title: DNA adenine methyltransferase (Dam) overexpression impairs Photorhabdus luminescens motility and virulence

city: Montpellier

first: Anne

last: Lanois

address: 75 rue du Truel CC54

institute: INRA

summary: Dam, the most described bacterial DNA-methyltransferase, is widespread in gamma-proteobacteria. Dam DNA methylation can play a role in various genes expression and is involved in pathogenicity of several bacterial species. In the entomopathogenic bacterium Photorhabdus luminescens, a dam ortholog was identified. Overexpression of dam in P. luminescens did not impair growth ability in vitro. In contrast, compared to a control strain harboring an empty plasmid, a significant decrease in motility was observed in the dam-overexpressing strain. In addition, the dam-overexpressing P. luminescens strain showed a delayed virulence compared to that of the control strain after injection in larvae of the lepidopteran Spodoptera littoralis. These results reveal that Dam plays a major role during P. luminescens insect infection.

sample_organism: Photorhabdus laumondii subsp. laumondii TTO1

overall_design:
Three independent RNA samples, each corresponding to a pool of total RNA extracted independently from 3 biological replicates cultures of:
[1] TT01 (pBBR1MCS-5) grown in LB supplemented with gentamycine harvested in exponential phase (OD= 0.5).
[2] TT01 (pBB-Dam) grown in LB supplemented with gentamycine harvested in exponential phase (OD= 0.5).
Deep sequencing, performed using Illumina HiSeq 2000.

first: Amaury

last: Payellevile

first: Marie

last: Gislard

first: Emeric

last: Dubois

first: Stéphane

last: Cruveiller

first: David

last: Roche

first: Alain

last: Givaudan

first: Julien

last: Brillard


title: DNA demethylation activates genes in seed maternal integument development in rice (Oryza sativa L.)

status: Public on Oct 10 2017

city: Hangzhou

first: Jian

last: zhang

state: Zhejiang

address: 28 shuidaosuo road,Fuyang, Hangzhou

department: State Key Lab of Rice Biology

country: China

institute: China National Rice Research Institute

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an important epigenetic modification that regulates various plant developmental processes. Rice seed integument determines the seed size. However, the role of DNA methylation in its development remains largely unknown. Here, we report the first dynamic DNA methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. Analysis of DNA methylation patterns identified 4238 differentially methylated regions underpin 4112 differentially methylated genes, including GW2, DEP1, RGB1 and numerous other regulators participated in maternal integument development. Bisulfite sanger sequencing and qRT-PCR of six differentially methylated genes revealed extensive occurrence of DNA hypomethylation triggered by double fertilization at IAP compared with IBP, suggesting that DNA demethylation might be a key mechanism to activate numerous maternal controlling genes. These results presented here not only greatly expanded the rice methylome dataset, but also shed novel insight into the regulatory roles of DNA methylation in rice seed maternal integument development.

overall_design: The global DNA methylomic profiling of seed integument before and after pollination of rice were generated by whole-genome deep bisulfite deep sequencing, in triplicate, using IlluminaHiSeqTM 2500.

first: Yifeng

last: Wang

first: Haiyan

last: Lin

last: Zhang


title: Epigenetic Targeting of Bromodomain Protein BRD4 Counteracts Cancer Cachexia and Prolongs Survival

status: Public on Oct 01 2017

city: Milan

first: Giuseppina

last: Caretti

address: Via Celoria 26

country: Italy

institute: University of Milan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cancer cachexia is a devastating metabolic syndrome characterized by systemic inflammation and massive muscle and adipose tissue wasting. Although cancer cachexia is responsible for approximately one third of cancer deaths, no effective therapies are available and the underlying mechanisms have not been fully elucidated.We have found that (+)-JQ1 administration protects tumor-bearing mice from body weight loss, muscle and adipose tissue wasting. Remarkably, in C26-tumor bearing mice (+)-JQ1 administration dramatically prolongs survival, without directly affecting tumor growth. By ChIP-seq analyses, we unveil that the BET proteins directly promote the muscle atrophy program during cachexia. Consistently, BET pharmacological blockade prevents the activation of catabolic genes associated with skeletal muscle atrophy and decreases IL6 systemic levels. Overall, these findings indicate that BET may represent a promising therapeutic target in the management of cancer cachexia.

overall_design: To examine BRD4 genome-wide distribution in skeletal muscle during cachexia, we compared BRD4 occupancy in control skeletal muscle, in muscles from C26-tumor bearing mice treated with JQ1 and in muscles from C26-tumor bearing mice treated with JQ1 inactive enantiomer. Tumor-bearing mice were inoculated with C26 tumor cells by dorsal s.c. injection. The day after tumor cells inoculation animals were treated either with JQ1 or the inactive enantiomer.

first: Marco

last: Segatto

first: Raffaella

last: Fittipaldi

first: Fabrizio

last: Pin

first: Roberta

last: Sartori

first: Kyung

middle: D

last: Ko

first: Hossein

last: Zare

first: Claudio

last: Fenizia

first: Giampietro

last: Zanchettin

first: Elisa

middle: S

last: Pierobon

first: Shinji

last: Hatakeyama

first: Cosimo

last: Sperti

first: Stefano

last: Merigliano

last: Sandri

first: Panagis

last: Filippakopoulos

first: Paola

last: Costelli

first: Vittorio

last: Sartorelli


title: Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche

status: Public on Oct 04 2017

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

institute: Northwest A&F University

type: Expression profiling by high throughput sequencing

summary: We sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis

overall_design: Mycelia from artificial inoculations onto apple fruit after 3 months in the field were used as ‘in planta’ samples for RNA sequencing. For ‘in vitro’ mycelium, R. luteum was cultured in liquid Czapek-Dox medium.Three independent biological samples were collected for RNA extraction and sequencing, using an Illumina HiSeq™ 2500 sequencing platform.

first: Bo

last: Wang

first: Guangyu

last: Sun


title: Differential expression analysis of haploid, diploid, and tetraploid yeast experimentally evolved in raffinose medium

city: Boulder

first: Amber

middle: Lynne

last: Scott

state: CO

address: 3415 Colorado Ave

department: Department of Molecular, Cellular, and Developmental Biology

country: USA

institute: University of Colorado

summary: Haploid, diploid, and tetraploid yeast were experimentally evolved in 2% raffinose medium. After 250 generations, we assessed the gene expression alterations in 2 evolved haploids, 2 evolved diploids, and 4 evolved tetraploids relative to the diploid ancestor.

overall_design: mRNA gene expression profiles of 2 evolved haploid, 2 evolved diploid, and 4 evolved tetraploid clones were compared to the expression profile of the diploid ancestral strain in 2% raffinose medium.

middle: L

first: Phillip

middle: A

last: Richmond

first: Anna

middle: M

last: Selmecki

first: Robin

last: Dowell


title: H3K27Ac ChIP-seq for TL-om1 cells and primary ATL cell samples

status: Public on Oct 05 2017

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

summary: ChIP-seq analysis was performed in adult T-cell leukemia/lymphoma cells to analyze acetylation of histone H3K27.

overall_design: TL-Om1 and primary ATL cells were crosslinked with formaldehyde for 10 min. DNA was enriched by chromatin-immunoprecipitation (ChIP) and analyzed by Illumina Hiseq 4000.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against histone H3 lysine 27 acetylation (H3K27Ac: Abcam, ab4729).

first: Regina

middle: W

last: Wong

middle: C

last: Ngoc

first: Wei

middle: Z

last: Leong

first: Alice

last: Yam

first: Takaomi

last: Sanda


title: High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast.

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

summary: While the protein composition of various yeast 60S ribosomal subunit assembly intermediates has been studied in detail, little is known about ribosomal RNA (rRNA) structural rearrangements that take place during early 60S assembly steps. Using a high-throughput RNA structure probing method, we provide nucleotide resolution insights into rRNA structural rearrangements during nucleolar 60S assembly. Our results suggest that many rRNA-folding steps, such as folding of 5.8S rRNA, occur at a very specific stage of assembly, and propose that downstream nuclear assembly events can only continue once 5.8S folding has been completed. Our maps of nucleotide flexibility enable making predictions about the establishment of protein-rRNA interactions, providing intriguing insights into the temporal order of protein-rRNA as well as long-range inter-domain rRNA interactions. These data argue that many distant domains in the rRNA can assemble simultaneously during early 60S assembly and underscore the enormous complexity of 60S synthesis.Ribosome biogenesis is a dynamic process that involves the ordered assembly of ribosomal proteins and numerous RNA structural rearrangements. Here the authors apply ChemModSeq, a high-throughput RNA structure probing method, to quantitatively measure changes in RNA flexibility during the nucleolar stages of 60S assembly in yeast.

overall_design: Three ribosomal RNA species were probed with 1M7 in vitro or incubated with DMSO. Biological replicates are provided for each sample.


title: Catalogue of differentially expressed long non-coding RNAs following activation of human and mouse innate immunity

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

institute: University of Bath

summary: Despite increasing evidence to indicate that long non-coding RNAs (lncRNAs) are novel regulators of immunity, there has been no systematic attempt to identify and characterise the lncRNAs whose expression are changed following the induction of the innate immune response. To address this issue, we have employed next generation sequencing data to determine the changes in the lncRNA profile in LPS-stimulated human macrophages, IL1beta-stimulated human airway A549 epithelial cells and and LPS-stimulated mouse RAW 264.7 macrophages

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNAseq was performed in human macrophages (Ribozero isolated), human alveolar A549 epithelial cells (polyA+ isolated) and mouse RAW 264.7 macrophages (polyA+ isolated) at 4h following exposure to media (control) or LPS (human macrophages and mouse RAW 264.7 macrophages) or IL1beta (human epithelial A549 cells)


title: Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq

status: Public on Oct 11 2017

city: St. Louis

first: Gary

middle: D.

last: Stormo

state: MO

address: 4515 McKinley Ave. Room 4208.

department: Genetics

institute: Washington University School of Medicine

summary: Spec-seq directly mesaures specificity by sequencing. We run an EMSA experiment on TF of interest with a library of DNA targets. Then we extract and sequence the bound and unbound portion of the DNA separately. Finally we count the occurences of each varient in the library and calculate the ratio and the relative binding energy.

overall_design: 15 independent Spec-seq experiments

first: Yiming

middle: K

last: Chang


title: Transcriptome analysis of fasted mouse livers

city: Neuherberg

first: Robert

last: Schneider

address: Ingolstaedter strasse 1

department: Institute of Functional Epigenetics

country: Germany

institute: Helmoltz Zentrum Muenchen

summary: We report application of RNA-seq to quantify gene expression changes in fasted mouse livers compared to re-fed controls.

