias revealed that Kdm2b regulates differentiation, lineage choice, cytokine signaling, and quiescence.

overall_design: Comparison of gene expression in wild-type and knockout HSPCs

first: Yan

last: Kai


title: Reducing Cytoplasmic Polyamine Oxidase Activity in Arabidopsis Increases Salt and Drought Tolerance by Reducing Reactive Oxygen Species Production and Increasing Defense Gene Expression.

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

institute: University Medicine Greifswald

summary: Arabidopsis thaliana polyamine oxidase 5 gene (AtPAO5) functions as a thermospermine (T-Spm) oxidase. Aerial growth of its knock-out mutant (Atpao5-2) is significantly repressed by low dose(s) of T-Spm but not by other polyamines. Massive analysis of 3’-cDNA ends (MACE) was performed. Cell wall, lipid and secondary metabolisms were dramatically affected in low dose T-Spm-treated Atpao5-2. Intriguingly Fe-deficient responsive genes and drought stress-induced genes were up-regulated, suggesting that vascular system loses the function. Histological observation showed that vascular system of the joint part between stem and leaves was structurally destroyed. The results indicate that T-Spm homeostasis by a balance of synthesis and catabolism, catalysed by AtPAO5 in Arabidopsis, is important for maintaining vascular system. Phylogenetic analysis showed that PAOs from vascular plants are classified into four clades (I-IV) and AtPAO5 belongs to the clade III. Clade III members show high identity to metazoan PAOs and are not found in non-vascular plants. Furthermore, all the clade III genes are intron-less or contain a single intron whereas the other three clade genes usually contain 7 to 9 introns. The data suggest the occurrence of a horizontal gene transfer of ancestral clade III PAO gene(s) from primitive animals. Fine tuning of T-Spm metabolism is critical for vascular plants and its catabolic gene was acquired from a certain Metazoan to equip the vascular system.

overall_design: 8 Samples analyzed by MACE (Massive Analysis of cDNA ends)

first: G

middle: H

last: Sagor

first: S

last: Zhang

last: Kojima

first: Thomas

last: Berberich

first: Tomonobu

last: Kusano


title: Comparative assessment of the transcriptome of pancreatic islets from Non-Obese Diabetic mice in the absence of immune infiltrate

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: The transcriptome of pancreatic islets from four mouse strains was compared - NODk.RagKO, B10k.RagKO, NODk.RagKO.insHEL and B10k.RagKO.insHEL. This comparison allows the assessment of altered transcriptome due to two factors - genetic background of NOD vs B10 strain, and the effect of the insHEL transgene. The use of the MHC k haplotype and the RagKO background remove contamination from infiltrating immune cells, in order to obtain a pure islet transcriptome.

overall_design: Three mice of each gentoype were analyzed in this study.

first: Lei

last: Tian

first: Joke

last: Allemeersch

first: Adrian

last: Liston


title: HsfA2 controls the activity of developmentally and stress-regulated heat stress protection mechanisms in tomato male reproductive tissues

summary: Male reproductive tissues are more sensitive to heat stress compared to vegetative tissues, however the basis of this phenomenon is poorly understood. Heat stress transcription factors (Hsfs) regulate the transcriptional changes required for protection and recovery from heat stress. HsfA2 has been characterized as co-activator of HsfA1a in tomato and is considered as one of the major Hsfs accumulating in response to elevated temperatures. The role of HsfA2 in heat stress response of different tissues was examined by exploring the composition and structure of the tissue-specific regulatory networks in transgenic tomato plants with suppressed HsfA2 expression (A2AS). Transcriptome analysis revealed that HsfA2 acts in condition- and tissue-specific manner and that only a subset of heat stress induced genes require HsfA2 for higher expression. Remarkably, although HsfA2 is not essential for thermotolerance in seedlings and flowering plants, it is required for maintenance pollen viability under stress conditions. We show that the activation of Hsf networks is important for the developmentally regulated priming of heat stress response occurring at early stages of anther and pollen development. Thereby, HsfA2 is involved in pollen thermotolerance by directly regulating heat stress responsive genes but also by stimulating the synthesis of molecular chaperones under non-stress conditions.

overall_design: 8 samples

first: Sotirios

last: Fragostefanakis

first: Enrico

last: Schleiff

first: Klaus

last: Scharf

first: Anida

last: Mesihovic


title: Comparison of genome-wide DNA methylation in MEFs derived from wildtype or estrogen receptor beta null mice using reduced representation bisulfite sequencing

city: Södertälje

first: Joëlle

last: Rüegg

address: Forskargatan 20

country: Sweden

institute: Karolinska Institutet/Swetox

summary:
Estrogen receptor beta (ERβ) is a ligand inducible transcription factor regulating gene expression in response to the female sex hormone estrogen. Previously, we found that ERβ deficiency results in changes in DNA methylation patterns at two gene promoters, implicating an involvement of ERβ in DNA methylation. In this study, we set out to explore this involvement on a genome-wide level, and to investigate the underlying mechanisms of this function.
Using reduced representation bisulfite sequencing (RRBS), we compared genome-wide DNA methylation in mouse embryonic fibroblasts (MEFs) derived from wildtype (wt) and ERβ knock-out (βerko) mice, and identified around 8000 differentially methylated positions (DMPs). This suggests that ERβ is involved in regulating DNA methylation at specific sites in the genome.

overall_design: Genome-wide DNA methylation was analysed in MEFs derived from wildtype and ERbeta null mice by educed representation bisulfite sequencing (RRBS) on an Illumina Genome Analyser IIx platform.

first: Yun

last: Liu

first: William

last: Duong

first: Claudia

last: Krawczyk

first: Nancy

last: Bretschneider

first: Gábor

last: Borbély

first: Mukesh

last: Varshney

first: Christian

last: Zinser

first: Primo

last: Schär


title: Role of the histone demethylase KDM2B in hematopoietic homeostasis and malignancies [ChIP-seq]

city: Washington

first: Alexandros

last: Tzatsos

overall_design: Identify the binding of KDM2B in seven human leukemia cell lines

first: Yan

last: Kai


title: Role of the histone demethylase KDM2B in hematopoietic homeostasis and malignancies

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-seq analysis of methanol-adapted Sporomusa ovata DSM-2662

city: Hørsholm

first: Pier-Luc

last: Tremblay

address: Kogle Alle 6

department: The Novo-Nordisk Foundation Center for Biosustainability

country: Denmark

institute: Technical University of Denmark

summary: Expression profile of wild-type S. ovata and methanol-adapted strain grown autotrophically with H2 as the source of electron.

overall_design: Illumina RNA-Seq of total RNA extracted from a strain of S. ovata evolved by adaptive laboratory evolution to grow faster with methanol 2% as the sole susbtrate and from the wild type. The adapted strain was transfer 18 times on methanol 2%.  Total RNA was extracted from both strains growing with H2/CO2.

