title: Linc-smad7 promotes myoblast differentiation and muscle regeneration via sponging miR-125b

city: Yangling

first: Chengchuang

last: Song

address: xinong road

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: Long noncoding RNAs (lncRNAs) are involved in the regulation of skeletal muscle development. In the present study, differentially expressed lncRNAs were identified from RNA-seq data derived from myoblasts and myotubes. We conducted studies to elucidate the function and molecular mechanism of action of Linc-smad7 during skeletal muscle development. Our findings show that Linc-smad7 is upregulated during the early phase of myoblasts differentiation. In in vitro studies, we showed that overexpression of Linc-smad7 promoted the arrest of myoblasts in G1 phase, inhibited DNA replication, and induced myoblast differentiation. Our in vivo studies suggest that Linc-smad7 stimulates skeletal muscle regeneration in cardiotoxin-induced muscle injury. Mechanistically, Linc-smad7 overexpression increased smad7 and IGF2 protein levels. On the contrary, overexpression of miR-125b reduced smad7 and IGF2 protein levels. Results of RNA immunoprecipitation analysis and biotin-labeled miR-125b capture suggest that Linc-smad7 could act as a competing endogenous RNA (ceRNA) for miRNA-125b. Taken together, our findings suggest that the novel noncoding regulator Linc-smad7 regulates skeletal muscle development.

overall_design:
We used RNA-seq to detect the transcriptome difference after Linc-smad7 gain of function in skeletal muscle damage. Compared to control group, existing 359 differential expressed genes, 121 genes and 238 genes were upregulated or down regulated respectively. GO analysis of genes showed that Linc-smad7 mainly participated in biological process such as skeletal muscle tissue development, skeletal muscle organ development, etc.
Six skeletal muscle samples from mouse (6w) of two groups, L7 (Linc-smad7) and Control, were purchased from the Fourth Military Medical University, Xi’An, P.R. China.

first: Hong

last: Chen


title: The hepatitis C viral protein NS5A stabilizes growth-regulatory human transcripts

status: Public on Nov 01 2017

city: minneapolis

first: Liang

last: Guo

state: MINNESOTA

address: 2001 6th Street SE

country: USA

institute: University of Minnesota

type: Expression profiling by high throughput sequencing

summary: Numerous mammalian proto-oncogene and other growth-regulatory transcripts are upregulated in malignancy due to abnormal mRNA stabilization.  In hepatoma cells expressing a hepatitis C virus (HCV) subgenomic replicon, we found that the viral nonstructural protein 5A (NS5A), a protein known to bind to viral RNA, also bound specifically to human cellular transcripts that encode regulators of cell growth and apoptosis, and this binding correlated with transcript stabilization.  An important subset of human NS5A-target transcripts contained GU-rich elements, sequences known to destabilize mRNA. We found that NS5A bound to GU-rich elements in vitro and in cells.  Mutation of the NS5A zinc finger abrogated its GU-rich element-binding and mRNA stabilizing activities. Overall, we identified a molecular mechanism whereby HCV manipulates host gene expression by stabilizing host transcripts in a manner that would promote growth and prevent death of virus-infected cells, allowing the virus to establish chronic infection and lead to the development of hepatocellular carcinoma.

overall_design: Calculate mRNA decay rate by examining RNA-seq expression levels of 2 samples (Huh and Huh-HCV) at 3 time points (0h, 3h, and 6h) after transcription arrest. RNA-IP followed by RNA-seq on 2 samples (Huh and Huh-HCV).

first: Paul

last: Bohjanen


title: Landscape of XUT lncRNAs in fission yeast

status: Public on Nov 09 2017

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

type: Non-coding RNA profiling by high throughput sequencing

summary: Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site. RNA profiling revealed that the resulting aslncRNAs mainly correspond to cryptic Xrn1/Exo2-sensitive transcripts (XUTs). ChIP-Seq analyses showed that antisense (as)XUTs expression is associated with specific histone modifications patterns. Finally, we showed that asXUTs are controlled by the histone chaperone Spt6 and respond to meiosis induction, in both cases anti-correlating with levels of the paired-sense mRNAs, supporting physiological significance to antisense-mediated gene attenuation. Our work highlights that antisense transcription is much more extended than anticipated and might constitute an additional non-promoter determinant of gene regulation complexity.

overall_design: Total RNA-Seq in WT & exo2-delta cells of S. pombe.

first: Camille

last: Gautier

first: Marc

last: Descrimes

first: Mayuko

last: Yoda

first: Hervé

last: Vennin-Rendos

first: Valérie

last: Migeot

first: Daniel

last: Gautheret

first: Damien

last: Hermand

first: Antonin

last: Morillon


title: ILC1 confer early host protection at initial sites of viral infection [RNA-Seq]

city: New York

first: Christina

last: Leslie

state: New York

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: We show that tissue-resident ILC1 serve a non-redundant early role in host immunity through rapid production of interferon (IFN)-γ following mouse cytomegalovirus (MCMV) infection.

overall_design: Comparative RNA-seq analysis of mature NK and ILC cells in adipose, liver, spleen, and peritoneal cavity.

first: Orr-El

last: Weizman

first: Tim

last: O'Sullivan

first: Colleen

last: Lau

first: Chirag

last: Krishna

first: Yuri

last: Pritykin


title: Improved Detection of Circulating Epithelial Cells in Patients with Intraductal Papillary Mucinous Neoplasms

city: Charlestown

first: Joseph

last: Franses

state: MA

address: 149 13th Street

department: Medical Oncology

institute: Massachusetts General Hospital

summary: Circulating epithelial cells (CECs) were purified using a microfluidic device from healthy donors, patients bearing intraductal papillary mucinous neoplasms, or pancreatic ductal adenocarcinoma and their transcriptomes were sequenced.