overall_design: RNA-seq from livers of re-fed and 48h fasted mice.

first: Adam

middle: F

last: Kebede


title: Transcription factors and stress response gene alterations in human keratinocytes following Solar Simulated Ultra Violet Radiation

city: New York

first: Hong

last: Sun

state: NY

address: 341 East 25 Street

department: Medicine

institute: NYU School of Medicine

summary: Ultraviolet radiation (UVR) from sunlight is the major effector for skin aging and carcinogenesis. However, genes and pathways altered by solar-simulated UVR (ssUVR), a mixture of UVA and UVB, are not well characterized. Here we report global changes in gene expression as well as associated pathways and upstream transcription factors in human keratinocytes exposed to ssUVR. Human HaCaT keratinocytes were exposed to either a single dose or 5 repetitive doses of ssUVR. Comprehensive analyses of gene expression profiles as well as functional annotation were performed at 24 hours post irradiation. Our results revealed that ssUVR modulated genes with diverse cellular functions in a dose-dependent manner. Gene expression in cells exposed to a single dose of ssUVR differed significantly from those that underwent repetitive exposures. While single ssUVR caused a significant inhibition in genes involved in cell cycle progression, especially G2/M checkpoint and mitotic regulation, repetitive ssUVR lead to extensive changes in genes related to cell signaling and metabolism. We have also identified a panel of ssUVR target genes that exhibited persistent changes in gene expression even at 1 week after irradiation. These results revealed a complex network of transcriptional regulators and pathways that orchestrate the cellular response to ssUVR.

first: Max

last: Costa


title: Transcriptomic profiles in dental pulp cells from one CCD patient with allelic RUNX2 deletion and one sex-age matched unaffected individual.

status: Public on Oct 03 2017

city: Vancouver

first: Mary

last: MacDougall

address: 2329 West Mall

country: Canada

institute: UUniversity of British Columbia

summary: The goal is to investigate the downstream targets of RUNX2 signaling which are potentially involved in the disease process of Cleidocranial Dysplasia (CCD). RNA-seq was performned to compare the mRNA profiles in human dental pulp cells from one CCD patient with allelic RUNX2 deletion (CCD-011) and sex-age matched unaffected individual(Control).   Of 25,643 genes analyzed, 11,039 genes had no detectable signal in both CCD and control samples tested leaving 14,604 genes that were evaluated for differential gene expression.  In the detectable genes, 60 transcripts (4.1%) were found to be statistically significantly dysregulated with 63% upregulated and 27% downregulated (fold change ≥ 2; q-value < 0.05).

overall_design: mRNA profiles of CCD-011 dental pulp cells and sex-age matched control cells were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Stephen

last: Greene


title: Polysome-profiling in small tissue samples - proof of concept experiment for the use of an optimized non linear gradient

city: Solna

first: Ola

last: Larsson

address: Tomtebodavägen 23A

institute: Karolinska Institute

summary: Polysome-profiling is commonly used to study translatomes, i.e. transcriptome-wide patterns of translational efficiency. The standard approach for collecting efficiently translated polysome-associated RNA results in laborious extraction of RNA from a large volume across many fractions. This property makes polysome-profiling inconvenient for larger experimental designs or samples with low RNA amounts such as primary cells or frozen tissues. To address this, we optimized a non-linear sucrose gradient which reproducibly enriches for mRNAs associated with >3 ribosomes in only one or two fractions, thereby reducing sample handling 5-10 fold. The technique can be applied to frozen tissue samples from biobanks, and generates polysome-associated RNA with a quality reflecting the starting material. When coupled with smart-seq2, a single-cell RNA sequencing technique, translatomes from small tissue samples can be obtained. Translatomes acquired using optimized non-linear gradients resemble those obtained with the standard approach employing linear gradients. Polysome-profiling using optimized non-linear gradients in serum starved HCT-116 cells with or without p53 showed that p53 status associated with changes in mRNA abundance and translational efficiency leading to changes in protein levels. Moreover, p53 status also induced translational buffering whereby changes in mRNA levels are buffered at the level of mRNA translation to maintain protein levels constant. Thus, here we present a polysome-profiling technique applicable to large study designs, primary cells and frozen tissue samples such as those collected in bio banks.

overall_design: We used two cell lines that differ in their p53 status (HCT-116 p53+/+ and HCT-116 p53-/-) and serum-starved them (16 h). We prepared cytosolic lysates from 6 plates (15 cm) from each cell type and divided the lysates equally between the optimized non-linear gradient and the linear gradient groups. We then collected fractions corresponding to mRNA associated with >3 ribosomes from the linear gradient, peak 0 and +1 from the optimized non-linear gradient as well as the cytosolic input. We repeated the experiment four times.

first: Shuo

last: Liang

first: Hermano

last: Bellato

first: Julie

last: Lorent

first: Fernanda

last: Lupinacci

first: Vincent

last: Van Hoef

first: Victor

last: Piana de Andrade

first: Martin

last: Roffe

first: Laia

last: Masvidal

first: Glaucia

last: Hajj


title: The planarian TCF/LEF factor Smed-tcf1 is required for the regeneration of dorsal-lateral neuronal subtypes

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: The adult brain of the planarian Schmidtea mediterranea (a freshwater flatworm) is a dynamic structure with constant cell turnover as well as the ability to completely regenerate de novo.  Despite this, function and pattern is achieved in a reproducible manner from individual to individual in terms of the correct spatial and temporal production of specific neuronal subtypes.  Although several signalling molecules have been found to be key to scaling and cell turnover, the mechanisms by which specific neural subtypes are specified remain largely unknown.  Here we performed a 6 day RNAseq time course on planarians that were regenerating either 0, 1, or 2 heads in order to identify novel regulators of brain regeneration.  Focusing on transcription factors, we identified a TCF/LEF factor, Smed-tcf1, which was required to correctly pattern the dorsal-lateral cell types of the regenerating brain.  The most severely affected neurons in Smed-tcf1(RNAi) animals were the dorsal GABAergic neurons, which failed to regenerate, leading to an inability of the animals to phototax away from light.  Together, Smed-tcf1 is a critical regulator, required to pattern the dorsal-lateral region of the regenerating planarian brain.

overall_design: control(RNAi), apc(RNAi) and Smed-Bcatenin1(RNAi) animals were fed 3 times over 1 week and amputated three days following their final feed. RNA was collected every 24 hours for 6 days from regenerating trunk fragments. Samples were sequenced to a depth of >43 million reads.  Each condition was biologically triplicated, but RNA was pooled prior to sequencing.

first: David

last: Brown


title: Characterizing the transcriptional profile of murine 3T3-L1 adipocytes with altered expression of Dnmt3a

city: Berkeley

first: Sona

last: Kang

state: CA

address: 316 Morgan Hall

department: Nutritional Sciences and Toxicology

institute: UC Berkeley

summary: We report RNA-Seq data file from 3T3-L1 adipocytes following overexpression and knock-down of Dnmt3a

overall_design: Transcriptional profiling of murine 3T3-L1 adipocytes with altered expression of Dnmt3a from biological triplicates. Overexpression or knockdown of Dnmt3a was achieved by lentivirus transduction in mature 3T3-L1 adipocytes.

first: Dongjoo

last: You

first: Danielle

last: Tenen

first: Anna

last: Lyubetskaya

first: Evan

last: Rosen


title: Genome-wide identification of bacterial membrane protein expression determinants

first: Heather

middle: Marie

last: Jensen

state: California

address: 1 Cyclotron Road, Mailstop 978-4110K

institute: Lawrence Berkeley National Laboratory

summary: Cellular membranes provide a barrier to toxins, play a central role in metabolism, and are essential for cell viability, making membrane proteins of key interest for microbial strain engineering. However, membrane protein expression often causes decreased cell viability and alterations to central metabolism. We hypothesized that some non-essential proteins may be antagonistic towards the expression of a desired membrane protein and thus expression stress may be alleviated by the deletion of the corresponding genes. To identify mutant Escherichia coli that tolerate greater expression of membrane proteins, we developed a generalizable method, FlowSeq, that utilizes a pooled, bar-coded transposon insertion library in tandem with cell sorting to access genome-wide impact on membrane protein expression. Five membrane proteins (CyoB, CydB, MdlB, YidC, and LepI) and one soluble protein (GST) fusted to GFP were screened with FlowSeq. We identified 15 gene deletion strains capable of increased membrane protein expresison, and 3 of these knockout strains also increased membrane protein function. To our knowledge, this study represents the first systematic approach to identify genetic deteminants of membrane protein expression.

overall_design: Examination of barcoded strain abundance after membrane protein expression stress.

first: Thomas

last: Eng

last: Chubukov

first: Robin

last: Herbert

first: Aindrila

last: Mukhopadhyay


title: Gene expression profile during wound-induced callus formation in Arabidopsis thaliana

city: Yokohama

first: Momoko

last: Ikeuchi

state: Kanagawa

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

department: CSRS

country: Japan

institute: RIKEN

summary: Wounding is a primary trigger of organ regeneration but how wound stress reactivates cell proliferation and promotes cellular reprogramming remains elusive. In this study we combined the transcriptome analysis with quantitative hormonal analysis to investigate how wounding induces callus formation in Arabidopsis thaliana. Our time-course RNA-seq analysis revealed that wounding induces dynamic transcriptional changes that can be categorized into five clusters with distinct temporal patterns. Gene ontology analyses uncovered that wounding modifies the expression of hormone biosynthesis and response genes, and quantitative analysis of endogenous plant hormones revealed accumulation of cytokinin prior to callus formation. Mutants defective in cytokinin synthesis and signalling display reduced efficiency in callus formation, indicating that de novo synthesis of cytokinin has major contribution in wound-induced callus formation. We further demonstrate that type-A ARABIDOPSIS RESPONSE REGULATOR (ARR)-mediated cytokinin signalling regulates the expression of CYCLIN D3;1 (CYCD3;1) and mutations in CYCD3;1 and its homologs CYCD3;2-3 cause defects in callus formation. Our transcriptome data, in addition, showed that wounding activates multiple developmental regulators, and we found novel roles of ETHYLENE RESPONSE FACTOR 115 (ERF115) and PLETHORA3 (PLT3), PLT5, PLT7 in wound-induced callus formation. Together, this study provides novel mechanistic insights into how wounding reactivates cell proliferation during callus formation.

overall_design: Examination of transcriptome at 0, 1, 3, 6, 12,24 h after wounding.