first: Anna

last: Koza

first: Tian

last: Zhang


title: Bcl6 is Required for Somatic Hypermutation and Gene Conversion in Chicken DT40 Cells

status: Public on Feb 21 2016

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: The activation induced cytosine deaminase (AID) mediates diversification of B cell immunoglobulin genes by the three distinct yet related processes of somatic hypermutation (SHM), class switch recombination (CSR), and gene conversion (GCV). SHM occurs in germinal center B cells, and the transcription factor Bcl6 is a key regulator of the germinal center B cell gene expression program, including expression of AID. To test the hypothesis that Bcl6 function is important for the process of SHM, we compared WT chicken DT40 B cells, which constitutively perform SHM/GCV, to their Bcl6-deficient counterparts. We found that Bcl6-deficient DT40 cells were unable to perform SHM and GCV despite enforced high level expression of AID and substantial levels of AID in the nucleus of the cells. To gain mechanistic insight into the GCV/SHM dependency on Bcl6, transcriptional features of a highly expressed SHM target gene were analyzed in Bcl6-sufficient and -deficient DT40 cells.  No defect was observed in the accumulation of single stranded DNA in the target gene as a result of Bcl6 deficiency.  In contrast, association of Spt5, an RNA polymerase II (Pol II) and AID binding factor, was strongly reduced at the target gene body relative to the transcription start site in Bcl6-deficient cells as compared to WT cells.  However, partial reconstitution of Bcl6 function substantially reconstituted Spt5 association with the target gene body but did not restore detectable SHM.  Our observations suggest that in the absence of Bcl6, Spt5 fails to associate efficiently with Pol II at SHM targets, perhaps precluding robust AID action on the SHM target DNA.  Our data also suggest, however, that Spt5 binding is not sufficient for SHM of a target gene even in DT40 cells with strong expression of AID.

overall_design: Sequencing of the IgL V region and mutationally active GFP transgene in WT, Bcl6-/- Pax5R, and  Bcl6-/- Pax5R Bcl6R chicken DT40 cells for evidence of AID dependent mutations. ChIP-seq proiles of RNA Pol II, Spt5, and pSer5 Pol II at a GFP transgene in WT, Bcl6-/- Pax5R, and  Bcl6-/- Pax5R Bcl6R chicken DT40 cells.

first: Alan

last: Williams

first: Jukka

last: Alinikula

first: David

middle: G

last: Schatz


title: Silcening RAC1 expression suppresses the proliferation of colon cancer cells by inducing gene differentially expressed.

status: Public on Feb 20 2016

city: Haikou

first: Yousheng

last: Huang

state: Hainan

address: The 3rd Xueyuan Road

department: Department of pathology

institute: Hainan Medical university

summary: In this study,RAC1 expression was silenced by RNA interference in colon cancer cell lines, and investigate the correlation between RAC1 expression and colon cancer proliferation,and differential expressed genes were analized by gene assay and qPCR technologe.The proliferation and colony formation ability of colon cancer cells were significantly reduced after RAC1 knockdown. More 1200 known genes were found to be involved in the RAC1 functions related tumorigenesis by genechip analysis, these genes related to cell proliferation/apoptosis and cell cycle process. qRT-PCR results showed an expression pattern consistent with that of the genechip analysis.

overall_design: Lentivirus-mediated RNA interference was used to knockdown RAC1 expression in colon cancer cell lines. And cell proliferation assays . GeneChip analysis were carried out for mRNA expression profiling, followed, the expressed levels of mRNA and protein were measured by Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot, respectively.

first: You

last: Xie


title: Hdac3 Interaction with p300 Histone Acetyltransferase Regulates the Oligodendrocyte and Astrocyte Lineage Fate Switch (RNA-Seq)

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary:
Establishment and maintenance of CNS glial cell identity ensures proper brain development and function, yet the epigenetic mechanisms underlying glial fate control remain poorly understood.
Here we show that the histone deacetylase Hdac3 controls oligodendrocyte-specification gene Olig2 expression, and functions as a molecular switch for oligodendrocyte and astrocyte lineage determination.
Our data suggest that Hdac3 cooperates with p300 to prime and maintain oligodendrogenic programs while inhibiting Stat3-mediated astrogliogenesis, and thereby regulate phenotypic commitment at the point of oligodendrocyte-astrocytic fate decision.

overall_design: Gene expression profiling of optic nerve from P12 control and Hdac3 cKO mice


title: Hdac3 Interaction with p300 Histone Acetyltransferase Regulates the Oligodendrocyte and Astrocyte Lineage Fate Switch (ChIP-Seq)

overall_design: Examination of Hdac3 and p300 genomewide occupancy in differentiating oligodendrocytes


title: Hdac3 Interaction with p300 Histone Acetyltransferase Regulates the Oligodendrocyte and Astrocyte Lineage Fate Switch

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH


title: Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation (Dnase-Seq)

summary: DHS enahncers to identify novel pathways in OB differentiation

overall_design: We examined DHS identified enhancers and promoters during OB differentiation

first: Lyuba

last: Varticovski

first: Bethtrice

last: Thompson

first: Gordon

last: Hager


title: Principles governing DNA methylation during neural lineage and subtype specification

city: New York

first: Shifra

middle: Liba

last: Klein

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell

summary: DNA methylation, in concert with other epigenetic regulators, controls the accessibility of transcription factors to DNA. While comprehensively described in the development of neuronal progenitors, the role of DNA methylation/demethylation in neuronal lineage/subtype specification is not known. By profiling two distinct neuronal lineages, and five neuron subtypes in the hippocampus and striatum, we uncovered a set of five principles that govern DNA methylation dynamics in neurodevelopment.  By dividing neurodevelopment to three alternating methylation and demethylation periods and applying the principles to each of these stages, we created a matrix that comprehensively describes the targets, genomic contexts, functional consequences and putative mechanisms of methylation/demethylation events.  The overarching theme is that the developmental methylation program is remarkably similar in the hippocampal and striatal lineages, with significant divergence only occurring during subtype specification. Our matrix can be cross-referenced with disease-associated epigenetic changes to specify the possible events and underlying principles compromised in disease.

overall_design: Compared tissue from C57BL6 male animals at differenent developmental timepoints and regions for differences in DNA methylation and RNA expression. Additionally Dnmt3a conditional knockdown mice were used to determine role of Dnmt3a during development.

first: Ali

last: Sharma

first: Luendreo

last: Barboza

first: Niraj

last: Lodhi

first: Miklos

last: Toth


title: Genome-wide maps of chromatin state during cardiac reprogramming of human fibroblasts by small molecules

status: Public on Feb 19 2016

city: San Francisco

last: Cao

address: 1650 Owens Street

department: Department of Pharmaceutical Chemistry

institute: gladstone institute of cardiovascular disease

summary: Cardiomyocyte-like cells can be reprogrammed from somatic fibroblasts by overexpression of cardiac genes, providing a new avenue for cardiac regenerative therapy. Here we report an alternative approach in which functional cardiomyocytes can be rapidly and efficiently generated from human fibroblasts by a specific combination of small molecules. ChIP-seq analysis has been used to understand the dynamic changes in chromatin state during early stage of reprogramming.

overall_design: We analyzed the genome-wide epigenetic changes by ChIP-seq analysis of H3K4me3 and H3K27ac (active chromatin marks) and H3K27me3 (inactive chromatin mark) at reprogramming Day 6 (D6) and day 11 (D11).