overall_design: examination of mRNA expression of mucin genes in the above samples

first: David

middle: T

last: Ting

middle: W


title: Pervasive transcription and endosiRNAs restrain transposons during global demethylation in embryonic stem cells [ChIP-Seq 2]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Genome binding/occupancy profiling by high throughput sequencing

summary: DNA methylation and other repressive epigenetic marks are erased in the mammalian germline and transposable elements (TEs) acquire the potential to be transcribed. This is a critical phase for genome defense and complementary TE silencing pathways are required to limit their activity. We find overlapping sense/antisense transcription in TEs in mouse embryonic stem cells, with an increase of sense transcription induced by acute deletion of Dnmt1, leading to increased abundance of small RNAs. These small RNAs are loaded into ARGONAUTE2 (AGO2) suggesting an endosiRNA based silencing mechanism. Reduction of Dicer and Ago2 levels reveals that small RNAs are involved in an immediate response to transposon activation by demethylation, while the deposition of repressive histone marks represents an ensuing chronic response. Dicer dependent endosiRNAs which map to TEs are also found in vivo during primordial germ cell development. Our results suggest that TE antisense transcription acts as a trap that restrains acute transposon activity through small RNAs during epigenetic reprogramming in the germline.

overall_design: ChIP-Seq (2 biological replicates of 6 samples with technical replicates, 1 biological replicate of 6 samples)

first: Rebecca

middle: V

last: Berrens

first: Simon

last: Andrews

first: Wolf

last: Reik


title: Next Generation Sequencing of total RNA from 9 bladder cancer cell lines and 3 fractionated bladder cancer cell lines

city: Århus N

first: Trine Line

middle: Hauge

last: Okholm

address: Palle Juul-Jensens Boulevard 99

department: Department of Molecular Medicine (MOMA)

country: Denmark

institute: Aarhus University Hospital

summary: We profile the cell line expression of 279 circRNAs, that are highly expressed across 457 bladder cancer patient samples. Additionally, we investigate their cellular location in fractionated cell lines

first: Trine

middle: H

first: Lars

middle: D

last: Andersen

first: Lise

last: Christensen

first: Morten

middle: M

last: Nielsen

first: Jakob

middle: S

last: Pedersen

first: Søren

last: Vang

last: Hedegaard


title: Pervasive transcription and endosiRNAs restrain transposons during global demethylation in embryonic stem cells [RNA-Seq 2]

overall_design: RNA Seq E14 Dicer KO Dnmt1KO


title: RNA-seq of maturation stage pituitary mouse cell lines and NIH-3T3

city: La Jolla

first: Pamela

middle: L

last: Mellon

address: 9500 Gilman Dr

institute: UCSD

summary: Proper expression of key reproductive hormones from gonadotrope cells of the pituitary is required for reproduction. We performed RNAseq of 3 maturaton staged gonadotrope cell lines,  a thyroptrope cell line and NIH-3T3 cells to establish the timing and expression levels of genes involved in gonadotrope maturation.

overall_design: Rna-seq of 3 mouse gonadotrope cell lines, 1 mouse thyrotrope cell line and NIH-3T3 cell line

first: Melissa

middle: J

last: Brayman


title: Pervasive transcription and endosiRNAs restrain transposons during global demethylation in embryonic stem cells [smallRNA-Seq 2]

overall_design: small RNA-seq libraires (2 biological replicates of 6 samples with technical replicates, 1 biological replicate of 6 samples)


title: Glass promotes the differentiation of both neuronal and non-neuronal cells in the Drosophila eye

first: Carolyn

last: Morrison

state: NY

address: 540 First Ave

department: Skirball Institute

institute: NYU School of Medicine

summary:
Multiple cell types can be specified from a single pool of progenitors through the combinatorial activity of transcriptional regulators, which activate distinct developmental programs to establish different cell fates.  The zinc finger transcription factor Glass is required
for neuronal progenitors in the Drosophila eye imaginal disc to acquire a photoreceptor identity.  Glass is also expressed in non-neuronal cone and pigment cells, but its role in these cells is unknown.  To examine how Glass activity is affected by the cellular context, we
misexpressed it in different tissues.  When expressed in neuroblasts of the larval brain or in epithelial cells of the wing disc, Glass activated both a common core set of target genes and distinct gene sets specific to each tissue.  In addition to photoreceptor-specific genes, Glass
induced markers of cone and pigment cells.  Cell type-specific glass mutations generated in cone or pigment cells using somatic CRISPR revealed autonomous developmental defects, and expressing Glass specifically in these cells partially rescued glass mutant phenotypes. Glass thus
acts in both neuronal and non-neuronal cells to promote their differentiation into functional components of the eye, suggesting that it is a determinant of organ identity.

overall_design:
6 samples in triplicate, 2 experimental (Glass misexpression (Gl ME) in the wing and Gl ME in the brain), 4 controls (wild-type (WT) eye discs, WT wing discs and WT brains and gl60j brains)
Drosophila melanogaster imaginal discs were isolated from Wandering 3rd Instar larvae (W3L) raised at 25C. Gl ME= Glass Misexpression, WT= wild-type. UAS-gl was expressed with tubulin (tub)-GAL4 in clones generated in the wing using Ultrabithorax-Flippase (Ubx-FLP).
The inscuteable (insc)-GAL4 driver was used to misexpress Gl in the larval brain in a gl60j background.