title: Generation of mature lung alveolar epithelial cells from human pluripotent stem cells

city: Boston

first: Anjali

last: Jacob

state: MA

address: 670 Albany St., 2nd Floor, CReM-232

department: Center for Regenerative Medicine

institute: Boston University School of Medicine

summary: We perform time-series global transcriptomic profiling of a directed differentiation protocol for generating alveolar epithelial type II cells (AEC2s) from pluripotent stem cells (PSCs). We analyzed 3 different timepoints in the RUES2 differentiation: 1) Day 0 undifferentiated cells, 2) Day 15 lung progenitors highly enriched in NKX2-1+ cells by CD47hi/CD26lo sorting, and 3) the outgrowth of these purified progenitors in 3D culture sorted again on Day 35 based on SFTPCtdTomato+ and SFTPCtdTomato- gating. For comparison to primary cells, we simultaneously sequenced RNA from purified primary fetal (21 week gestation) distal alveolar epithelial progenitors and purified adult human (HTII-280 sorted) AEC2s. In order to evaluate the effect of cell culture on primary fetal alveolar cells, parallel aliquots of the fetal cells were also exposed to 4 days of culture in DCI media. We find that AEC2 maturation involves downregulation of Wnt signaling activity, and that the highest differentially expressed transcripts in iPSC-derived AEC2s encode genes associated with lamellar body and surfactant biogenesis.

overall_design: Analysis of global transcriptomes of PSCs and their differentiated progeny (primordial lung progenitors and alveolar cells) compared to primary fetal (21 week) and adult alveolar epithelial type 2 cells in triplicate

first: Darrell

middle: N

last: Kotton


title: U1 snRNP telescripting regulates size-function stratified human genome

status: Public on Oct 02 2017

city: Philadelphia

first: Christopher

middle: Conrad

last: Venters

state: Pennsylvania

address: 415 Curie Boulevard

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

summary: This project looks into how U1 snRNP inhibition causes a loss of telescripting through premature cleavage and polyadenylation based on the size and function of human genes.

overall_design: Knockdown of U1 snRNP by antisense morpholino followed by examining transcriptome changes by RNA-seq and RNA pol II profile changes by ChIP-seq.

first: Jung-Min

last: Oh

first: Chao

last: Di

first: Jiannan

last: Guo

first: Chie

last: Arai

first: Byung Ran

last: So

first: Anna Maria

last: Pinto

first: Zhenxi

last: Zhang

first: Lili

last: Wan

first: Ihab

last: Younis

first: Gideon

last: Dreyfuss


title: Cerebellar differentiation in Ataxia-Telangiectasia

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

summary: Control (CRL2429 C11) and A-T (MC3/AT30) iPSC were differentiated according to Erceg et al to generate cerebellar precursors

overall_design: Examination of changes in gene expression after a 34 day differentiation protocol in control and A-T iPSC

first: Samuel

last: Nayler

first: Darya

last: Vanichkina


title: Tracheal gene expression after Wls deletion

city: Cincinnati

first: Debora

last: Sinner

state: OH

address: 3333 Burnet Ave

department: Neonatology and Pulmonary Biology

institute: CCHMC

summary: Wls is required for patterning of the developing trachea

overall_design: E11.5 and E13.5 mouse trachea control vs WlsShhCre

first: John

last: Snowball

first: Jeffrey

last: Whitsett


title: Genome-wide binding analysis of Arabidopsis GATA transcription factors GNC and CGA1

city: Toronto

first: Zhenhua

last: Xu

state: ON

address: 25 Willcocks St.

department: Cell and Systems Biology

institute: University of Toronto

summary: GATA transcription factors are involved in multiple processes in plant growth and development. Two GATA factors, nitrate-inducible, carbon metabolism-involved (GNC) and CYTOKININ-RESPONSIVE GATA FACTOR 1 (CGA1, also named GNL) are important regulators in greening, flowering, senescence and hormone signaling. However, their direct target genes in regulating these biological processes are poorly characterized. Here, we report a genome-wide identification of the target genes of Arabidopsis GNC and CGA1.

overall_design: INPUT DNA and ChIP-DNA from 2 biological replicates of Arabidopsis myc-GNC and myc-CGA1 transgenic lines were subjected for sequencing.

first: Jose

last: Casaretto

first: Yong-Mei

last: Bi

first: Steven

last: Rothstein


title: RNA-sequencing analysis of response to P.falciparum infection in Fulani and Mossi ethnic groups, Burkina Faso

city: Stockholm

first: Ann-Kristin

last: Östlund-Farrants

address: Svante Arrheniusväg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

institute: Stockholm University

summary: The Fulani ethnic group is relatively protected from Plasmodium falciparum malaria, however a genetic basis for this is unknown. Therefore, we have performed a pilot study to examine global transcription and DNA methylation patterns in specific immune cell populations in the Fulani, compared to a sympatric ethnic group, the Mossi. When we compared uninfected and infected individuals in Fulani and Mossi, a strong transcriptional response was only detected in the monocyte fraction of Fulani, and this was not related to differences in DNA methylation.

overall_design:
RNA sequencing analysis of CD14+ (monocyte) and CD14- (predominantly lymphocyte), and DNA-methylation analysis of CD14+ (monocyte) fractions of PBMCs,  from of Fulani and Mossi individuals, uninfected or infected with P.falciparum.
This Series represents the RNA-Seq dataset.


title: The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pest

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

summary: Synergists can counteract metabolic insecticide resistance by inhibiting detoxification enzymes or transporters. In this study we used Illumina RNA-sequencing to investigate genome-wide transcriptional responses in an acaricide resistant strain (JP-R) of the spider mite Tetranychus urticae upon exposure to synergists such as S,S,S-tributyl phosphorotrithioate (DEF), diethyl maleate (DEM), piperonyl butoxide (PBO) and cyclosporin A (CsA).

overall_design: In total 24 RNA-seq samples (6 treatments, 4 biological replicates per treatment) from Tetranychus urticae, were generated. RNA was collected from adult T. urticae females 24h after being sprayed with a synergist compound (PBO, DEF, DEM or CsA) or with formulation only (FORM). Unsprayed mites served as an additional control (CON). For each sample, Illumina mRNA-seq libraries were constructed and strand-specific paired reads of 2x125 bp were generated. The obtained reads were used to quantify gene expression in each sample.

first: Simon

last: Snoeck

first: Robert

last: Greenhalgh

first: Luc

last: Tirry

first: Richard

last: Clark

first: Thomas

last: Van Leeuwen


title: Elucidating the direct target regulon of NtcA during the early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803

city: Pozuelo de Alarcón

first: joaquín

last: Giner Lamia

state: Madrid

address: Campus de Montegancedo

department: Biotecnologia

country: Spain

institute: CBGP-Universidad Politecnica de Madrid

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

overall_design: Refer to individual Series


title: Single cell analysis of SFTPC+ cells and CPM-high progenitor cells derived from human induced pluripotent stem cells (hiPSCs)

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

summary: We stepwisely induced SFTPC+ cells from hiPSCs via CPM-high progenitor cells with or without coculturing human fetal lung fibroblasts. Single-cell RNA-seq of CPM-high progenitor and hiPSC-derived SFTPC+ cells demonstrated their differentiation process and cellular heterogeneity.

overall_design:
scRNA-seq: 6 sample.
FF-SFTPC_scRNA-seq : 1 sample.

first: Yuki

last: Yamamoto

first: Yutaka

last: Suzuki


title: Genome-wide analysis of SAGA subunits: ada2b, spt3, nonstop, and sgf11, as well as RNA pol II in 1-3 hr embryos of Drosophila melanogaster.

city: Kansas City

first: Chris

last: Seidel

department: Genomics

institute: Stowers Institute

summary: The Spt-Ada-Gcn5-acetyltransferase (SAGA) chromatin-modifying complex is a transcriptional coactivator that contains four different modules of subunits. The intact SAGA complex has been well characterized for its function in transcription regulation and development. However, little is known about the roles of individual modules within SAGA and if they have any SAGA independent functions. Here we demonstrate that the two enzymatic modules of Drosophila SAGA are differently required in oogenesis. Loss of the HAT activity blocks oogenesis, while loss of the DUB activity does not. However, the DUB module regulates a subset of genes in early embryogenesis and loss of the DUB subunits causes defects in embryogenesis. ChIP-seq analysis of ada2b, spt3, nonstop, and sgf11revealed that both the DUB and HAT modules bind most SAGA target genes even though many of these targets do not require the DUB module for expression. Furthermore, we found that the DUB module can bind to chromatin and regulate transcription independently of the rest of SAGA. Our results suggest that the DUB module has functions within SAGA as well as independent functions.

overall_design: ChIP Seq analysis of 4 different chromatin modification factors and RNA polymerase II in drosophila embryos was performed with 2 to 4 replicates of each factor.

first: Xuanying

last: Li

first: Leanne

middle: T

last: Well

first: Jerry

last: Workman

first: Susan

last: Abmayr


title: Genome-wide analysis of SAGA subunit ada2b, and histones ubH2B, H2b, H3, H3K9ac, and H3K14ac in wt and Ataxin 7 mutants of 1-3 hr embryos of Drosophila melanogaster

overall_design: ChIP Seq analysis of 6 different chromatin associated factors in wt and Ataxin 7 mutant drosophila embryos was performed with 2 to 3 replicates of each factor.


title: Cross-talk between species that do not share often the same environment

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

institute: UMA

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida DOT-T1E and E. coli growing in co-cultures

sample_organism:
Pseudomonas putida
Escherichia coli

platform_organism:
Pseudomonas putida
Escherichia coli

overall_design: P. putida DOT-T1E and E. coli mRNA profiles comparing their growth in single-cultures and in co-cultures in LB at exponential phase

last: Molina-Santiago

first: Juan

last: Ramos


title: Elucidating the direct target regulon of NtcA during the early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 [ChIP-Seq]

summary: Cyanobacteria are oxygenic photoautotrophs responsible for a substantial proportion of nitrogen fixation and primary production in the hydrosphere. Non-nitrogen fixing cyanobacteria, such as Synechocystis sp. PCC 6803, depend of the availability of nitrogenized species to survive. Therefore, an intricate regulatory network around the transcriptional factor NtcA maintains the homeostasis of nitrogen in these organisms. The mechanisms controlling NtcA activity are well understood but a comprehensive study of its regulon is missing in Synechocystis. To define NtcA regulon during the early stage of nitrogen starvation, we have performed chromatin immunoprecipitation followed by sequencing (ChiP-seq), in parallel with genome level transcriptome analysis (RNA-seq). By combining both methods we assigned 51 activated and 28 repressed genes directly by NtcA. Most of direct targets included genes involved in nitrogen and carbon metabolism and photosynthesis. NtcA regulon also included 8 ncRNAs, of which ncr0710, Syr6 and NsiR7 were experimentally validated. Intriguingly, we identified several NtcA intragenic binding sites suggesting that NtcA can modulate transcriptional expression by binding along the whole transcript and not only in the promoter region as previously though. Finally, the transcriptional implication of PipX was analyzed in some NtcA-targets genes, revealing that PipX assists NtcA in the global nitrogen regulation in Synechocystis.