first: Jiashun

last: Zheng

first: Sheng

last: Ding


title: Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts.

city: Aurora

first: Peter

last: Kabos

state: CO

address: 12801 E. 17th Avenue

department: Division of Medical Oncology

institute: University of Colorado School of Medicine

summary: High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) allows for high resolution, genome-wide mapping of RNA-binding proteins. We found that substantial mispriming during reverse transcription results in the overrepresentation of sequences complementary to the primer used for reverse transcription. Up to 45% of peaks in publicly available HITS-CLIP libraries are attributable to this artifact, and the majority of libraries have detectable levels of mispriming. We also found that standard techniques for validating miRNA-target interactions fail to differentiate between artifactual peaks and physiologically relevant peaks. Here, we present a modification to the HITS-CLIP protocol that effectively eliminates this artifact.

overall_design: Argonaute HITS-CLIP on the MCF-7 breast cancer cell line treated with 17β-estradiol for 0, 6 or 24 hours using a nested reverse transcriptions pimer and protected or unprotected reverse PCR primers for library amplification.

first: Austin

middle: E

last: Gillen

first: Tomomi

last: Yamamoto

first: Enos

last: Kline

first: Jay

last: Hesselberth


title: Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells

city: Tarrytown

first: Yurong

last: Xin

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

summary: This study provides an assessment of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells. The system combines microfluidic technology and nanoliter-scale reactions. We sequenced 622 cells allowing identification of 341 islet cells with high-quality gene expression profiles. The cells clustered into populations of alpha-cells (5%), beta-cells (92%), delta-cells (1%) and PP-cells (2%). We identified cell-type specific transcription factors and pathways primarily involved in nutrient sensing and oxidation and cell signaling. Unexpectedly, 281 cells had to be removed from the analysis due to low viability (23%), low sequencing quality (13%) or contamination resulting in the detection of more than one islet hormone (64%). Collectively, we provide a resource for identification of high-quality gene expression datasets to help expand insights into genes and pathways characterizing islet cell types. We reveal limitations in the C1 Fluidigm cell capture process resulting in contaminated cells with altered gene expression patterns. This calls for caution when interpreting single-cell transcriptomics data using the C1 Fluidigm system.

overall_design: Single-cell RNA sequencing of mouse C57BL/6 pancreatic islet cells

first: Jesper

last: Gromada


title: How C/EBPa creates an elite cell state for reprogramming to pluripotency [RNAseq]

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

country: France

institute: Ecole Normale Superieure

summary: Mouse Bcell, upon ectopic expression of the transcription factor Cebpa for 18h, can be reprogrammed to iPS with extremely high efficiency. To understand the molecular control of this phenomena we performed multiple high throughtput functionnal genomic analysis.

overall_design: Transcriptomic by RNAseqencing (polyA+, non stranded) in Bcell, Bcell+Cebpa18h, Bcell+Cebpa18h+OKSM1d, Bcell+Cebpa18h+OKSM2d, ES cells

first: Bruno

last: di Stefano

first: Samuel

first: Janus

last: Jakobsen

first: Andreas

last: Lackner

first: Thomas

last: Graf


title: How C/EBPa creates an elite cell state for reprogramming to pluripotency [ChIPseq]

overall_design: Genome binding/occupancy of transcription factors and histones by ChIPseq in Bcell, Bcell+Cebpa18h, Bcell+Cebpa18h+OKSM1d, Bcell+Cebpa18h+OKSM2d, ES cells


title: How C/EBPa creates an elite cell state for reprogramming to pluripotency [ATACseq]

overall_design: Chromatin accessibility by ATACseq in Bcell, Bcell+Cebpa18h, Bcell+Cebpa18h+OKSM1d, Bcell+Cebpa18h+OKSM2d, ES cells


title: Transcriptomics analysis of developing wild type and val1 mutant Arabidopsis embryos

city: Blacksburg

first: Delasa

last: Aghamirzaie

state: VA

address: 101L Price Hall, Virginia Tech

department: GBCB

institute: virginia Tech

summary: Developing Arabidopsis seeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism.  Seed development and metabolism are positively regulated by transcription factors belonging to the LAFL regulatory network.  The VAL gene family encodes repressors of the seed maturation program in germinating seeds, although they are also expressed during seed maturation.  VAL1 functions as a repressor of seed metabolism, as val1 mutant seeds accumulated elevated levels of storage proteins compared to the wild type.  Two VAL1 splice variants were identified through RNA sequencing analysis: a full-length and a truncated form lacking the plant-homeodomain-like domain associated with epigenetic repression.  None of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos.  Instead, activation of VAL1 by FUSCA3 appears to result in repression of a subset of seed maturation genes downstream of core LAFL regulators as 39% of transcripts in the FUSCA3 regulon were de-repressed in the val1 mutant.  The LEC1 and LEC2 regulons also responded but to a lesser extent.  Additional 832 transcripts that were not LAFL targets were de-repressed in val1 mutant embryos.  These transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression.

overall_design: 2 genotypes, 7 time points, 3 biological and 4 technical replicates

first: Andrew

last: Schneider

first: Haitham

last: Elmarakeby

first: Arati

middle: N

last: Poudel

first: Abraham

middle: J

last: Koo

first: Lenwood

last: Heath

first: Ruth

last: Grene

first: Eva

last: Collakova


title: Measure transcript integrity using RNA-seq data

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: Achieved biospecimens annotated with patient clinical characteristics are unique resources for translational research. However, RNA extracted from the achieved tissues is often degraded. RNA degradation can have a significant impact on the measure of transcript abundance that can lead to an increase rate of erroneous differentially expressed genes.  Here, we are presenting the transcript integrity number (TIN) algorithm to measure the RNA degradation at transcript level. When applied to RNA-seq datasets generated from human brain Glioblastome cell line, human peripheral blood mononuclear cells, and metastatic castration resistant prostate cancer (mCRPC) clinical tissues, TIN provided a more reliable and more sensitive measure of RNA degradation than RIN, as demonstrated by much higher concordance with the RNA fragment size estimated from read pairs. More importantly, when comparing 10 mCRPC samples with lower RNA quality to another 10 samples with higher RNA quality, we demonstrated that calibrating gene quantification with TIN scores could mitigate RNA degradation effects and greatly improve gene expression analysis. The detected differentially expressed genes before TIN correction were predominantly ribosomal genes. However, when we adjusted gene quantifications with the corresponding TIN scores, we found differentially expressed genes were highly enriched in prostate cancer specific pathways. When further evaluating the performance of TIN correction using synthetic spike-in transcripts with predetermined abundance in RNA-seq data generated from Sequencing Control Consortium (SEQC), we found TIN adjustment had a better control of false positives and false negatives (sensitivity = 0.89, specificity = 0.91), as compared to gene expression analysis results without TIN correction (sensitivity =0.98, specificity = 0.50).

overall_design: RNA sequencing of 20 bone-metastatic castration resistant prostate cancer (mCRPC) using Illumina HiSeq 2500. Out of 20 mCRPC samples, 10 samples have relative low RNA integrity and another 10 samples have relative higher RNA integrity as measured by Agilent RIN score.