middle: A

first: Hao

last: Chen

first: Stuart

last: Brown

first: Jessica

middle: E

last: Treisman


title: The Conserved Intron Binding Protein EMB-4 Plays Differential Roles in Germline Small RNA Pathways of C. elegans

city: Toronto

first: Julie

last: Claycomb

state: ON

address: MaRS Centre, West Tower 661 University Ave, Room 1535

department: Department of Molecular Genetics

country: Canada

institute: University of Toronto

summary: Proper regulation of the germline transcriptome is essential for the maintenance of fertility and survival of a species. In C. elegans, germline transcriptome homeostasis hinges on a complex repertoire of small RNA pathways that act in both activating and silencing capacities. Our understanding of how fundamental RNA processing steps intersect with these small RNA machineries in the germline remains relatively limited. Here, we link the conserved intron binding protein and splicing factor, EMB-4/AQR/IBP160 to two key 22G-RNA pathways in the C. elegans germline. EMB-4 associates with the Argonautes CSR-1 and HRDE-1, and is enriched at the genomic loci of CSR-1 and HRDE-1 target genes. Loss of emb-4 leads to distinct alterations in CSR-1 vs. HRDE-1 small RNA and mRNA transcriptomes. Our transcriptome-wide analysis shows that EMB-4 is enriched along pre-mRNAs of nearly 10,000 transcripts. For a subset of these genes, including mostly CSR-1 pathway targets, EMB-4 enriches for intronic, but not exonic, sequences. Together these data point to EMB-4 as a factor that may help to distinguish the targets of these two germline small RNA pathways.

overall_design: For mRNA and small RNA-seq experiments, total RNA was extracted from N2 and emb-4(hc60) mutant worms harvested as young adults. EMB-4 IPs were performed on RNA extracted from gravid adult N2 worms.

first: Katarzyna

last: Tyc

first: Amena

last: Nabih

first: Monica

middle: Z

last: Wu

first: Christopher

last: Wedeles

first: Julia

last: Sobotka


title: A prostate cancer risk element functions as a repressive loop that regulates HOXA13

city: Los Angeles

first: Zhifei

last: Luo

state: CA

address: 1450 Biggy Street, NRT 6514

institute: University of Southern California

summary: Prostate cancer (PCa) is the leading cancer among men in the United States, with genetic factors contributing to ~42% of the susceptibility to PCa. To understand the causal genetic factors associated with PCa, we have focused on a PCa risk region located at 7p15.2. We performed Hi-C analysis and demonstrated that this region has long range interactions with the HOXA locus, located ~873 kb away. Using the CRISPR/Cas9 system, we deleted a 4 kb region encompassing several prostate cancer risk-associated SNPs and performed RNA-seq to investigate transcriptomic changes in RWPE1 prostate cells lacking the regulatory element. Our results suggest that the risk element affects the expression of HOXA13 and HOTTIP, but not other genes in the HOXA locus, via a repressive loop. Forced expression of HOXA13 was also performed to gain insight into the mechanisms by which this risk element affects prostate cancer risk.

overall_design: Examination of normal prostate epithelial cell RWPE-1 genomic interactions by Hi-C. A prostate cancer risk region at 7p15.2 was deleted and HOXA13 gene was forced expressed in RWPE-1 cells, the transcriptomic changes were investigated by RNA-seq.

first: Fides

last: Lay

first: Suhn

middle: K

last: Rhie

first: Peggy

last: Farnham


title: Transcriptomic analysis of Drosophila imaginal wing discs cultured in insulin or 20-hydroxyecdysone

city: Dresden

first: Natalie

middle: Anne

last: Dye

address: Pfotenhauerstrasse 108

country: Germany

institute: MPI-CBG

summary: We identified a role for low concentrations of 20-hydroxyecdysone (20E) in promoting growth of the Drosophila larval wing imaginal disc using genetics and in vitro explant culture. We found that 20E alone could promote proliferation in the absence of added insulin, a well known regulator of growth. To investigate the mechanism by which these hormones promote growth, we sequenced the transcriptomes of mid-third instar wing discs cultured in no hormone, 20E alone or insulin alone at two timepoints (4hr and 9hr). We also sequenced the transcriptomes of freshly dissected wing discs (not cultured). We found that within 4hr of culture without hormone, the expression of 1604 genes goes down and 1409 genes goes up, relative to uncultured discs. Changes in the expression of 1911 genes could be prevented, at least transiently, by the addition of either 20E or insulin. The transcriptional response to insulin was remarkably transient, decreasing by rougly 50% from 4hr to 9hr of culture. The response to 20E was smaller than that induced by insulin, but longer lasting. Insulin-induced genes are most significantly enriched in GO-terms describing DNA replication, ribosome biogenesis, translation, purine biosynthesis, and mitochondrial biogenesis. Insulin-repressed genes are enriched in genes involved in autophagy and cell death. 20E-regulated genes were also enriched for genes involved in DNA replication. Unlike insulin, however, 20E was found to promote the expression of genes in GO categories describing a variety of developmental processes. These data represent the first description of the direct transcriptional response of the wing disc to either insulin or low doses of 20E.

overall_design: Illumina RNA-seq was performed on mRNA isolated from wing discs that were either freshly dissected (uncultured) or cultured in no hormone (4hrs), 20E (4hr or 9hr) or insulin (4hr or 9hr). Three biological replicates were performed for all conditions and timepoints.