overall_design: Cells from Synechocystis sp. PCC 6803 wild type (WT) cultured in ammonium and after 4 h of nitrogen starvation were used to perform chromatin immunoprecipitation with anti-NtcA antibody. Four ChIPs were performed from four independent sets of Synechocystis cells. For each experimental condition, a sample of total DNA (not subjected to immunoprecipitation) was used as a control (Input samples). The immunoprecipitated material was sequenced using Illumina Hiseq 2500.

first: Joaquín

last: Giner-Lamia

first: Rocio

last: Robles-Rengel

first: Miguel

last: Hernández-Prieto

first: M

middle: I

last: Muro-Pastor

first: Francisco

last: Florencio

first: Matthias

middle: E

last: Futschick


title: RNA-seq data for tumor tissues from mice fed with normal diet (ND) or high cholesterol diet (HCD)

city: shanghai

first: Fu

last: jing

address: No.225 Changhai road

department: Liver Centre of SMMU

institute: Eastern Hepatobiliary Surgery Hospital

summary: To address how serum cholesterol affected tumor progression, C57BL/6J mice were placed on either normal diet or high cholesterol diet for 4 weeks, and then B16F10 cells were subcutaneously injected into the right flanks of mice. We performed transcriptome sequencing analysis (RNA-seq) on tumor tissues from ND and HCD groups.

overall_design: Three tumor tissues from ND group (ND-1,ND-2,ND-3) and three tumor tissues from HCD group (HCD-1,HCD-2,HCD-3) were analyzed.

first: Wenhao

last: Qin

first: Zhishi

last: Yang

first: Jing

last: Fu

first: Hongyang

last: Wang


title: RNA-seq profiles of  Arabidopsis thaliana wild-type and trm4b-4

city: Singapore

first: Hao

last: Yu

address: Science Drive 4

country: Singapore

institute: National University of Singapore

summary: Methylation of carbon 5 in cytosine (5-methylcytosine; m5C) is a well-characterized DNA modification, and is also predominantly reported in highly abundant noncoding RNAs, such as rRNA and tRNA, in both prokaryotes and eukaryotes. However, the distribution and biological functions of m5C in plant mRNAs remain largely unknown. Here we develop an m5C RNA immunoprecipitation followed by deep sequencing approach (m5C-RIP-seq) to achieve transcriptome-wide profiling of RNA m5C in Arabidopsis thaliana. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and dot blot analyses reveal a dynamic pattern of m5C mRNA modification in various tissues and at different developmental stages. m5C-RIP-seq analysis identifies 6,045 putative m5C peaks in 4,465 expressed genes in young seedlings. m5C is enriched in coding sequences with two peaks located immediately after start codons and before stop codons, and is associated with mRNAs with low translation activity. We further show that a RNA (cytosine-5)-methyltransferase, tRNA specific methyltransferase 4B (TRM4B), exhibits the m5C mRNA methyltransferase activity. Mutations in TRM4B display defects in root development and decreased m5C levels in root mRNA. Furthermore, TRM4B affects transcript levels of the genes involved in root development, which is positively correlated with their mRNA stability and m5C levels. Our results suggest that m5C in mRNA is a new epitranscriptome marker widely distributed in plant genes, and that regulation of this modification is an integral part of gene regulatory networks underlying plant development.

overall_design: RNA-seq in Arabidopsis thaliana (Col-0) wild-type and  trm4b-4, two replicates for each sample

first: Xuean

last: Cui

first: Zhe

last: Liang

first: Lisha

last: Shen

first: Qian

last: Zhang

first: Shengjie

last: Bao

first: Yuke

last: Geng

first: Bin

first: Vonny

last: Leo

first: Leah

middle: A

last: Vardy

first: Tiegang

last: Lu

first: Xiaofeng

last: Gu


title: Ribosomal profiling of adipocytes

first: Yi

last: Chen

state: Massachusetts

address: 450 Brookline Ave CLS 11116

institute: Dana-Farber Cancer Institute

summary:
Purpose: To generate gene expression profiles of inguinal white, epididymal white and interscapular brown adipocytes

Methods: Translating ribosomal affinity purification (TRAP) using an adipocyte-specific cre in adult wildtype mice followed by RNA-Seq

Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) using Tophat and assembled reads into transcripts using Cufflinks.

overall_design: ribosomal affinity purified mRNA profiles of adult mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500.

first: Sara

last: Serag


title: Substrate-based regulation in gut fungi

city: Santa Barbara

first: John

last: Henske

address: Engineering II Building

department: Department of Chemical Engineering

institute: University of California, Santa Barbara

summary: Differential expression analysis of overall transcriptome in response to varying carbon source

sample_organism:
Neocallimastix californiae
Anaeromyces robustus

overall_design: RNAseq of Neocallimastix californiae (G1) and Anaeromyces robustus (S4) grown on glucose, maltose, cellobiose, cellulose, reed canary grass, switchgrass, and corn stover as carbon sources. RNA was isolated during exponential growth and sequenced on an Illumina NextSeq.

first: Kevin

middle: V

last: Solomon

first: Michelle

last: O'Malley


title: Post-transcriptional regulation of adult CNS axonal regeneration by Cpeb1

city: Heidelberg

first: Ana

last: Martin-Villalba

state: Deutschland

address: Im Neuenheimer Feld 280

department: Molekulare Neurobiologie (A290)

institute: German Cancer Research Center (DKFZ)

summary: Profiling of injury response of the localized transcriptome from wild-type and Cpeb1 knockout neurites

overall_design: RNA-sequecing of naïve and injured neurites from wild-type and Cpeb1 knockout neurons

first: Wilson

middle: P

last: Lou

first: Sheng

last: Zhao


title: RNA Sequencing looking at differential gene expression between p65+/+ and p65-/-  mouse embryonic fibroblasts (MEFs)

city: Columbus

first: Denis

last: Guttridge

address: Biomedical Research Tower, 460 West 12th Avenue

institute: The Ohio State University

summary: We look at differential gene expression between immortalized p65+/+ and p65-/- MEFs to identify potential NF-kB regulated genes which when grouped based on biological function indicates candidates involved in protecting p65+/+ cells from macrophage-mediated killing

overall_design: Examination of differential gene expression between two cell types either in the presence or absence of p65

middle: C

first: David

last: Wang

first: Nivedita

middle: M

last: Ratnam


title: Aid is a key regulator of myeloid/erythroid differentiation and DNA methylation in murine hematopoietic stem/progenitor cells (ERRBS)

city: New York

first: Francine

middle: E.

last: Garrett-Bakelman

address: 413 East 69th street, BRB 1426

department: Medicine

institute: Weill Cornell Medicine

summary: Recent studies have uncovered that activation-induced cytidine deaminase (AID) and ten-eleven-translocation (TET) family members regulate active DNA demethylation. Genetic alterations of TET2 in various myeloid malignancies and aberrant hematopoietic stem cell (HSC) self-renewal/differentiation in mice with hematopoietic tissue specific loss of Tet2 have been reported, indicating that TET2 is a master regulator of normal and malignant hematopoiesis. Despite a functional link between AID and TET in epigenetic gene regulation, the role of AID loss in normal hematopoiesis and myeloid transformation remains to be investigated. Here, we show that Aid loss in mice leads to expansion of myeloid cells and contraction in erythroid progenitors resulting in pathologic anemia possibly due to dysregulated expression of Cebpa and Gata1, myeloid/erythroid lineage specific transcription factors. Consistent with data in the murine context, silencing of AID skews differentiation towards myelomonocytic lineage in human BM cells. However, in contrast to Tet2, Aid loss does not contribute to enhanced HSC self-renewal or cooperate with Flt3-ITD in myeloid leukemogenesis. Genome-wide transcription and differential methylation analysis uncover critical role of Aid as a key epigenetic regulator. These results indicate that AID and TET2 share common effects on myeloid and erythroid lineage differentiation, and that their role is non-redundant in regulating HSC self-renewal and in myeloid transformation.

overall_design: We utilized germ line Aid knockout mice for our study and examined transcriptome of FACS-sorted LSK populations from WT, Aid(+/-) and Aid(-/-) animals at 12 months of age.

first: Hiroyoshi

last: Kunimoto

first: Cem

last: Meydan

first: Caroline

last: Sheridan

first: Tak

last: Lee

first: Yaseswini

last: Neelamraju

first: Ari

last: Melnick

first: Ross

middle: L

last: Levine


title: Aid is a key regulator of myeloid/erythroid differentiation and DNA methylation in murine hematopoietic stem/progenitor cells


title: Enzymatic modules of the SAGA chromatin-modifying complex play distinct roles in Drosophila gene expression and development

first: Chris

middle: W

last: Seidel


title: RNA Seq analysis of whole ovaries following mutation of SAGA subunits: Ada2b, Ataxin-7, or non-stop in Drosophila melanogaster

summary: The Spt-Ada-Gcn5-acetyltransferase (SAGA) chromatin-modifying complex is a transcriptional coactivator that contains four different modules of subunits. The intact SAGA complex has been well characterized for its function in transcription regulation and development. However, little is known about the roles of individual modules within SAGA and if they have any SAGA independent functions. Here we demonstrate that the two enzymatic modules of Drosophila SAGA are differently required in oogenesis. Ada2b is part of the HAT module (Histone Acetyl Transferase), whereas Ataxin-7 and non-stop are members of the DUB  module (Deubiquitinase). Loss of the HAT activity blocks oogenesis, while loss of the DUB activity does not. However, the DUB module regulates a subset of genes in early embryogenesis and loss of the DUB subunits causes defects in embryogenesis. ChIP-seq analysis of ada2b, spt3, nonstop, and sgf11revealed that both the DUB and HAT modules bind most SAGA target genes even though many of these targets do not require the DUB module for expression. Furthermore, we found that the DUB module can bind to chromatin and regulate transcription independently of the rest of SAGA. Our results suggest that the DUB module has functions within SAGA as well as independent functions.

overall_design: Gene expression was assessed by RNA Seq analysis in ovaries mutant for either Ada2b, Ataxin-7, or non-stop, relative to wt (FRT) background in three separate experiments, each in triplicate.

first: Xuanying

last: Li

first: Leanne

last: Well

first: Jerry

last: Workman

first: Susan

last: Abmayr


title: RNA Seq analysis of 2.5 hour embryos of Drosophila melanogaster in the absence of Ataxin-7 or non-stop.