first: Manish

last: Kohli

first: Liguo

last: Wang


title: How C/EBPa creates an elite cell state for reprogramming to pluripotency [4C]

first: samuel

overall_design: Circularized chromosome conformation capture assay (4C) taking as view point Klf4 promoter and a putative enhancer situated a -100kb upstream

first: Ralph

last: Stadhouders


title: Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

summary: Both prokaryotic and eukaryotic organisms take deterministic decisions to reprogram cell fates. A macroscopic manifestation of such an event is the remodelling of the cells’ morphology and it typically is governed at the molecular scale by massive reorganization of the cellular transcriptome. With the regulation at the level of transcription initiation representing the most common form for such developmental reprogramming, cells typically rely on one or several master regulators to coordinate the the activity of hundreds of genes simultaneously by directly binding to their promoters. Despite the apparent simplicity of prokaryotes and their reduced genome size compared to that of their eukaryotic counterparts, free-living bacteria typically encode hundreds of transcription factors (TFs) in their genomes that could act as master TFs.  By contrast, obligate intracellular bacteria such as Chlamydiae have a drastically reduced genome due to their intimate association with the host and thus a smaller number of TF genes. The genomes of members of the Chlamydiaceae family, which include the well-known bacterial pathogens Chlamydia trachomatis and Chlamydia pneumoniae, are only 1-1.2 Mbp. By contrast, members of the environmental Chlamydiae Waddlia chondrophila and Parachlamydia acanthamoebae have a 2-fold and 3-fold larger genome, respectively, likely allowing for an expansion of the host range while still retaining their host dependence and parasitic life style. Moreover, they all exhibit a characteristic chlamydial developmental cycle via two functionally specialized morphotypes, the infectious non-dividing elementary bodies (EBs) and the non-infectious dividing reticulate bodies (RBs). This developmental cycle is usually divided in three stages: the early stage during which EBs enter host cells and differentiate into RBs; the mid-stage where RBs proliferate inside a vacuole called inclusion and the late stage where RBs differentiate back into EBs and are released after exocytosis or cell lysis. Chlamydial genes are thus classified into three different temporal classes (early, mid and late expressed genes), likely reflecting the need of these transcripts in each of the three developmental stages. W. chondrophila, an emerging pathogen implicated in abortion in bovine and miscarriage in humans, encodes less than 20 TFs, 10 of which are conserved among the Chlamydiae. In light of this low TF multiplicity in the chlamydial pan-genome along with the common developmental cycle and parasitic life style, we aimed to define the regulatory pan-genome of each these conserved TFs to identify the elusive chlamydial master regulator and to characterize underling specificity for its target promoters using chromatin-immunoprecipitation followed by deep-sequencing (ChIP-Seq) of chlamydial cells growing inside the host. The immunochemistry of ChIP-Seq has the advantage of minimizing the contaminating nucleic acids compared to chlamydial transcriptome studies, it has the added benefit of providing the first unambiguous glimpse into the regulatory landscape of a bacterium inside host, offering a solid framework in understanding the stochastic and/or deterministic switches that bacteria rely on during infections.

overall_design: Examination of the regulatory network of an intracellular pathogen

first: Marie

last: De Barsy

first: Gael

last: Panis

first: Laurence

last: Theraulaz

first: Trestan

last: Pillonel

first: Gilbert

last: Greub

first: Patrick

last: Viollier


title: Breast Cancer Suppressor Role of RUNX1: Estrogen-dependent Regulation of AXIN1 and b-catenin

city: Duarte

first: Dustin

last: Schones

address: 1500 E Duarte Rd.

institute: City of Hope

summary: The transcription factor RUNX1 exhibits recurrent loss-of-function mutations in estrogen receptor-positive (ER+) breast cancer (BCa).  Its knockdown in vitro decreased AXIN1 expression in estrogen-dependent manner.  Consistently, RUNX1 and AXIN1 mRNA levels are strongly correlated in ER+, not ER- tumors.  RUNX1 occupies AXIN1’s second intron in living cells, abutting an ERa-binding site.  Potentially promoting BCa progression, decreased AXIN1 expression after RUNX1 knockdown associated with upregulation of b-catenin, and this was preventable by AXIN stabilizers. Unlike in colon cancer, however, deregulation of b-catenin in BCa cells affect neither c-Myc, nor CCND1, nor G1/S cell cycle phase transition. Instead, cyclin B1 was decreased and the G2/M checkpoint was compromised as indicated by mitotic slippage in the presence of microtubule disruptors. Thus, combined analysis of the RUNX1 transcriptome, its cistrome, and differential mRNA expression in tumors with wild type versus mutant RUNX1, altogether highlight a role for the RUNX1/AXIN1/b-catenin axis in ER+ BCa. Significance: Three recent exome sequencing studies assigned to RUNX1 a BCa suppressor role. The present study begins to uncover the underlying molecular mechanisms, offers an explanation for the specificity to ER+ tumors, and marks AXIN1 as a therapeutic target for ER+/RUNX1- BCa.

overall_design: Examination of RUNX1 binding in MCF7 cells

first: Nyam-Osor

last: Chimge

first: Gillian

last: Little

first: Sanjeev

middle: K

last: Baniwal

first: Helty

last: Adisetiyo

first: Tian

last: Zhang

first: Andie

last: O’Laughlin

first: Peaches

last: Ulrich

first: Zhi

last: Liu

first: Anthony

last: Martin

first: Paulette

last: Mhawech-Fauceglia

first: Matthew

last: Ellis

first: Debu

last: Tripathy

first: Chengyu

last: Liang

first: Baruch

last: Frenkel


title: Profiling of soma and neurite transcriptomes

last: Taliaferro

address: 12801 E 17th Ave, RC1 South Room 10403D

institute: University of Colorado Anschutz Medical Campus

summary: We report mRNA profiles of subcellularly localized transcriptomes (soma and neurite) of two mouse cell lines, N2A and CAD, as well as primary cortical neurons from E18.5 mice.  We also performed this fractionation and sequencing after RNAi knockdown (cell lines) or in knockout mice (primary cortical neurons) of the RNA-binding proteins muscleblind 1 and 2 (Mbnl1 and Mbnl2).

overall_design: Fractionate neurons using porous transwell membranes.  Isolate poly-A RNA.

first: Christopher

last: Burge


title: Gene expression profiling of optic nerve from Tcf7l2 mutant and control mice

first: Richard

last: Lu

summary: We performed gene expression pofiling of of optic nerve from Tcf7l2 mutant and control mice and identified significantly changed genes in mutant.

overall_design: RNA-seq of P12 optic nerve from control and mutant mice.

first: Chuntao

last: Zhao


title: Occupancy of Mll1 in ESCs and transcriptome of ESCs, EpiSCs and reverted ES by MM401 (Mll1 inhibitor)

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

institute: University of Michigan

overall_design: Refer to individual Series


title: How C/EBPa creates an elite cell state for reprogramming to pluripotency

first: samuel

last: Collombet


title: PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage.