first: Suzanne

last: Eaton


title: A general transcription co-factor, Smad3, potentiates master transcription factor mediated cell identity conversions

status: Public on Nov 02 2017

city: Edinburgh

first: Keisuke

last: Kaji

state: Midlothian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

institute: University of Edinburgh

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

overall_design: Refer to individual Series


title: Root-specific overexpression of OsERF48 causes regulation of OsCML16, a calmodulin-like protein gene that enhances root growth and drought tolerance

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

summary: The AP2/ERF family is one of the plant-speciﬁc transcription factors (TFs) whose members have been associated with various developmental processes and stress tolerance. Here, we functionally characterized the drought-inducible OsERF48, a group Ib member of the rice ERF family that contains four conserved motifs, CMI-1, 2, 3 and 4. Transactivation assay in yeast revealed that the CMI-1 at the C-terminal end was essential for its transcriptional activity. When the OsERF48 was overexpressed in an either root-specific (ROXOsERF48) or whole-body (OXOsERF48) expression manner, both transgenic plants showed a longer and denser root phenotype than the nontransgenic (NT) controls. When plants were grown on a 40% PEG-infused medium, an in vitro drought condition, ROXOsERF48 plants showed a more vigorous root growth over OXOsERF48 and NT plants. In addition, the ROXOsERF48 plants exhibited higher grain yield under field-drought conditions than OXOsERF48 and NT plants. We constructed a putative regulatory network of OsERF48 by cross-referencing of RNA-seq data of ROXOsERF48 roots with a co-expression network database, revealing an involvement of 20 drought-related genes. These include genes for stress signaling, carbohydrate metabolism, cell-wall proteins, and drought-response. More importantly, OsCML16, a key gene for calcium signaling during abiotic stress, was identified to be the direct target of OsERF48 by the ChIP-qPCR and the protoplast transient assay. Thus, our results demonstrated that OsERF48 regulates OsCML16, a calmodulin-like protein gene that enhance root growth and drought tolerance.

overall_design: RNA-Seq on roots of nontransgenic control (NT) and root-specific OsERF48 overexpression transgenic rice.

first: Harin

last: Jung

first: Ju-Kon

last: Kim


title: A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [BS-Seq]

first: Felix

last: Krueger

type: Methylation profiling by high throughput sequencing

summary: DNA methylation and other repressive epigenetic marks are erased genome-wide in mammalian primordial germ cells (PGCs), the early embryo and in naïve embryonic stem cells (ESCs). This is a critical phase for transposon element (TE) defense since presumably alternative pathways need to be employed to limit their activity. It has been reported that pervasive transcription is enriched for TEs in ESCs in comparison to somatic cells. Here we test the hypothesis that pervasive transcription overlapping TEs forms a sensor for loss of their transcriptional repression. Overlapping sense and antisense transcription is found in TEs, and the increase of sense transcription induced by acute deletion of DNMT1 leads to the emergence of small RNAs. These small RNAs are loaded into ARGONAUTE 2 suggesting an endosiRNA mechanism for transposon silencing. Indeed, deletion of DICER reveals this mechanism to be important for silencing of certain transposon classes, while others are additionally repressed by deposition of repressive histone marks. Our observations suggest that pervasive transcription overlapping with TEs resulting in endosiRNAs is a transposon sensor that restrains their activity during epigenetic reprogramming in the germline.

overall_design: Bisulfite-seq (2 biological replicates of 8 samples, 1 replicate of 2 samples)

first: Rebecca

last: Berrens

first: Simon

last: Andrews

first: Wolf

last: Reik


title: In Vivo Chemical Screen Nominates Valproic Acid as Pharmacologic Modulator of Hematopoietic Stem and Progenitor Cell Activity

first: Guruchandar

last: Arulmozhivarman

address: Fetscherstraße 74

department: Hematology department

institute: TU Dresden - Faculty of Medicine

summary: The identification of small molecules which either increase the number and/or enhance the activity of CD34+ hematopoietic stem and progenitor cells (HSPCs) during ex-vivo expansion has remained challenging. Applying an unbiased in vivo chemical screen in a transgenic (c-myb:EGFP) zebrafish embryo model, histone deacetylase inhibitors (HDACI) (valproic acid, resminostat and entinostat) were shown to significantly amplify the number of phenotypic hematopoietic precursors. The identified HDACIs were confirmed to significantly enhance also the expansion of human HSPCs during ex vivo treatment. Long-term functionality of ex vivo expanded human HSPCs was verified in a xenotransplantation model using NSG mice. However, the HDACI induced proliferation of HSPCs was associated with short-term functional changes. One of the identified hits, valproic acid (VPA), increased the adhesion capacity of CD34+ cells on primary mesenchymal stromal cells and reduced their chemokine-mediated migration capacity in vitro. In line with the reduced migratory potential in vitro, homing as well as early engraftment of VPA treated human CD34+ cells was significantly impaired in the xenotransplantation model. Our data confirms that HDACI treatment leads to a net expansion of HSPCs cells with long-term engraftment potential across different species. However impaired homing and short-term-engraftment has to be kept in mind when designing clinical transplantation protocols. In addition, our gene expression analysis (RNA-Seq) revealed expression of several genes that were altered in CD34+ cells by VPA treatment including cell adhesion molecules and Notch and wnt genes which has been shown to be involved in preservation of stem cell properties.