overall_design: Gene expression was assessed by RNA Seq analysis in embryos mutant for either Ataxin-7, or non-stop, relative to wt in separate experiments, each in triplicate.


title: Genome-wide characterization of cis-acting DNA targets of Opaque11 in maize

city: Shanghai

first: Weiwei

last: Qi

address: 333 Nanchen Road

institute: Shanghai University

summary: Opaque11 (O11) is a bHLH transcription factor that plays important roles in maize endosperm development, nutrient metabolism, and stress response.

overall_design:
Examination of 15 days after pollination (DAP) wild type maize endosperm with O11 specific antibody.  o11 mutant seeds which have no O11 protein were used as negtive control.
Please note that  antibody for O11 was custom-made as following.  Full-length O11 cDNA was cloned into the EcoR I and Xho I sites of the pET-32a vector (Novagen) and transformed into BL21. The 6xHis fusion recombinant O11 protein was purfied with the   KTA purfication system using a 1 mL HisTrap FF crude column (GE Healthcare). Antibodies were prepared in rabbits by Shanghai ABclonal Biotechnology.

first: Fan

last: Feng


title: A mutually exclusive stem loop arrangement in roX2 RNA is essential for X chromosome regulation in Drosophila

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: The X chromosome provides an ideal model system to study the contribution of RNA-protein interactions in epigenetic regulation. In male flies, roX lncRNAs harbor several redundant domains to interact with the ubiquitin ligase MSL2 and the RNA helicase MLE for X-chromosomal regulation. However, how these interactions provide the mechanics of spreading remains unknown. By employing the uvCLAP methodology, which provides unprecedented information about RNA secondary structures in vivo, we identified the minimal functional unit of roX2 RNA. By using wild type and various MLE mutant derivatives including a catalytic inactive MLE derivative MLEGET we show that the minimal roX RNA contains two mutually exclusive stem-loops which exist in a peculiar structural arrangement: when one stem-loop is unwound by MLE, an alternate structure can form, likely trapping MLE in this perpetually structured region. We show that this functional unit is necessary for dosage compensation as mutations that disrupt this formation lead to male lethality. Thus, we propose that roX2 lncRNA contains an MLE-dependent affinity switch to enable reversible interactions of the MSL complex to allow dosage compensation of the X chromosome.

overall_design: UV crosslinking and affinity purification (uvCLAP) for MLE wildtype and 4 MLE mutants in Drosophila melanogaster.

first: Ilik

last: Ibrahim

first: Maticzka

last: Daniel


title: Systematic identification of molecular pathways driving GBM invasion

city: Amsterdam

first: Nora

last: Pencheva

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Glioblastoma multiforme (GBM) is the most prevalent and deadliest adult brain tumor. To systematically characterize the pathways governing brain invasion, we developed a three-dimensional (3D) ex vivo organotypic invasion model with clinical relevance to GBM. We used this model to enrich for highly invasive GBM cell population. Using next-generation sequencing to transcriptomically profile highly invasive and poorly invasive GBM cell populations, we have identified a network of extracellular matrix (ECM) components, including multiple collagens and collagen-interacting proteins, which are upregulated by invading GBM cells and strongly correlate in expression with clinical glioma progression outcomes. We identify the interferon regulatory factor 3 (IRF3) as a direct transcriptional repressor of ECM factors in GBM and show that IRF3 acts as an endogenous suppressor of GBM invasion. Therapeutic activation of IRF3 by inhibiting casein kinase 2 (CK2) -- a negative regulator of IRF3 phosphorylation -- downregulated the expression of ECM factors and suppressed GBM invasion in ex vivo and in vivo models across a panel of patient-derived GBM cell lines representative of the main molecular GBM subtypes in the clinic. Our findings illustrate an integrated and systematic approach for the discovery of novel pathways regulating brain tumor invasion and provide a strong mechanistic insight into the notorious, yet poorly understood, invasion capacity of GBM tumors.

overall_design: Next-gen sequencing and mRNA transcriptome analysis on 2 independently derived highly invasive GBM cell populations (invasive clones 1 and 2) and 2 poorly invasive control populations (controls 1 and 2). U87 control 1 was analyzed together with and serves as a control for U87 invasive clone 1, and U87 control 2 was analyzed together with and serves as a control for U87 invasive clone 2.

first: R

last: Bernards


title: RNA-seq Analysis of the Salt Stress Induced Transcripts in Fast Growing Bioenergy Tree, Paulownia elongata

city: Tucson

first: Kerry

middle: Kevin

last: Cooper

state: AZ

address: 1117 E. Lowell St.

department: School of Animal and Comparative Biomedical Sciences

institute: University of Arizona

summary: Paulownia elongata is a fast-growing tree species native to China that is grown in different climates, types of soils, and can be easily re-grown. The versatility of the P. elongata species makes it an ideal candidate for biofuel production. High soil salinity is known to inhibit plant growth dramatically or lead to death. Salinity in soil is a detrimental abiotic stress affecting crop production worldwide and a hindrance for potential crop candidates used for biofuel production. The purpose of this study was to characterize the salt-induced transcriptome of P. elongata. Transcriptome differences in response to salt stress were determined by RNA sequencing (RNA-seq) using next generation sequencing and bioinformatics analysis. A total of 646 genes were found to have significant altered expression in response to salt stress, and expression levels of a selective subset of these genes were chosen and confirmed using quantitative real-time PCR. To the best of our knowledge, this is the first report of salt-induced transcriptome analysis in P. elongata. The current study indicates that the differential expression of certain genes may have an important role in the adaptation of P. elongata in response to salt stress. Functional characterization of these genes will assist in future development of salt tolerance in P. elongata, which could be used to enhance biofuel production.

overall_design: Transcriptomes of 3-year old Paulownia elongata pots wild type (WT) and salt stressed (SS) by next generation sequencing, in duplicate using Illumina MiSeq

first: Michel

last: Chaires

first: Dinesh

last: Gupta

first: Nirmal

last: Joshee

first: Chhandak

last: Basu


title: RNA-seq of IL-4 complex treated tissue resident macrophages vs. monocytic macrophages from LysM Cre+ (WT litermate control) and LysM Cre+ RICTOR KO (myeloid specifically RICTOR deleted) mice

city: Baltimore

first: Maureen

middle: R.

last: Horton

state: MD

address: 1830 E. Monument Street, 5th floor

department: Department of Medicine

institute: Johns Hopkins University School of Medicine

summary: RNA-seq was performed on sorted peritoneal tissue resident macrophages (CD11b+F4/80hiTIM4+) and monocytic macrophages (CD11b+F4/80loTIM4-) from IL-4c (recombinant IL-4 (5µg) and anti-IL-4 ab (12.5µg) IP injection on days 0 and 2 and sorted on day 4) treated 6-8wks old LySM Cre+ and LysM Cre+ RICTOR KO  (C57BL/6 background) for expression profiling

overall_design: Expression profiling by high throughput sequencing (Illumina NextSeq 500  V2 - PE 150 Cycle) on sorted peritoneal macrophages from WT and LysM RICTOR KO

first: Jonathan

last: Powell

first: Min-hee

last: Oh


title: Targeting Glioma Stem Cells through Combined BMI1 and EZH2 Inhibition [RNA-seq]

city: Cleveland

first: Briana

last: Prager

address: 9500 Euclid Ave.

institute: Cleveland Clinic

summary: Glioblastomas are lethal cancers defined by angiogenesis and pseudopalisading necrosis.  Here, we demonstrate that these features are associated with distinct transcriptional programs, with vascular regions showing a Proneural profile and hypoxic regions a Mesenchymal pattern.  As these regions harbor glioma stem cells (GSCs), we investigated the epigenetic regulation of these two niches.  Proneural, perivascular GSCs activated EZH2, whereas Mesenchymal GSCs in hypoxic regions expressed BMI1 protein, which promoted cellular survival under stress.  Using both genetic and pharmacologic inhibition, we found that Proneural GSCs are selectively sensitive to EZH2 disruption, whereas Mesenchymal GSCs are sensitive to BMI1 inhibition.  Given that glioblastomas contain both Proneural and Mesenchymal GSCs, combined EZH2 and BMI1 targeting proved more effective than either agent alone both in culture and in vivo, suggesting that strategies that simultaneously target multiple epigenetic regulators within glioblastomas may be necessary to overcome resistance to therapies caused by intratumoral heterogeneity.

overall_design: RNA-seq of CD133 positive cells from intracranial xenografts of patient-derived glioblastoma stem cells

first: Xun

last: Jin

first: Leo

last: Kim

first: Tyler

last: Miller

first: Stephen

last: Mack

first: Daniel

last: Factor

first: Jeremy

last: Rich


title: Elucidating the direct target regulon of NtcA during the early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 [RNA-Seq]

first: joaquín

last: Giner Lamia

institute: CBGP-Universidad Politecnica de Madrid

overall_design: mRNA profiles of Synechocystis sp. PCC6803 wild type (WT) cells growth in ammonium and after 4 hours of nitrogen depletion were generated by deep sequencing, in duplicate, using Ion Torrent PGM Machine.

first: Joaquín

last: Giner-Lamia

first: Rocio

last: Robles-Rengel

first: Miguel

last: Hernández-Prieto

first: M

last: Muro-Pastor

first: Francisco

middle: J

last: Florencio

first: Matthias

last: Futschick


title: Hyperactive FOXO1 results in lack of tip stalk identity and deficient microvascular regeneration

city: Cambridge

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

summary: Inhibition of FOXO1 activity in kidney microvascular endothelial cells improves angiogenesis

overall_design: Kidney microvascular endothelial cells were serum starved and treated with DMSO control or FOXO1 inhibitor for one hour, then stimulated with VEGF for 30 minutes

first: Lan

last: Dang

first: Takahide

last: Aburatani

first: Giovanni

last: Ligresti

first: Graham

last: Marsh

first: Bryce

middle: G

last: Johnson

first: Angela

last: Huang

first: Stella

last: Alimperti

first: Christine

last: Yoon

first: Naoki

last: Nakagawa

first: Ivan

last: Gomez

first: Shuyu

last: Ren

first: Sarah

middle: K

last: Read

first: Chris

last: Sparages

first: Alfred

last: Aplin

first: Roberto

middle: F

last: Nicosia

last: Chen

middle: S

last: Duffield


title: Comparison of mRNA expression profiles of 3q21q26 and 3q21q26::Gata2+/– mouse leukemic cells

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: The 3q21q26 mice harboring a transgene recapitulating GATA2 enhancer-drived EVI1 overexpression in inv(3)(q21q26) allele develop leukemia. Gata2 heterogenous deletion accelerates leukemogenesis of the 3q21q26 mice. To get insights into the couse of the acceleration of leukemogenesis, RNA-sequencing analysis was performed using B220+Gr1–cKit+ populations containing leukemia-initiating cells in bone marrows of leukemic 3q21q26 and 3q21q26::Gata2+/– mice.