city: Pittsburgh

first: Hun-Way

last: Hwang

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

summary: Accurate and precise annotation of 3' UTRs is critical for understanding how mRNAs are regulated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). Here, we describe a method, poly(A) binding protein-mediated mRNA 3' end retrieval by crosslinking immunoprecipitation (PAPERCLIP), that shows high specificity for mRNA 3' ends and compares favorably with existing 3' end mapping methods. PAPERCLIP uncovers a previously unrecognized role of CstF64/64tau in promoting the usage of a selected group of non-canonical poly(A) sites, the majority of which contain a downstream GUKKU motif. Furthermore, in the mouse brain, PAPERCLIP discovers extended 3' UTR sequences harboring functional miRNA binding sites and reveals developmentally regulated APA shifts, including one in Atp2b2 that is evolutionarily conserved in humans and results in the gain of a functional binding site of miR-137. PAPERCLIP provides a powerful tool to decipher post-transcriptional regulation of mRNAs through APA in vivo.

overall_design: PAPERCLIP protocol and RNA-Seq on human cell lines and mouse whole brain cortex.

first: Robert

middle: B

last: Darnell


title: Alternative routes to induced pluripotent stem cells revealed by reprogramming of neural lineage

status: Public on Feb 18 2016

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Department of Regenerative Biology

institute: University of Wisconsin

summary: During the reprogramming of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells, the activation of pluripotency genes such as Nanog occurs after the mesenchymal to epithelial transition (MET). Here we report that both adult stem cells (neural stem cells- NSCs) and differentiated cells (astrocytes) of the neural lineage can activate Nanog in the absence of cadherin expression during reprogramming. Gene expression analysis revealed that only the Nanog+Ecadherin+ populations expressed stabilization markers and had upregulated several cell cycle genes; and were transgene independent. Inhibition of Dot1L activity, which has previously been shown to increase MET, enhanced both the numbers of Nanog+ and Nanog+E-cadherin+ colonies, suggesting a MET independent pathway for activation of Nanog in NSCs.  Expressing Sox2 in MEFs prior to reprogramming does not alter the ratio of Nanog colonies that express E-cadherin obtained. Taken together these results provide a novel pathway for reprogramming taken by cells of the neural lineage.

overall_design: Neural Stem Cells (NSCs) were induced to reprogram by the induction of Oct4, Sox2, c-Myc and Klf4. Reprogramming colonies that expressed either Nanog alone (N+E-) or Nanog and E-cadherin (N+E+) were sorted by flow cytometry and used as input for RNA-sequencing. There are 3 replicates each for the N+E- and N+E+ samples.


title: Long non-coding RNA landscape in human monocytes

city: Baltimore

first: Srikanth

middle: Srinivas

last: Manda

state: Maryland

address: 733 N Broadway

department: School of Medicine

institute: Johns Hopkins University

summary:
We report the lncRNAs transcribed in the human primary monocyte cells. We performed deep RNA sequencing from four healthy individuals. In addition, the raw RNA-Seq data from 11 human monocyte samples were selected from public databases and generated a total ~1.7 billion reads. We identified ~ 8,000 lncRNAs from all the datasets of which more than 1,000 of them have not been previously reported in monocytes. We also validated a few of these novel lncRNAs in monocytes and other hematopoetic cell types.

The other 11 datasets were taken from the following:

ENCSR000CUC 6 samples
E-MTAB-2399 4 samples
GSM1526678

overall_design: mRNA profiling of monocytes cells  from 4 healthy individuals

first: Hoda

last: Mirsafian

first: Srinivas

middle: S

first: Sreelakshmi

last: Sreenivasamurthy

first: Adiratna

middle: M

last: Ripen

first: Saharuddin

last: Mohamad

first: Amir

middle: F

last: Merican

first: Akhilesh

last: Pandey


title: Cohesin releases DNA through asymmetric ATPase-driven ring opening

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: Cohesin stably holds together the sister chromatids from S phase until mitosis. To do so, cohesin must be protected against its cellular antagonist Wapl. Eco1 acetylates cohesin’s Smc3 subunit, which locks together the sister DNAs. We used yeast genetics to dissect how Wapl drives cohesin from chromatin and identified mutants of cohesin that are impaired in ATPase activity but remarkably confer robust cohesion that bypasses the need for the cohesin protectors Eco1 in yeast and Sororin in human cells. We uncover an unexpected functional asymmetry within the heart of cohesin’s highly conserved ABC-like ATPase machinery and show that an activity associated with one of cohesin’s two ATPase sites drives DNA release from cohesin rings. This key mechanism is conserved from yeast to humans. We propose that Eco1 locks cohesin rings around the sister chromatids by counteracting an asymmetric cohesin-associated ATPase activity.

overall_design: Effect of mutations in Smc1 and Smc3 on cohesin loading onto chromosomes

first: Naomi

last: Petela

first: Christophe

last: Chapard

first: Benjamin

last: Rowland


title: Releasing activity disengages cohesin’s Smc3/Scc1 interface in a process blocked by acetylation

summary: Sister chromatid cohesion conferred by entrapment of sister DNAs within a tripartite ring formed between cohesin’s Scc1, Smc1, and Smc3 subunits is generated during S and eventually destroyed at anaphase through cleavage of Scc1 by separase. Throughout the cell cycle, cohesin’s association with chromosomes is controlled by opposing activities: loading by the Scc2/4 complex and release by a separase independent releasing activity. Co-entrapment of sister DNAs during replication is accompanied by acetylation of Smc3 by Eco1, which blocks releasing activity and ensures that sisters remain stably connected. Because fusion of Smc3 to Scc1 prevents release and bypasses the requirement for Eco1, we suggested that release is mediated by disengagement of the Smc3/Scc1 interface. We now show that all mutations capable of bypassing Eco1, be they in cohesin’s Smc1, Smc3, Scc1,Wapl, Pds5, or Scc3 subunits, greatly reduce dissociation of N-terminal cleavage fragments of Scc1 (NScc1) from Smc3. We show that this process involves interaction between Smc ATPase heads and is inhibited by Smc3 acetylation

overall_design: Effect of mutations QQ and EQ in Smc3 on cohesin loading onto chromosomes

first: Bin

last: Hu


title: mRNA sequencing of the global effect of SET1A on gene expression in mouse ES cells

city: Shanghai

first: Jiemin

last: Wong

address: 500 Dongchuan Road

institute: Institute of Biomedical Sciences and School of Life Sciences, East China Normal University

summary: Gene expression profiling reveals that SET1A regulates gene expression, metabolism and development programs in mouse ES Cells

overall_design: To analyze the global effect of SET1A on gene expression in ES cells, we compared the gene expression profiles in CGR8 cells treated with control and Set1A siRNA by RNA-seq.

first: Lan

last: Fang


title: Control of Smc Coiled Coil Architecture by the ATPase Heads Facilitates Targeting to Chromosomal ParB/parS and Release onto Flanking DNA

city: Martinsried

first: Stephan

last: Gruber

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

summary: Smc/ScpAB promotes chromosome segregation in prokaryotes, presumably by compacting and resolving nascent sister chromosomes. The underlying mechanisms, however, are poorly understood. Here, we investigate the role of the Smc ATPase activity in the recruitment of Smc/ScpAB to the Bacillus subtilis chromosome. We demonstrate that targeting of Smc/ScpAB to ParB/parS loading sites is strictly dependent on engagement of Smc head domains and relies on an open organization of the Smc coiled coils. We find that dimerization of the Smc hinge domain stabilizes closed Smc rods and hinders head engagement as well as chromosomal targeting. Conversely, the ScpAB sub-complex promotes head engagement and Smc rod opening and thereby facilitates recruitment of Smc to parS sites. Upon ATP hydrolysis, Smc/ScpAB is released from loading sites and relocates within the chromosome—presumably through translocation along DNA double helices. Our findings define an intermediate state in the process of chromosome organization by Smc.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: ChIP-Seq experiments were performed on wild type and mutant cells of Bacillus subtilis 1A700.