overall_design: Gene expression analysis of in vitro expanded human HSPCs (CD34+ cells) by valproic acid

first: Dimitra

last: Alexopoulou

first: Andreas

last: Dahl

first: Martin

last: Bornhäuser


title: A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [smallRNA-Seq]

overall_design: small RNA-seq libraires (3 biological replicates of 14 samples, 2 biological replicate of a 2 samples, 1 biological replicate of 6 samples)


title: Lamins organize the three dimensional genome from nuclear periphery in ES cells

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

summary: Lamins are the major structural components of the nuclear lamina (NL) beneath the inner nuclear membrane. Although lamins are believed to regulate genome organization and transcription, how they perform these functions remains poorly understood. Combining Hi-C with fluorescence in situ hybridization (FISH) and Histone and Lamina landscape (HiLands) analyses of chromatin domains, we show that lamins differentially regulate the NL-associated HiLands-P and -B domains in mouse ES cells (mESCs). Lamin loss leads to HiLands-P expansion at the NL, detachment of HiLands-B from the NL, and genome-wide changes of 3D chromatin interactions in NL-associated and interior HiLands in mESCs. Further epigenome and transcriptome analyses show that lamins can function from the NL to maintain the boundaries of active and repressive chromatin domains, thereby influencing gene expression throughout the genome. These findings should provide the basis to further understand how changes in the NL-associated chromatin influence transcription in development and NL-associated diseases.

overall_design: Comparison of transcriptome (RNA-seq, 2 replicates), histone modifications(H3K4me3, H3K27me3, H3K9me3, H3K4me1, H3K27Ac, each 3-4 replicates), and 3D genome organization (Hi-C, 2 replicates) in WT and lamin-B1/B2/A triple knockout mESCs.

first: Xiaobin

first: Jiabiao

last: Hu

first: Youngjo


title: RNA-seq analysis of hypertension induced by a high calcium intake in Chicken broiler kidney under varied calcium intake

city: Wanju-Gun

first: woncheoul

last: park

state: Iseo-Myeon

address: 1500 kongjwipatjwi-Ro

department: Animal genomics and Bioinformatics

institute: National Institute of Animal Science

summary: Chicken (Gallus gallus) were first domesticated from a wild form called red jungle fowl that still runs wild in most of southeast Asia. After then the grey jungle fowl (G. sonneratii) was hybridized, which was occurred probably about 8,000 years ago, and domestic chickens have been selected to have ideal economic traits such as a meat and a laying breed. In these breeds, a meat breed such as broiler is the most distributed in poultry industry. In addition, calcium is essential for normal cellular function and blood coagulation. However, it caused the hypocalcemia and the hypercalcemia if calcium intake was less and more than adequate calcium intake such as hypocalcemia and hypercalcemia, which is related to hypertension and blood pressure. So, we generated RNA-seq data from nine chicken broilers according to calcium intake (0.8, 1.0 and 1.2percent) for gene expression profiling. As a result, we identified differentially expressed genes (DEGs) using cufflinks (128 DEGs between 0.8 versus 1.0 percent, 141 DEGs between 0.8 versus 1.2 percent and 103 DEGs between 1.0 versus 1.2 percent), also 12 DEGs were identified by generalized linear model (GLM) within edgeR. We identified that these DEGs were related to hypertension and blood pressure through the KEGG pathway enrichment, the co-occurrence and the protein/protein interaction (PPI) network analysis. In summary, the objective of this study was to investigate the influence of increasing calcium intake in chicken broilers kidney. Therefore, we suggested that higher calcium intake than adequate in chicken broilers can caused the hypertension and high blood pressure.

overall_design: whole mRNA sequencing profiles of 10 chicken broiler (nine profiles of kidney tissue)

first: Ki-Duk

last: Song

first: Hak-Kyo

last: Lee

first: Woncheoul

last: Park


title: Dimethyl fumarate increases fetal hemoglobin, provides heme detoxification, and corrects anemia in sickle cell disease

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

summary: Sickle cell disease (SCD) results from a point mutation in the β-globin gene forming hemoglobin S (HbS), which polymerizes in deoxygenated erythrocytes, triggering recurrent painful vaso-occlusive crises and chronic hemolytic anemia. Reactivation of fetal Hb (HbF) expression ameliorates these symptoms of SCD. Nuclear factor (erythroid derived-2)–like 2 (Nrf2) is a transcription factor that triggers cytoprotective and antioxidant pathways to limit oxidative damage and inflammation and increases HbF synthesis in CD34+ stem cell–derived erythroid progenitors. We investigated the ability of dimethyl fumarate (DMF), a small-molecule Nrf2 agonist, to activate γ-globin transcription and enhance HbF in tissue culture, murine and primate models. DMF recruited Nrf2 to the γ-globin promoters and the locus control region of the β-globin locus in erythroleukemia cells, elevated HbF in SCD donor–derived erythroid progenitors, and reduced hypoxia-induced sickling. Chronic DMF administration in SCD mice induced HbF and increased Nrf2-dependent genes to detoxify heme and limit inflammation. This improved hematological parameters, reduced plasma-free Hb, and attenuated inflammatory markers. Chronic DMF administration to nonanemic primates increased γ-globin mRNA in BM and HbF protein in red cells. DMF represents a potential therapy for SCD to induce HbF and augment vasoprotection and heme detoxification