overall_design: mRNA profiles of B220+Gr1–cKit+ populations in bone marrows of leukemic 3q21q26 and 3q21q26::Gata2+/– mice were generated by deep sequencing, in triplicate.

first: Saori

last: Katayama

first: Mikiko

last: Suzuki

first: Fumiki

last: Katsuoka

first: Akihito

last: Otsuki


title: Non-Cell-Autonomous Tumor Suppressor Activity of the Homeobox Gene Cdx2 in the Gut

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

summary: This dataset describe the transcriptomic profiling of cecum, stomach and ileum from wild type, cdx2 conditional knock out and cdx2 ; apc deficient mice, by mRNA-seq. Each condition was analyzed in triplicated experiment to analyze the role of cdx2 in colorectal cancer susceptibilities

overall_design: Biological samples from dissected tissue were tested by RNASeq in triplicates resulting into a total of 24 samples.

first: Olivier

last: Armant

first: Jean-Noel

last: Freund

first: Isabelle

last: Duluc


title: RNA-Seq analysis of sorted cortical projection neuron subtype specific responses in a mouse model of ALS over the course of disease progression

status: Public on Sep 30 2017

first: Loyal

last: Goff

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: Neocortical hyperexcitability is a prominent feature of inherited and sporadic amyotrophic lateral sclerosis (ALS) and is inversely correlated with patient survival. Cell-type specific changes in neuronal function have been proposed to underlie these functional abnormalities and contribute to the selective degeneration of corticospinal and spinal motor neurons. We analyzed the physiological properties of distinct classes of neurons in the motor cortex of hSOD1G93A mice and found that they exhibit robust physiological changes that depend on disease stage. Targeted recordings and in vivo calcium imaging revealed that neurons adapt their properties to normalize cortical excitability as disease progresses. Although different neuron classes exhibited similar functional changes, transcriptional profiling and pharmacological manipulations indicate that the molecular mechanisms underlying these changes are cell-type specific. These widespread, stage-dependent alterations in neuronal function in ALS mice highlight the dynamic changes cortical circuits experience during neurodegeneration and expand potential therapeutic strategies for normalizing circuit function.

overall_design: RNA-Seq analysis of wildtype and Sod1 mutant corticospinal neurons sorted for Ctip2 or Satb2.

first: Juhyun

last: Kim

first: Ethan

last: Hughes

first: Ashwin

last: Shetty

first: Paula

last: Arlotta

first: Dwight

last: Bergles

first: Solange

last: Brown


title: Aid is a key regulator of myeloid/erythroid differentiation and DNA methylation in murine hematopoietic stem/progenitor cells (RNA-Seq)

first: Francine

last: Garrett-Bakelman

first: Hiroyoshi

last: Kunimoto

first: Cem

last: Meydan

first: Caroline

last: Sheridan

first: Tak

last: Lee

first: Yaseswini

last: Neelamraju

first: Ari

last: Melnick

first: Ross

last: Levine


title: The Influence of a Cryptochrome on the Gene Expression Profile in the Diatom Phaeodactylum tricornutum under Blue Light and in Darkness

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

summary: Diatoms, albeit being only distantly related with higher plants, harbour a plant-like cryptochrome (CryP) that was proposed to act as a photoreceptor required for the regulation of photosynthetic proteins. Importantly, plant cryptochromes are assumed to be involved in the regulation of developmental processes that are only needed in multicellular organisms; their role in the unicellular diatoms to date is mostly enigmatic. To elucidate the function of this plant-like cryptochrome in a unicellular species, we examined the role of CryP in the regulation of transcription in the diatom Phaeodactylum tricornutum by comparative RNA-seq of wild type and CryP knock-down mutants, under prolonged darkness and one hour after onset of blue light. In total, mRNAs of 12,298 genes were identified and more than 70% of the genes could be sorted into functional bins. We here show that CryP influences gene expression in three different ways: some genes are regulated by CryP under blue light only, others independent of the light condition and surprisingly some are regulated by CryP only in darkness. Changes under blue light included only around 4% of total genes, and genes regulated in any condition were distributed over almost all functional categories. Expression of photosynthesis genes was lowered by CryP under BL, in contrast to the overall enhancement in wild-type cells under the same conditions. Interestingly, CryP also exerted an influence on two other photoreceptors: the genes for phytochrome (Pt-DPH) and CPF1, another cryptochrome of Phaeodactylum tricornutum, were down-regulated by CryP independent of the light condition. However, the regulatory effects of the different photoreceptors on transcriptional output were independent. The influence of CryP on the expression of other photoreceptors hints to the existence of a regulatory signalling network in diatoms that includes several cryptochromes and phytochrome, whereby CryP acts as a regulator of transcript abundance under light as well as in darkness.

overall_design: Transcriptomes of Phaeodactylum tricornutum wild type (WT) and antisense mutants in the plant-like cryptochrome CryP (Na1, Ta3)  grown for 4 d in a dark/light cycle, then kept for 72h in darkness and then shifted to blue light conditions for 1 h. WT samples and Na1 blue light samples were sequenced in biological triplicates, all other samples in biological duplicates.

first: Sarah

last: König

first: Marion

last: Eisenhut

first: Andrea

last: Bräutigam

first: Samantha

last: Kurz

first: Claudia

last: Büchel


title: Comparative analysis the transcriptomes of the hyperaccumulator Sedum plumbizincicola and the non-hyperaccumulator Sedum alfredii (NHE)

first: Jiming

last: Gong

address: Fenglin Road 300

department: National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: The aim of this study is to investigate whether the known mechanisms of hyperaccumulaion in Brassicaceae hyperaccumulators (Arabidopsis halleri and Noccaea caerulescens) are conserved among different hyperaccumulating species or if there exist unknown mechanismsin other metal hyperaccumulating species.The comparison of transcriptomes between hyperaccumulator Sedum plumbizincicola and non-hyperaccumulator S. alfredii (NHE) was performed by taking advantage of next-generation sequencing.The data suggested that increased active uptake, long-distance transport and efficient chelation of heavy metals might represent common mechanisms occurred in various hyperaccumulators. Moreover, we found that those genes showing constitutively higher expression in S. plumbizincicola shoots are significantly enriched in processes related to cell wall metabolism, including biosynthesis/modification of cellulose, lignin, pectin, glucan, and other cell wall related components.

sample_organism:
Sedum alfredii
Sedum plumbizincicola

platform_organism:
Sedum alfredii
Sedum plumbizincicola

overall_design: Roche-454 was adopted to sequence the pooled root and shoot samples of S. plumbizincicola.Illumina sequencing was used to characterize the transcriptomes of root and shoot tissues of the two Sedum species with/out 10μM Cd treatment.Biological replicates: 2 replicates for S. plumbizincicola samples.

first: Jia-Shi

last: Peng

first: Yue-Jun

last: Wang

first: Yi-Jing

last: Zhang

first: Ji-Ming


title: RNA Sequencing Quantitative Analysis of RNA editing sites of Wild Type and ADAR1 editing deficient (ADAR1E861A) murine fetal RNA of various tissues

city: STANFORD

first: Jin

middle: Billy

last: Li

address: 300 Pasteur Dr.

department: Genetics

institute: Stanford University

summary: The Adar1 deaminase inactive mutant mouse tissue samples were obtain from the Walkley lab as described in http://www.ncbi.nlm.nih.gov/pubmed/26275108. We performed mmPCR-seq on the samples and measured the editing levels of.

overall_design: Fetal mRNA profiles of E12.5 wild type (WT) and ADAR E861A mutant mice were generated by deep sequencing using Illumina HiSeq 2000.

first: Meng

middle: H

last: Tan

first: Qin

first: Ankita

last: Gupte

first: Carl

middle: R

last: Walkley

middle: B


title: SMC1A ChIP-seq in primary human keratinocytes

city: La Jolla

first: George

last: Sen

address: 9452 Medical Center Dr.

department: Dermatology

institute: University of California San Diego

summary: This study examines the DNA binding regions of SMC1A, a subunit of the Cohesin complex, in undifferentiated human keratinocytes.

overall_design: ChIP-seq was used to determine the localization of SMC1A in the genome

first: Maria

last: Noutsou


title: Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes

city: Nashville

first: Yongchao

last: Dou

state: Tennessee

address: 2525 west end

institute: vanderbilt medical center

summary: Recent studies have shown that circular RNAs (circRNAs) are abundant, widely expressed in mammals, and can display cell-type specific expression. However, how production of circRNAs is regulated and their precise biological function remains largely unknown. To study how circRNAs might be regulated during colorectal cancer progression, we used three isogenic colon cancer cell lines that differ only in KRAS mutation status. Cellular RNAs from the parental DLD-1 cells that contain both wild-type and G13D mutant KRAS alleles and isogenically-matched derivative cell lines, DKO-1 (mutant KRAS allele only) and DKs-8 (wild-type KRAS allele only) were analyzed using RNA-Seq. We developed a bioinformatics pipeline to identify and evaluate circRNA candidates from RNA-Seq data. Hundreds of high-quality circRNA candidates were identified in each cell line. Remarkably, circRNAs were significantly down-regulated at a global level in DLD-1 and DKO-1 cells compared to DKs-8 cells, indicating a widespread effect of mutant KRAS on circRNA abundance. This finding was confirmed in two independent colon cancer cell lines HCT116 (KRAS mutant) and HKe3 (KRAS WT). In all three cell lines, circRNAs were also found in secreted extracellular-vesicles, and circRNAs were more abundant in exosomes than cells. Our results suggest that circRNAs may serve as promising cancer biomarkers.

overall_design: RNAseq deep sequencing for both cell and exosome mRNAs

first: Diana

last: Cha

first: Jeffrey

last: Franklin

first: James

middle: N

last: Higginbotham

first: Dennis

last: Jeppesen

first: Alissa

last: Weaver

first: Nripesh

last: Prasad

first: Shawn

last: Levy

first: Robert

last: Coffey

last: Patton

first: Bing


title: Identification of regenerative roadblocks via repeat deployment of limb regeneration in axolotls

city: Boston

first: Jessica

last: Whited

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

summary: We sought to determine if we could experimentally compromise the axolotl’s ability to regenerate limbs and, if so, discover the molecular changes that might underlie their inability to regenerate.  We found that repeated limb amputation severely compromised axolotls’ ability to initiate limb regeneration.  Using RNA-seq, we observed that a majority of differentially expressed transcripts were hyperactivated in limbs compromised by repeated amputation, suggesting that mis-regulation of these genes antagonizes regeneration.  To confirm our findings, we additionally assayed the role of amphiregulin, an EGF-like ligand, which is aberrantly upregulated in compromised animals.