first: Anita

last: Minnen

first: Frank

last: Bürmann

first: Larissa

last: Wilhelm

first: Anna

last: Anchimiuk

first: Marie-Laure

last: Diebold-Durand


title: Identifying molecular mechanisms of neural crest (NC) EMT and cell migration

city: Salt Lake City

first: Rodney

last: Stewart

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

institute: University of Utah

summary:
Purpose: To identify differntially expressed transcripts in TP-0903 treated embryos that impair cranila NC EMT and cell migration in zebrafish embryos
Methods: zebrafish embryos treated at 13 hpf with 5-7uM TP-0903 and DMSO for 1-, 4- and 8-hrs at 28°C. 35 embryos were collected for each treatment.
Results: TP-0903 increases expression of several retinoic acid target genes including genes from within the retinoid pathway
Conclusions: TP-0903 causes a direct increase in RA signaling that impairs cranial NC EMT and cell migration in zebrafihs embryos

overall_design: mRNA profiles of zebrafish embryos treated with TP-0903 and DMSO were generated by RNA-Seq, in quadruplicates, using Illumina Hi Seq

first: Laura

last: Jimenez


title: Genome wide binding sites of NF-κB subunits RelA, RelB, p50, and p52 in the Hodgkin lymphoma cell line L1236

city: Berlin

first: Marina

last: Kolesnichenko

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Center

summary: The malignant cells of Hodgkin's lymphoma are characterized by a constitutive activation of the canonical as well as the non-canonical NF-κB signaling cascades. We carried out genome-wide localization and expression profiling experiments in the Hodgkin lymphoma cell line L1236 for the canonical and non-canonical NF-κB pathway components p65, p50 and p52, RelB, respectively. We found that the single NF-κB subunits bind to overlapping, but distinct cistromes by using consensus motifs of high similarity.

overall_design: ChIP-Seq analysis of 4 NF-κB subunits with 2 biological replicates each

first: Eva

last: Kärgel

first: Matthias

last: Heinig

first: Giannino

last: Patone

first: Norbert

last: Huebner

first: Claus

last: Scheidereit


title: Effect of drought on herbivore-induced plant gene expression: Population comparison for range limit inferences

city: SPEARFISH

first: Gunbharpur

middle: Singh

last: Gill

state: SOUTH DAKOTA

address: 1200 UNIVERSITY STREET

department: SCHOOL OF NATURAL SCIENCES

institute: BLACK HILLS STATE UNIVERSITY

summary: Low elevation “trailing edge” range margin populations typically face increases in both abiotic and biotic stressors that may contribute to range limit development.  We hypothesize that selection may act on ABA and JA signaling pathways for more stable expression needed for range expansion, but that antagonistic crosstalk prevents their simultaneous co-option.  To test this hypothesis, we compared high and low elevation populations of Boechera stricta that have diverged for constitutive levels of glucosinolate defenses and root:shoot ratios; neither population has high levels of both traits. If constraints imposed by antagonistic signaling underlies this divergence, one would predict that high constitutive levels of traits would coincide with lower plasticity.  To test this prediction, we compared the genetically diverged populations in a double challenge drought-herbivory growth chamber experiment.  Although a glucosinolate defense response to the generalist insect herbivore Spodoptera exigua was attenuated under drought conditions, the plastic defense response did not differ significantly between populations.  Similarly, although several potential drought tolerance traits were measured, only stomata aperture behavior, as measured by carbon isotope ratio, was less plastic as predicted in the high elevation population. However, RNAseq results on a small subset of plants indicated differential expression of relevant genes between populations as predicted.  We suggest that the ambiguity in our results comes from a weaker link between the pathways and the functional traits compared to transcripts.

overall_design: Examination of four different treatments on two different populations

last: Singh Gill

first: Riston

last: Haugen

first: Steven

middle: L

last: Matzner

first: Abdelali

last: Barakat

first: David

last: Siemens


title: Next generation sequencing reveals gene transcription activities and alternative splicing events in germinating barley embryos

city: South Perth

first: Qisen

last: Zhang

state: WA

address: 3 naron Hay Court

country: Australia

institute: Australian Export Grain Innovation Center

summary: Seed germination triggers a transition of growth and metabolic activities from quiescent to active statuses. Germinating seeds is a good system to study many biological and biochemical processes including hormone metabolic activities and cell wall biosynthesis. Next generation sequence technology is used to study these processes. We have examined gene transcription activities and alternative splicing events in germinating embryos

overall_design: We dissected barley embryos from four barley varieties at 2 time points 24 h and 48 h

first: Chengdao

last: Li

first: Xiaoqi


title: Nematostella vectensis high resolution developmental transcriptomic time-course

city: Haifa

first: Itai

last: Yanai

address: Technion City

institute: Technion - Israel Institute of Technology

summary: Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage, however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum, including a segmented worm, a flatworm, a roundworm, a water bear, a fruitfly, a sea urchin, a zebrafish, a sea anemone, a sponge, and a comb jelly. For each species, we collected the embryonic transcriptomes at ~100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly, we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation, and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes, also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility.

overall_design: 123 single embryo samples.

first: Michal

last: Levin

first: Leon

last: Anavy


title: Caenorhabditis elegans high resolution developmental transcriptomic time-course

overall_design: 139 single embryo samples.


title: Schmidtea polychroa high resolution developmental transcriptomic time-course

overall_design: 132 single embryo samples.


title: Strongylocentrotus purpuratus high resolution developmental transcriptomic time-course

overall_design: 165 single embryo samples.


title: Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

summary: The mammalian heart has poor regenerative capacity following injury. In contrast, certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA-dependant regulatory circuits in the heart. We identified novel miRNA-dependant networks involved in critical biological pathways, which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart.

overall_design: 2 conditions, 3 biological replicates per condition

first: Stefania

last: Crippa

first: Samir

last: Ounzain

first: Mohammed

last: Nemir

first: Corinne

last: Berthonneche

first: Alexandre

last: Sarre

first: Gaëlle

last: Boisset

first: Keith

last: Harshman

first: Ioannis

last: Xenarios

first: Dario

last: Diviani

first: Daniel

last: Schorderet

first: Thierry

last: Pedrazzini


title: Mnemiopsis leidyi high resolution developmental transcriptomic time-course

overall_design: 40 single embryo samples


title: Platynereis dumerilii high resolution developmental transcriptomic time-course

overall_design: 97 single embryo samples.


title: Drosophila melanogaster high resolution developmental transcriptomic time-course

overall_design: 91 single embryo samples.


title: Amphimedon queenslandica high resolution developmental transcriptomic time-course

overall_design: 124 single embryo samples.