overall_design: RNA-Seq of 30 samples

first: Sriram

last: Krishnamoorthy

first: Betty

last: Pace

first: Dipti

last: Gupta

first: Sarah

last: Sturtevant

first: Biaoru

last: Li

first: Levi

last: Makala

first: Julia

last: Brittain

first: Nancy

last: Moore

first: Benjamin

middle: F

last: Vieira

first: Timothy

last: Thullen

first: Ivan

last: Stone

first: Huo

first: William

last: Hobbs

first: David

middle: R

last: Light


title: A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [RNA-Seq]

first: Felix

last: Krueger

overall_design: Total RNA-seq libraires (2 biological replicates of 16 samples, 1 biological replicate of 1 sample)

first: Rebecca

last: Berrens

first: Simon

last: Andrews

first: Wolf

last: Reik


title: A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [ChIP-Seq]

overall_design: Chip-Seq (2 biological replicates of  6 samples, 1 replicate 7 samples)


title: Hepatocellular carcinoma tissues: tumor tissues vs. non-tumor tissues

city: GuangZhou

first: Shunwang

last: Cao

state: GuangDong

address: 1838 Guangzhoudadaobei road

department: Laboratory Medicine Center

country: China

institute: Nanfang Hospital, Southern Medical University,Guangzhou, China

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: LncRNAs and mRNAs profiling of tissues from HCC patients comparing tumor tissues with non-tumor tissues

overall_design: Two-condition experiment, tumors vs. non-tumors. Biological replicates: 3 tumor replicates, 3 non-tumor replicates.

first: Qian

last: Wang


title: Gene expression profile of doxycycline inducible shHNF4G hairpins in 22RV1 prostate cancer cells

first: Shipra

last: Shukla

address: 417 East 68th Street

institute: MSKCC

summary: To determine genes regulated by HNF4G, we performed doxycycline induced shRNA mediated knockdown of HNF4G using two lentiviral constructs as well as a scrambled shRNA in duplicate. Two pLKO.1 constructs against HNF4G (HNF4Gsh1: TRCN0000019243,  targeting CACCAGCATCTCTCCAAACAA in coding DNA sequence (CDS); and HNF4Gsh2: TRCN0000420190, targeting GATGAGCTGGTTAGACCATTTC in CDS) were purchased from Sigma Aldrich MISSION® shRNA Plasmid DNA and pLKO.1 shScr (targeting CCTAAGGTTAAGTCGCCCTCG) was purchased from Addgene.  RNA was harvested 3 days after doxycycline treatment and gene expression profiling was performed.

overall_design: 22Rv1 sublines expressing doxycycline inducible hairpins against HNF4G (HNF4Gsh1 and HNF4Gsh2) and SCR control were treated with doxycycline or vehicle for three days after which cells were harvested for gene expression analysis.

first: Yu

last: Chen


title: Smad5 acts as an intracellular pH messenger and maintains bioenergetic homoeostasis

city: Shanghai

first: Xiaobai

last: Zhang

address: 1239 Siping Road

institute: Tongji University

summary: we report here that Smad5 acts as a pHi messenger and maintains bioenergetic homeostasis of a cell by regulating cytoplasmic metabolic machinery

overall_design: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

first: Yujiang

last: Fang

first: Zhongliang

last: Liu

first: Zhenyu

first: Xiangjie

last: Xu

first: Mengtao

last: Xiao

first: Yanyan

last: Yu

first: Yuanyuan

first: Yanhua

last: Du

first: Cizhong

last: Jiang

first: Yuzheng

last: Zhao

first: Yiran

first: Beibei

last: Fan

first: Daniel

last: Terheyden-Keighley

first: Yang

first: Lei

last: Shi

first: Yi

last: Hui

first: Xin

first: Bowen

first: Hexi

last: Feng

first: Lin

last: Ma

first: Quanbin

first: Guohua

last: Jin

last: Yang

first: Bin

last: Xiang

first: Ling

first: Xiaoqing


title: miR-93 Targets in Human Endothelial Cells

city: Kuopio

first: Suvi

last: Kuosmanen

address: Neulaniementie 2

country: Finland

institute: University of Eastern Finland

summary: miR-93-5p controls endothelial glycolysis and proliferation

overall_design: For identification of miR-93 targets and affected biological functions, HUVECs were transfected with miR-93-5p mimic and inhibitor and respective controls. In addition, mock transfection and non-treated cells were prepared as control samples. RNA-seq was performed in duplicate or triplicate.

first: Emilia

last: Kansanen

first: Anna-Liisa

last: Levonen


title: The Transgenerational Effects of Prenatal Synthetic Glucocorticoids

first: Stephen

last: Matthews

state: Ontario

address: 1 King's College Circle

summary: First generation animals (F1) were exposed to multiple courses of synthetic glucocorticoids in utero. Animals were then bred to produce second (F2) and third (F3) generation offspring. These animals underwent behavioural assessmenets before sacrifice. In this experiment the paraventricular nucleus of the hypothalamus fo F1, F2, and F3 female anmials (Beta and Control) have been extracted via micro-punch and RNA has been extracted.

overall_design: F1 Control n=5 vs F1 Beta n=5, F2 Control n=5 vs F2 Beta n=5, F3 Control n=6 vs F3 Beta n=6

first: Vasilis

middle: G

last: Moisiadis

first: Andrea

last: Constantinof

first: Moshe

last: Szyf


title: Gene expression profile of LNCaP prostate cancer cells with exogenous HNF4G  expression

first: Shipra

last: Shukla

summary: To determine genes regulated by HNF4G, we retrovirally infected LNCaP cells in triplicates to express HNF4G  and empty vector  as  control. cDNA for HNF4G in pDONR201 vector was obtained from Harvard medical school Plasmid database (ID:HsCD00022314) and was cloned into an murine stem cell virus (MSCV)-based retroviral vector with puromycin selection marker (Addgene) using Gateway technology.

overall_design: LNCaP cells were infected with retroviruses in triplicates for HNF4G and control empty vector expression. After three days of infection cells were selcted with puromycin for two days and later on RNA was harvested for gene expression analysis.

first: Yu

last: Chen


title: Transcriptomic profiling of BRC+, BRC-, DRC+ and DRC- FACS-sorted samples

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: BRcells and DRcells show distinct transcriptomic profiles. We assessed transcriptome changes, by deep-sequencing, of different subpopulations of Staphylococcus aureus strain Newman from multicellular aggregates.