overall_design: There are two conditions, with four biological replicates per condition.  Condition 1 samples, "Multi-amp"  in the sample names, are derived from axolotl limbs that have undergone six rounds of amputation-regeneration and mRNA was extracted at three days following the last amputation.  Condition 2 samples, "Contol" in the sample names, are age- and size-matched sibling animals that have undergone a single amputation and mRNA was extracted at three days following this amputation.

first: Donald

middle: M

last: Bryant


title: CFP1 Regulates Histone H3K4 Trimethylation and Developmental Potential in Mouse Oocytes

city: Beijing

first: Xiaoying

last: Fan

state: Beijing

address: 5 Yiheyuan Road

department: College of Life Sciences

institute: Peking University

summary: Through RNA-seq of wildtype and CFP1-deleted GV oocytes of different ages, zygotes and 2-cell embryos and  whole genome bisulfite sequencing of GV oocytes, We show here that CFP1 is responsible for epigenetic maturation in oocytes. Deletion of CFP1 directly decreased histone H3K4 trimethylation and caused global down-regulation of gene expression in oocytes.These genes are involved in cytoplasmic lattice formation, maternal-zygotic transition and epigenetic maturation. Maternal CFP1-deleted oocytes had fewer CPLs in the cytoplasm and the organelles were severely aggregated, which further caused defects in α-tubulin polymerization and aneuploidy in meiosis II. The genome was less methylated and methylation of maternal DNA was impaired after CFP1 deletion. Therefore CFP1-deleted oocytes fail to complete epigenetic maturation as well as cytoplasmic maturation and nuclear maturation and unable to gain developmental competence during oogenesis.

overall_design: GV oocyte, zygote and 2-cell embryonic transcriptome profiles wild type (WT) and CFP1-depleted mice were generated by deep sequencing, in duplicate or triplicate on Illumina platform.

first: Chao

last: Yu


title: Regulation of gene expression by FOXC1 in mouse mammary epithelial cells.

city: Los Angeles

first: Xiaojiang

last: Cui

address: 3884 Fredonia  Dr#F

department: Surgery Dept

institute: Cedars Sinai Medical Center

summary: The FOXC1 transcription factor plays a critical role in basal-like breast cancer development and metastasis. However, it is not clear whether its overexpression alters normal mammary development and mammary cell function in vivo. We used MMTV-FOXC1 transgenic mice to adddress this question. In association with the lobuloalveologenesis and lactation-related phenotype in the transgenic mice, we also found marked gene expression changes in mammary epithelial cells of the transgenic mice compared with wildtype mice at the lactation stage. Differentially expressed genes identified by RNA-Seq analysis include those involved in fatty acid metabolism, PPAR, cytokine, chemokine, inflammation, and NF-κB signaling. These data suggest that FOXC1 is an important regulator of mammary cell function.

overall_design: Comparison of gene expression profiles in mammamry epithelial cells from MMTV-FOXC1 transgenic and wildtype mice at the lactation stage.

first: Bowen

last: Gao

last: Deng


title: Complete atrio-ventricular canal defects in mouse hearts lacking G-protein receptor kinases

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: Combined ablation of all 3 cardiac-expressed GRKs in the developing mouse heart impaired Hedgehog/Smoothened and GATA signaling, recapitulating heart abnormalities of human Complete Atrioventricular Septal Defect.

overall_design: Cardiac transcriptomes from mouse E13.5 hearts (8 wt, 8 haploinsufficient  GRK2+/-GRK5-/-GRK6-/- and 7 GRK-triple knockout GRK2-/-GRK5-/-GRK6-/-) were generated via Illumina RiboZeroGold rRNA depletion and subsequent single-end 50 nt sequencing on Illumina HiSeq 2500

first: Gerald

last: Dorn


title: ChIPSeq data from melanoma cancer cell line CHL-1 after Bromodomain and extra terminal (Bet) domain inhibitor treatment

city: Berlin

first: Ralf

last: Lesche

address: Muellerstr 178

institute: Bayer Pharma AG

summary:
Bromodomain and extra terminal domain (BET) inhibition reduces occupancy of BET-family proteins at promoter and enhancer sites finally leading to genome wide changes in gene transcription.
We used ChIPSeq profiling to investigate genome wide changes in promoter and enhancer occupancy induced by BET inhibitors BAY 1238097 and OTX-015, respectively.

overall_design: CHL-1 cells were treated with BAY 1238097 or OTX-015, potent and selective Bromodomain and extra terminal domain (BET) inhibitors, before chromatin immunoprecipitation using antibodies directed against BRD4 and acetylated H3K27.

first: Kathy

last: Gelato

first: Olaf

last: Klingbeil

first: Bernard

last: Haendler


title: RNA-Seq analysis of iMOS T1-Myc ESC mosaic cultures

status: Public on Sep 29 2017

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

summary: The goal of this study is to analyse the transcriptome of WT and Myc-overexpressing ESCs in iMOS T1-Myc mosaic cultures.

overall_design: Homozygous iMOS T1-Myc ESC cultures (Claveria et al., 2013) were treated with 20μM 4-hydroxytamoxifen for 24 hours to generate a mosaic of cell populations containing two, one or no extra Myc and EYFP copies. 24 hours after tamoxifen removal, cells were sorted according to their EYFP expression levels and populations with two extra Myc and EYFP copies and with no extra Myc and EYFP copies were collected. Uninduced homozygous iMOS T1-Myc ESC cultures were also sorted and collected as a control. Three biological replicas were included for each condition.

first: Cristina

last: Claveria

first: Miguel

last: Torres


title: Notch1 haploinsufficiency causes aortic aneurysms in mice

city: Columbus

first: Vidu

last: Garg

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

summary: Ascending aortic aneurysms (AscAA) are a life-threatening disease whose molecular basis is poorly understood. Mutations in NOTCH1 have been linked to bicuspid aortic valve (BAV), which is associated with AscAA. Here, we describe a novel role for Notch1 in AscAA. We found that Notch1 haploinsufficiency exacerbated the aneurysmal aortic root dilation seen in the Marfan syndrome mouse model and that heterozygous deletion of Notch1 in the second heart field (SHF) lineage recapitulated this exacerbated phenotype. Lineage tracing analysis showed that loss of Notch1 in the SHF reduces the number of SHF-derived smooth muscle cells in the aortic root, and RNA-seq analysis demonstrated distinct in vivo expression patterns between lineage-specific regions of the ascending aorta. Finally, Notch1+/- mice in a predominantly 129S6 background develop aortic root dilation, indicating that loss of Notch1 independently predisposes to AscAA. These findings are the first to demonstrate a SHF lineage-specific role for Notch1 in AscAA and suggest that genes linked to the development of BAV may also contribute to the associated aortopathy.

overall_design: To determine why dilation was localized to the aortic root in Notch1.129S6+/- mice, RNA-sequencing was performed on proximal and distal ascending aortic tissue from Notch1.129S6+/- mice and wildtype littermates at 2 months of age. Transcriptome analysis was utilized to better understand why the dilation was localized to the aortic root. Hierarchical cluster analysis grouped these samples based on location first and then genotype, and showed that cells of the proximal and distal ascending aorta have distinct gene expression patterns in vivo.

first: Sara

last: Koenig

first: Stephanie

last: LaHaye

first: James

middle: D

last: Feller

first: Patrick

last: Rowland

first: Kan

last: Hor

first: Aaron

last: Trask

first: Paul

last: Janssen

first: Freddy

last: Radtke

first: Brenda

last: Lilly


title: Atheroprotective flow alters EZH2/H3K27me3 dependent transcriptional profile in human endothelial cells

city: Rochester

first: Suowen

last: Xu

state: NY

address: 603 Elmwood Avenue

institute: University of Rochester

summary: Atherosclerosis is a focal disease that preferentially develop in the regions of atheroprone disturbed flow, but less in regions of atheroprotective laminar flow. The mechanisms by which atheroprotective laminar flow prevents atherosclerosis at the epigenetic level remain largely unknown. In this study, we observed that laminar flow decreased histone methyltransferase EZH2, which imposes a repressive epigenetic mark of histone 3 lysine 27 trimethylation (H3K27me3) onto target gene promoters, leading to transcriptional silencing. To evaluate the effect of atheroprotective flow on EZH2 and H3K27me3 dependent genome-wide transcriptional profile, we performed RNA-sequencing study on laminar flow and EZH2 siRNA treated human endothelial cells. Venn diagram was used to compare the common regulated genes by both laminar flow and EZH2 depletion. We found atheroprotective flow and EZH2 depletion altere endothelial gene landscape, which include upregulating atheroprotective genes while downregulating pro-atherosclerotic genes.

overall_design: Human Umbilical Vein Endothelial Cells (HUVEC, passage 3 to passage 5) were seeded in 0.2% gelatin-coated dishes the day before experiment. The next day, HUVECs were changed with new complete media and then exposed to atheroprotective laminar flow (shear stress=12 dyne/cm2) for 48 hours using a cone and plate viscometer. For EZH2 siRNA experiment, HUVECs at 80% confluence were transfected with control siRNA or EZH2 siRNA for 48 h. After treatment, RNA was isolated using the RNA-Easy Mini Plus kit (QIAGEN). High quality RNA samples (pre-assessed by Nanodrop measurements) were further processed in the Genome Research Center of the University of Rochester Medical Center. The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3’ adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome. Sequenced reads were cleaned using Trimmomatic-0.32 before mapping some of to the human reference genome (GRCh38.p2) with STAR-2.4.2a. Raw read counts were obtained using HTSeq and gencode 23 human gene annotations. DESeq2-1.10.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05. Then, Cufflinks-2.0.2 Software was used with the gencode 23 human gene annotations to perform differential expression analysis with an FDR cutoff of 0.05.

first: Zheng

last: Jin

first: John

last: Ashton

first: Jason

last: Myers


title: Genetic circuit 0x58

city: Bristol

first: Thomas

middle: Edward

last: Gorochowski

address: 24 Tyndall Avenue

department: Biological Sciences

institute: University of Bristol

summary: We report the characterization of a synthetic genetic circuit using RNA-Seq data. Data is collected for all input inducer combinations and cells harboring the circuit are grown in two conditions (14 ml culture tubes and 250 ml Erlenmeyer flasks).

overall_design: Examination of 8 different inducer combinations for 2 grown conditions (culture tubes and Erlenmeyer flasks)

middle: E

first: Yongjin

last: Park

first: Alec

last: Nielsen


title: Role of N-α-acetyltransferase 10 Protein in DNA Methylation and Genomic Imprinting