first: Nagayasu

last: Nakanishi

first: Selene

last: Fernandez-Valverde

first: Bernard

last: Degnan


title: Growth control switch by a DNA damage-inducible toxin-antitoxin system in Caulobacter

status: Public on Feb 17 2016

first: Antonio

last: Frandi

summary: Bacterial toxin-antitoxin systems (TASs) are thought to respond to various stresses, often inducing growth-arrested (persistent) sub-populations of cells whose housekeeping functions are inhibited. However, it is not always clear whether specific targets of orthologous RNAse toxins are responsible for their phenotypic effect, which has made it difficult to accurately place the multitude of TASs within cellular and adaptive regulatory networks. Here we show that the TAS HigBA can promote and inhibit bacterial growth dependent on the dosage of HigB, a toxin regulated by the DNA damage (SOS) repressor LexA in addition to its antitoxin HigA, and the target selectivity of HigB’s mRNA cleavage activity. HigB reduced the expression of an efflux pump that is toxic to a polarity control mutant, cripples the growth of cells lacking LexA and targets the cell cycle circuitry. Thus, TASs can have outcome switching activity in bacterial adaptive (stress) and systemic (cell cycle) networks.

overall_design: DNA binding of the antitoxin HigA and the SOS regulator LexA was analysed by chromatin immunoprecipitation-deep sequencing, and found to overlap at only one locus, the HigBA TA system promoter

first: Clare

last: Kirkpatrick

last: Martins

first: Peter

last: Redder

first: Johann

last: Mignolet

first: Julien

last: Bortoli Chapalay

first: Marc

last: Chambon

first: Gerardo

last: Turcatti

first: Patrick

last: Viollier


first: Mark

last: Ibberson

overall_design: 2 conditions, 4 biological replicates per condition

first: Stefania

last: Crippa

first: Samir

last: Ounzain

first: Mohammed

last: Nemir

first: Corinne

last: Berthonneche

first: Alexandre

last: Sarre

first: Gaëlle

last: Boisset

last: Harshman


title: Danio rerio high resolution developmental transcriptomic time-course

first: Itai

last: Yanai

overall_design: 106 single embryo samples

first: Michal

last: Levin

first: Leon

last: Anavy


title: ASNase treatment in PC3 cells

city: Amsterdam

first: Koos

last: Rooijers

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: Ribosome profiling performed on control and L-Asparaginase treated PC3 cells

overall_design: 2 individual batches: (i) 1 control and 1 treated sample, (ii) 1 control and 2 treated samples

first: Fabricio

last: Loayza-Puch

first: Jelle

last: Zijlstra

first: Joachim

last: Oude Vrielink

first: Rui

last: Lopes

first: Alejandro

middle: P

last: Ugalde

first: Axel

last: Bex

first: Reuven

last: Agami


title: Ribosome profiling on polysomes extracted via sucrose gradient and IP

summary: Technical feasibility study to determine data quality and reproducibilty. Ribosome profiling was performed by either sucrose gradient (SG) or immunoprecipitation (IP).

overall_design: 1 sucrose gradient sample, 2 immunoprecipitation samples in two concentrations of beads


title: Deep sequencing data for PAM-SCANR tested CRISPR-Cas systems

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive, Partners II Rm 2109

department: Chemical and Biolmolecular Engineering

institute: North Carolina State University

summary: In this work, we analyzed recognized PAM sequences from four CRISPR-Cas systems: E. coli I-E, B. halodurans I-C, S. thermophilus CR1 II-A, and F. novicida V. Cells containing functional PAMs were sorted using FACS and subsequently sequenced.

sample_organism:
Francisella tularensis subsp. novicida
Escherichia coli
Streptococcus thermophilus
Halalkalibacterium halodurans

overall_design: Ranking of recognized PAMs from a positive screen

first: Ryan

middle: T

last: Leenay

first: Kenneth

middle: R

last: Maksimchuk

first: Rebecca

middle: A

last: Slotkowski

first: Roma

last: Agrawal

first: Ahmed

last: Gomaa

first: Alexandra

last: Briner

first: Rodolphe

last: Barrangou


title: PAR-CLIP analysis of YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 in human HeLa cells

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: Label the cells overexpressed Flag tagged YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 with 4-SU, the RNA bound by YTHDC1 and SRSF proteins can be got by Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

overall_design: Discovery of the binding motif of YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 or SRSF10  in overexpressed Human HeLa cells

first: Wen

last: Xiao

first: Yun-Gui

last: Yang


title: Ribosome profiling on SUM159PT cells grown in vitro or in vivo

first: Koos

last: Rooijers

summary: SUM159PT cells were grown either in vitro (in culture) or in vivo (mouse), after which RPL10a tagged with GFP was used to perform extraction by immoprecipitation and subsequent ribosome profiling

overall_design: Two batches of in vitro grown cells, each having 2 replicates. Two batches of in vivo grown cells from tumors grown in two individual mice, each having tumors on left (first batch) and right side (second batch). Extraction and ribosome profiling was done independently for the two batches of samples.

first: Fabricio

last: Loayza-Puch

first: Jelle

last: Zijlstra


title: Global analysis of pre-mRNA subcellular localization upon splicing inhibition by spliceostatin A

city: Toyoake

first: Rei

last: Yoshimoto

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake

department: Institute for Comprehensive Medical Science

country: Japan

institute: Fujita Health University

summary: RNA-Seq analysis of SSA treated cells

overall_design: HeLa cells, nuclear and cytoplasmic fractions, treated with SSA or MeOH

first: Minoru

last: Yoshida


title: Ribosome profiling on glutamine-starved panel of luminal and basal breast cancer cell lines

summary: Four different breast cancer cell lines were grown either under unrestricted growth conditions or in medium lacking glutamine, and ribosome profliling was performed on material extracted from these samples

overall_design: 1 replicate per condition

first: Joachim

last: Oude Vrielink

first: Rui

last: Lopes

first: Alejandro

last: Ugalde

first: Axel

last: Bex

first: Reuven

last: Agami


title: Transcriptomics analysis of gene expression in normal and YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 or SRSF10 deficient human HeLa cells

summary: RNA was isolated from and YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 deficient human HeLa cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read or paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

overall_design: Examination of gene expressive levels in normal and YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 or SRSF10 deficient Human HeLa cells