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: Transcriptmic profiles of [Pica-yfp and Ppsma-yfp labeled-strains samples belonging to high and low-fluorescence populations sorted by FACS] were generated by deep sequencing, using Illumina HiSeq 2500.

first: Daniel

last: Lopez

first: Juan

middle: C

last: Garcia-Betancur

first: Malvika

last: Sharan


title: Profiling the target genes for MTA2 and EZH2 in HCT116

city: Beijing

first: Tingting

last: Li

address: 38 Xueyuan Rd

department: Medical informatics

institute: Peking University

summary: Using ChIP-seq technology, we tried to find out the whole genome targets for MTA2 and EZH2 in human colon cancer cells. More than 1700 genes were defined as the target of both MTA2 and EZH2, implying that MTA2 and EZH2 coordinate to participate in regulating a common set of target genes. Our results demonstrate a coordinated histone regulating model of gene transcriptional repression.

overall_design: ChIP-seqs using antibodies against MTA2, EZH2 and IgG.

first: Wei-Guo

last: Zhu


title: Investigating B cell stimulation in ubiquilin-1 KO mice

city: South San Francisco

first: Janina

last: Reeder

address: 1 DNA Way

institute: Genentech

summary: Ubiquilins are a family of proteins involved in proteasomal degradation of mislocalized membrane proteins. Here, Greer et al. demonstrate that Ubqln1 is required for BCR-driven B cell proliferation through maintenance of protein synthesis following stimulation. In the absence of Ubqln1, mitochondrial proteins accumulate in the cytosol, which may account for the observed proteostasis. BCR stimulation of murine B cells induced a long-lasting mitochondrial depolarization that did not occur in response to LPS.  We hypothesize that in the absence of Ubqln1, mitochondrial depolarization leads to an accumulation of mitochondrial membrane proteins in the cytosol, which leads to translational inhibition and a cell cycle block.

overall_design: For RNASeq, cells were stimulated in triplicate in 2*10e6 cells/mL for 4 hours with either 10 μg/mL anti-IgM F(ab)2 or 20 μg/mL LPS, or no stimulation. There were 18 total samples, 9 Knockout samples, 9 WT samples, 3 biological replicates per treatment group: no stimulation, 10 ug/mL a-Igm, 20 ug/mL LPS.

first: Alexandra

last: Greer

first: Ivan

last: Peng

first: Alexander

last: Abbas

first: Benjamin

last: Haley

first: Mike

last: Reichelt

first: Anand

last: Katakam

first: Meredith

last: Sagolla

first: Zora

last: Modrusan

first: Dong

middle: Y

last: Lee

first: Merone

last: Roose-Girma

first: Donald

last: Kirkpatrick

first: Brent

last: McKenzie

first: Eric

last: Brown


title: Single-cell and bulk RNA-seq of sorted and micro-dissected mouse bone marrow and fetal liver cells

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We here systematically studied the interaction network of bone marrow cells. To this end, we micro-dissected many small interacting structures (cell doublets, triplets etc.) into single cells, and sequenced their mRNAs, to infer cell identity. After grouping the cells into cell types (based on the single-cell transcriptomes), we identified actual physical interactions that occurred more, or less, than what would be expected by chance.

overall_design: After mild dissociation of the bone marrow or fetal liver, we micro-dissected many small interacting structures (cell doublets, triplets etc.) into single cells, and sequenced their mRNAs. We also sorted single bone marrow cells.

first: Judith

last: Vivié

first: Dominic

last: Grün

last: van Oudenaarden


title: Systems analysis of high-fat diet-induced hepatic insulin resistance

city: Bethesda

first: Anthony

middle: Robert

last: Soltis

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

summary: We profiled the transcriptomes and genome-wide H3K4me1, H3K27Ac, and H3K4me3 (chow diet only) enrichments from chow diet and 16 week high-fat diet-fed mouse livers.

overall_design: Liver mRNA and H3K4me1, H3K27Ac, and H3K4me3 were profiled by sequencing from chow diet and 16 week high-fat diet mouse livers.


title: Hybrid performance in maize predicted with combinations of omics data

status: Public on Oct 31 2017

city: Hamburg

first: Stefan

last: Scholten

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

institute: University of Hamburg

summary: We explored genomics, transcriptomics (mRNA and sRNA) and metabolomics of maize parent lines as predictors for agronomic performance of single-cross hybrids. Our results indicate that the merit of any individual predictor is trait dependent and that combining predictors has advantages for application across traits. We conclude that downstream “omics” can complement genomics for hybrid prediction and thereby contribute to more efficient selection of hybrid candidates.