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

summary: Genomic imprinting is an allelic gene expression phenomenon primarily controlled by allele-specific DNA methylation at the imprinting control region (ICR). How allele-specific DNA methylation at ICR is regulated is largely unknown. Mammalian N-α-acetyltransferase 10 protein (Naa10p) catalyzes N-α-acetylation of nascent proteins. Mutation of human Naa10p is linked to severe developmental defects and mental retardation, including the Ogden syndrome. Here we report that Naa10-null mice display partial embryonic lethality, growth retardation, brain disorder and maternal-effect lethality, phenotypes commonly observed in defective genomic imprinting. Genome-wide analyses reveal global DNA hypomethylation and enriched dysregulation of imprinted genes in Naa10p-null embryos and ES cells. Naa10p regulates global DNA methylation by stimulating DNA methyltransferase 1 (Dnmt1) activity, while maintaining imprinted allele methylation by binding to GCXGXG and recruits Dnmt1. Clinical mutation of Naa10p disrupts its H19-ICR binding and Dnmt1 recruitment. Our study thus links Naa10p mutation-associated human diseases to defective DNA methylation and genomic imprinting.

overall_design: In this data set, we include RRBS data of both WT and Naa10-KO mESCs

first: Chen-Cheng

last: Lee

first: Shih-Huan

last: Peng

first: Chung-Fan

first: Ting-Huei

last: Du

first: Ming-Lun

last: Kang

first: Guoliang

first: Azusa

last: Inoue

first: Anup

last: Upadhyay

first: Xiaodong

last: Cheng

first: Yu-Ting

last: Yan

first: Yi

last: Zhang

first: Li-Jung

last: Juan


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

first: Sandra

last: Cortijo

address: Bateman Street

institute: Sainsbury Laboratory, Cambridge University

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

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

first: Phil

last: Wigge

first: Varodom

last: Charoensawan


title: RNA-SEQ analysis of E14.5 ALL Ret-positive (EGFP-labeled) FACSd dorsal root ganglia neurons.

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The goal of this set is to build expression data using FACS isolated Ret-positive cells harvested from a Ret-EGFP reporter mouse (embryonic day E14.5). These can be used as a time point in comparative analysis of ontogeny of genes expressed at various developmental time points.

overall_design: RNA was extracted from E14.5 FACS isolated dorsal root ganglia dissected from Ret-EGFP C57BL/6J mice (EGFP knocked-in Ret locus-heterozyotes) and sequenced using Illumina Hiseq 2500 platform. Refer to protocols on the GUDMAP website under Jain.

first: Eric

last: Tycksen

first: Masato

last: Hoshi

first: Judy

last: Golden

first: Amanda

last: Knoten

first: Sanjay

last: Jain


title: Expression profiles of retinal neuronal cells

first: Yi-Rong

last: Peng

state: CA

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

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

overall_design: Refer to individual Series


title: The transcriptome comparison between wildtype Hb9-GFP and Satb1-/-Hb9-GFP retinal ganglion cells (RGCs).

summary: The goal of this experiment was to define genes differentially expressed between P6 Hb9-GFP and Satb1-/-Hb9-GFP cells, which were dissociated and FACS sorted from mice retinae.

overall_design: Mice retinae from P6 Hb9-GFP and Satb1-/-Hb9-GFP were dissected, GFP labeled RGCs were purified by flow cytometry. Five biological replicates, origniating from different litters, were collected for each genotype. RNA was extracted from ~1000 sorted cells and cDNA was synthesized and amplified using Nugen Ovation RNAseq kit. Libraries were prepared using Nugen Ultralow System V2 kit.

first: Josh

last: Sanes


title: Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo

status: Public on Sep 28 2017

city: Barcelona

first: Marta

last: Sese

state: Barcelona

address: Pg. Vall Hebron, 119

department: Translational Molecular Pathology

institute: Vall Hebron Institute of Research (VHIR)

summary: We performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. Paired-end reads were mapped against the reference human genome (GRCh38) with STAR v2.5.1b (ENCODE parameters for long RNA) and GENCODE v24 annotation. Gene quantification was performed using RSEM v1.2.28 with default parameters. Only protein-coding genes were included in the analysis. Normalization of the count matrix was performed with the TMM method of the edgeR R package. Polysomal RNA (P) and RNA total (T) fold changes across conditions were calculated with edgeR. Significant genes (FDR < 5% for MCF10A cells and FDR < 10% for MDA-MB-231 cells) in polysomes were selected for translational efficiency calculation (log2FC RNA polysomes/log2FC RNA total). Genes with a z-score > 1.5 were considered to have an increased translational efficiency and genes with a z-score < –1.5 were considered to have a decreased translational efficiency. GO enrichment analysis of significant genes was performed with the DAVID database.

overall_design: RNA-Seq profiles in polysomes vs total in Normoxia, Hypoxia, Hypoxia + PP242, Normoxia + PP242 in MCF10A and MDA-MB-231 cell lines

first: Santiago

last: Ramón y Cajal

last: Sesé


title: Inflammation-modulated Metabolic Reprogramming is Required for DUOX-dependent Gut Immunity in Drosophila

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

summary: DUOX, a member of the NADPH oxidase family, acts as the first line of host defense against enteric pathogen by producing microbicidal reactive oxygen species. Despite the extensive research conducted, the elucidation of the DUOX regulatory mechanism remains incomplete. Here, by taking advantages of the Drosophila genetic tools, we showed that enteric infection acts as a ‘pro-catabolic’ signaling capable of initiating metabolic reprogramming of enterocytes toward lipid catabolism through activation of complex signaling cascades involving TNF receptor-associated factor 3, AMP-activated protein kinase, Warts kinase of the Hippo pathway, and ATG1 kinase of autophagy. We further showed that inflammation-modulated metabolic reprogramming is necessary for cellular NADPH homeostasis, which is essential for sustained DUOX activity and host survival during enteric infection. The discovery of signaling cascades governing inflammation-induced metabolic reprogramming will provide a novel perspective on physiology and pathophysiology of immune-metabolic interactions in microbe-laden gut epithelia.

overall_design: mRNA expression profiles of Drosophila anterior midgut at 2, 4, and 16 hr after infection with Ecc15 (Erwinia carotovora carotovora strain 15; Ecc) and sucrose treatment (Suc) were examined by Illumina HiSeq2000.

first: Won

last: Lee

first: Daehee

last: Hwang


title: Identification of viral ncRNA-mRNA interactions in Herpesvirus saimiri-infected marmoset T cells

city: Salt Lake City

first: Demian

last: Cazalla

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

summary: Viruses express several classes of non-coding (nc) RNAs1. For most of them, the functions and mechanisms by which they act are unknown. Herpesvirus saimiri (HVS), a g-herpesvirus that establishes latency in T cells of New World primates and has the ability to cause aggressive leukemias and lymphomas in non-natural hosts2, expresses seven small nuclear (sn), U-rich ncRNAs called HSURs in latently infected cells3-5. HSURs associate with Sm proteins and share biogenesis and structural features with cellular Sm-class snRNAs4,6. One of these viral snRNAs, HSUR 2, base-pairs with two host microRNAs (miRNAs), miR-142-3p and miR-167. However, HSUR 2 does not affect the abundance or activity of these two cellular miRNAs, suggesting alternative functions for these interactions. Here we show that HSUR 2 also base-pairs with messenger RNAs (mRNAs) in infected cells. We combined in vivo psoralen-mediated RNA-RNA crosslinking and high-throughput sequencing to identify mRNAs targeted by HSUR 2. HSUR 2 targets include mRNAs encoding Retinoblastoma (pRb) and factors involved in p53 signaling and apoptosis. We show that HSUR 2 represses expression of target mRNAs. Base-pairing between HSUR 2 and miR-142-3p and miR-16 is essential for HSUR 2-mediated mRNA repression, suggesting that HSUR 2 recruits these two cellular miRNAs to target mRNAs. Moreover, we show that HSUR 2 utilizes this mechanism to inhibit apoptosis. Our results uncover a role for a viral Sm-class RNA as a miRNA adaptor in post pre-mRNA-processing regulation of gene expression.

overall_design: Three independent samples of marmoset T cells infected with H. saimiri and expressing HSUR 2 as well as three independent samples of control T cells in which HSUR 2 was depleted with antisense oligonucleotide were crosslinked in the presence of psoralen at 365 nm for 1 hour at 4°C (6 samples total).  Samples were distributed in 100-µl aliquots and lysed with 3 M guanidinium-HCl and 1 % SDS in the presence of 1.8 mg/ml of proteinase K and incubated for 1 hour at 65°C.  One-milliliter of Trizol was added to each sample and then stored at -80°C until used.  Total RNA was purified from each sample following the standard protocol and pooled before capturing polyA+ RNA using oligo-dT magnetic beads.  The polyA+ was suspended in water and 10% of each polyA+ sample was retained as input RNA and stored in 1 ml of Trizol.  The remainder of each sample was suspended in binding buffer plus 500 pmoles of a biotinylated oligonucleotide complementary to HSUR 2 (GGTTTTTAAATATGTACACCC-3’-Bio) (three WT samples containing HSUR 2 and three samples from HSUR 2-depleted cells) and incubated for 4 hours at room temperature.  Samples were then incubated overnight at 4°C with streptavidin-conjugated magnetic beads.  Bound RNA was eluted from the beads by adding 1 ml Trizol.  RNA was purified from each sample (a total of 12 samples: six inputs and the corresponding HSUR 2-pulldowns) and the crosslinking was reverted by shining 254-nm UV light on the samples for 10 min.  RNA was recovered by ethanol-acetate precipitation and used with Illumina's TruSeq Stranded mRNA LT kit to prepare libraries for sequencing.

first: Demián

first: Carlos

last: Gorbea

first: Tim

last: Mosbruger


title: Genes under positive selection and their recruitment order during C4 emergence in Grass

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

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

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

institute: Shanghai Institutes for Biological Sciences, CAS

summary: The C4 CO2 concentrating mechanism (C4-CCM) requires the coordinated function of multiple enzymes and transporters, which were gradually recruited during evolution. However, critical genes involved and their recruitment order remains elusive. Here we address this question with molecular evolution approaches, we identified all the positive selected genes in C4 species from grass.

sample_organism:
Bothriochloa ischaemum
Arundinella nepalensis
Arundinella hirta
Capillipedium parviflorum
Imperata cylindrica
Arundinella anomala
Arundinella fluviatilis
Arundinella pubescens

overall_design: eight C4 species, RNA-seq from leaves

first: Ming-Ju

middle: A

last: Lyu

first: Yimin

last: Tao

first: Yaling

last: Wang

first: Xin-Guang

last: Zhu