title: Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis 18b

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

institute: University of Bern

summary:
Introduction: Tuberculosis (TB) is a serious human disease caused by the bacterium Mycobacterium tuberculosis (Mtb). One third of the world’s population is estimated to be latently infected with Mtb. Exact mechanisms and properties of latent TB infection (LTBI) are not fully elucidated. In essence, the pathogen can enter a dormant or latent state characterized by limited growth and metabolism, resulting in absence of clinical symptoms in the host, and most importantly by increased phenotypic tolerance to the commonly used medications, thereby allowing indefinite persistence in the human body. This persistence is the main reason why the current treatment of new-onset pulmonary TB is very long, consisting of a six months therapy of four antibiotics (rifampicin, isoniazid, pyrazinamide, and ethambutol for the first two months, and only rifampicin and isoniazid for the last four months).
Current state of the art: To fight TB globally and more efficiently, it is essential to shorten the treatment for TB with new drugs that are efficient also against LTBI. To facilitate discovery of such drugs, in vitro models for LTBI can be used for high throughput screening of chemical libraries. Current in vitro models such as nutrient starvation (Betts et al. 2002), nutrient depletion (Hampshire et al. 2004; Rifat, Bishai, and Karakousis 2009), progressive hypoxia (Wayne and Hayes 1996), nitric oxide treatment (Martin I. Voskuil et al. 2003) and multiple stress (Deb et al. 2009) mimic the dormant state of Mtb, but the technical settings and equipment required for these models obstruct high throughput applications.
Proposed model: The streptomycin (STR)-starved 18b model (SS18b) is a simple and drug discovery efficient Mtb latency model successfully applicable to both in vitro and in vivo settings (Zhang et al. 2012). It is based on the Mtb strain 18b, which is a STR-dependent mutant that enters a viable but nonreplicating state in the absence of STR (Hashimoto 1955). Despite the successful model, we know very little about 18b. How well does SS18b mimic the bacterial response to the complex host-pathogen interactions underlying LTBI, and how does the SS18b response compare to that of other dormancy models are still open questions. In this work we analyse the complete genome of 18b and describe the transcriptomic response of 18b to STR depletion.

overall_design: 12 samples were analyzed. Four biological replicates were sampled during the exponential growth phase, in presence of streptomycin. Four biological replicates derived after 2 weeks of streptomycin depletion, and two biological replicates derive after 4 weeks of streptomycin depletion. Two replicates derive from the resubmission of streptomycin after four weeks of depletion.

first: Swapna

last: Uplekar

first: Ming

last: Zhang

first: Jérémie

last: Piton

first: Stewart

last: Cole

first: Claudia

last: Sala


title: Ribosome profiling on sections taken from a kidney tumor

overall_design: For two tumors: 2 sections of normal tissue and 4 samples of tumor tissue, for another two tumors 1 section of normal tissue and 1 section of tumor tissue


title: Gene expression analysis of wild-type and Beta-2-spectrin homozygous knockout (β2SP-/-) mouse embryonic fibroblasts

city: Houston

first: Jian

last: Chen

state: TX

address: 1515 Holcombe Blvd

department: Gastroenterology

institute: UT MD Anderson Cancer Center

summary: Gene expression profiling was carried out in wild and β2SP-/- (Sptbn1 -/-) mouse embryonic fibroblast (MEF) cells. Beta-2-spectrin (β2SP) is a dynamic intracellular non-pleckstrin homology (PH)-domain protein that belongs to a family of polypeptides that have been implicated in conferring cell polarity. Spectrins have been linked to multiple signaling pathways, including cell cycle regulation, DNA repair and TGFβ signaling. In this study, we report a major role of the TGFβ/Smad3 adaptor β2-Spectrin in conserving genomic integrity from alcohol-induced DNA damage and describe a novel pathway that protects genomes from genotoxic stresses.

overall_design: Whole-transcriptome RNA sequencing of wild-type and β2SP knockout (β2SP-/-) mouse embryonic fibroblasts was carried out on an Illumina HiSeq 2000 sequencer. The raw data quality was assessed using a FastQC software. Adaptor presence was tested using Trimmomatic. The readings were then aligned to the NCBI mouse reference genome build 37.2 using the splice-aware aligner Tophat2 v2.0.10. Transcript quantification, normalization and assembly were carried out with Cufflinks. A gene model gtf file corresponding to the NCBI mouse reference genome build 37.2 was used in the quantification. Cuffdiff2, part of the Cufflinks suite of tools, was used to identify significant differences in gene expression profiles between the wild-type and β2SP-/- MEF cells.

first: Lopa

last: Mishra


title: Large-scale profiling of intracellular signalling pathway activation reveals major distinctions between airway smooth muscle cells of asthmatics and non-asthmatics.

city: Portici

first: Elena

last: Alexandrova

state: Napoli

address: Viale Stazione, 22

department: Faculty of Medicine and Surgery

country: Italy

institute: University of Salerno

summary: Signalling pathways regulate all major cellular events in health and disease, including asthma development and progression. Complexity of human intracellular signalization can be explored using novel systemic approaches that exploit whole-transcriptome analysis. Cap-analysis-of-gene-expression (CAGE) is a method of choice for generating transcriptome libraries, as it interrogates only terminally capped mRNAs that have the highest probability to be translated into protein. In this study we for the first time systematically profiled differentially activated Intracellular Signalling Pathways (ISPs) in cultured primary human airway smooth muscle (ASM) cells from asthmatic (n=8) and non-asthmatic (n=6) subjects in a high-throughput assay, highlighting asthma-specific co-regulatory patterns. CAGE-libraries from primary human ASM cells were subject to massive parallel next generation sequencing, and a comprehensive analysis of ISP activation was performed using a recently developed technique OncoFinder. Analysis of 270 ISPs led to discovery of multiple pathways clearly distinguishing asthmatic from normal cells. In particular, we found 146 (p<0.05) and 103 (p<0.01) signalling pathways differentially active in asthmatic vs non-asthmatic samples. We identified seven clusters of coherently acting pathways functionally related to the disease. Pathways down-regulated in asthma mostly represented cell death-promoting pathways, whereas the up-regulated ones were mainly involved in cell growth and proliferation, inflammatory response and some specific reactions, including smooth muscle contraction and hypoxia - related signalization. Most of interactions uncovered in this study were not previously associated with asthma, suggesting that these results may be pivotal to development of novel therapeutic strategies that specifically address the ISP signature linked with asthma pathophysiology.

overall_design: Capped mRNA profiles of primary bronchial smooth muscle cells from 8 asthmatic and 6 healthy donors were generated by deep sequencing using Illumina HiSeq1500.


title: Impact of Prnp genetic ablation in the hippocampus transcriptome of congenic B6.129-PrnpZH1/ZH1 or coisogenic C57BL/6-PrnpZH3/ZH3 mice

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

summary: To study the effect of Prnp genetic ablation on different aspects of RNA metabolism, we performed RNA sequencing of the hippocampus of wild-type C57BL/6J, congenic B6.129-PrnpZH1/ZH1 and coisogenic C57BL/6J-PrnpZH3/ZH3 mice. We analyzed differential gene expression, exon usage and RNA editing.

overall_design: RNA sequencing on hippocampus of wild-type C57BL/6 mice, congenic B6.129-PrnpZH1/ZH1 and coisogenic C57BL/6-PrnpZH3/ZH3 mice (3 month-old males, n=4 per genotype).

first: Mario

last: Nuvolone

first: Giancarlo

last: Russo

first: Adriano

last: Aguzzi


title: Ribosome profiling and RNA sequencing of MCF10A cells treated with torin or by serum starvation

first: Koos

last: Rooijers

summary: MCF10A were either untreated, treated with torin or by starvation, to induce autophagy. RNA sequencing and ribosome profiling was performed.

overall_design: 1 biological replicate for each condition

first: Fabricio

last: Loayza-Puch

first: Jelle

last: Zijlstra

first: Joachim

last: Oude Vrielink

first: Rui

last: Lopes