overall_design: This dataset reports on the analysis of sRNAs in 64 Dent and 41 Flint inbred lines from a maize breeding population with 10 replicated samples


title: Frequent miRNA-convergent fusion gene events in breast cancer

city: Lund

first: Carlos

last: Rovira

address: Medicon Village, Byggnad 404

department: Department of Clinical Sciences, Lund

country: Sweden

institute: Lund University

summary: Studies of fusion genes have mainly focused on the formation of fusions that result in the production of hybrid proteins or, alternatively, on promoter-switching events that put a gene under the control of aberrant signals. However, gene fusions may also disrupt the transcriptional control of genes that are encoded in introns downstream of the breakpoint. By ignoring structural constraints of the transcribed fusions, we highlight the importance of a largely unexplored function of fusion genes. Using breast cancer as an example, we show that miRNA host genes are specifically enriched in fusion genes and that many different, low-frequency, 5' partners may deregulate the same miRNA irrespective of the coding potential of the fusion transcript. These results indicate that the concept of recurrence, defined by the rate of functionally important aberrations, needs to be revised to encompass convergent fusions that affect a miRNA independently of transcript structure and protein-coding potential.

overall_design:
Illumina paired-end RNA-sequencing was performed on 1600 sequencing libraries (49 technical replicates, 1552 tumour samples) for fusion gene detection analysis. miRNA sequencing was performed on a subset of the fusion detection samples, 191 sequence libraries (5 technical replicates, 186 tumour samples), for miRNA transcript expression estimation.
------------------------------------
This represents the miRNA sequencing component of 191 libraries only.
--------------------------------------
The authors state "due to Swedish law, the patient consent, and the risk that the   sequencing data contains personally-identifiable information   andhereditary mutations, we cannot deposit the short sequencing read   data in a repository".
Thus, this submission is incomplete.

first: Helena

last: Persson

first: Jari

last: Häkkinen

first: Johan

last: Vallon-Christersson

first: Åke

last: Borg

first: Rolf

last: Søkilde

first: Anna

last: Pirona

first: Mattias

last: Höglund

first: Felix

last: Mitelman

first: Fredrik

last: Mertens

first: Anders

last: Kvist


title: Transcriptomes of major renal collecting duct cell types in mouse  identified by single-cell RNA-Seq

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary:
Purpose: Transport processes in the renal collecting duct are responsible for precise regulation of blood pressure and body fluid composition.  The collecting duct is composed of at least three cell types, type A intercalated cells (A-IC), type B intercalated cells (B-IC) and principal cells (PC). To identify the genes that are selectively expressed in each cell type, including cell-surface receptors, transcription factors, transporters and secreted proteins, we used cell surface markers necessary for isolation of each of the three cell types using fluorescence-activated cell sorting and carried out single-cell RNA-Seq to measure the mRNA species in each of these cell types.

Methods: We enriched each of the three cell types using fluorescence-activated cell sorting. Subsequently, we carried out single-cell RNA-Seq of those cells using a microfluidic chip (Fluidigm C1 system). Single-cell cDNA libraries were constructed for paired-end sequencing and sequenced on Illumina HiSeq3000 platform. In addition, we also microdissected mouse CCDs and cTALs and carried out single-tubule RNA-Seq. Reads were mapped to mouse Ensembl Genome by STAR and transcript abundances were calculated in the units of transcripts per million (TPM) using RSEM (https://github.com/deweylab/RSEM). Single-cell RNA-Seq data anaysis were carried out using Seurat package in R.

Results and conclusion: Single-cell cDNA libraries were constructed for paired-end sequencing and at least 10-million sequence reads per cell were mapped to the mouse genome (Ensembl, GRCm38.p5). On average, cells were sequenced to a depth of 3000 genes (TPM>1). Unsupervised clustering analysis revealed five different cell types, namely type A intercalated cells (n=87), type B intercalated cells (n=23), principal cells (74), proximal tubule cells (n=19), and non-epithelial cells (n=32). The identified patterns of gene expression among A-ICs, B-ICs and PCs provide a foundation for understanding physiological regulation and pathophysiology in the renal collecting duct.

overall_design: Single-cell RNA-Seq data were generated from separate fludigm chips. 11 microdissected mouse CCDs and 8 cTALs were included for for single-tubule RNA-Seq.

first: Jae Wook

last: Lee

first: Chung-Lin

last: Chou

first: Anil

middle: V

last: Nair

first: Maria

last: Battistone

first: Teodor

last: Păunescu

last: Merkulova

first: Sylvie

last: Breton

first: Jill

middle: W

last: Verlander

first: Susan

last: Wall

first: Brown

last: Dennis

first: Maurice

middle: B

last: Burg

first: Mark

last: Knepper


title: Enhanced chromatin accessibility of the dosage compensated Drosophila male X chromosome requires the CLAMP zinc finger protein [MNase-SEQ]

city: Boston

first: Michael

last: Tolstorukov

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: The essential process of dosage compensation is required to equalize gene expression of X-chromosome genes between males (XY) and females (XX). In Drosophila, the conserved Male-specific lethal (MSL) histone acetyltransferase complex mediates dosage compensation by increasing transcript levels from genes on the single male X-chromosome approximately two-fold. Consistent with its increased levels of transcription, the male X-chromosome has enhanced chromatin accessibility, distinguishing it from the autosomes. Here, we demonstrate that the non-sex specific CLAMP (Chromatin-linked adaptor for MSL proteins) zinc finger protein that recognizes GA-rich sequences genome-wide promotes the specialized chromatin environment on the male X-chromosome. In contrast, MSL complex is not required for global male X-chromosome chromatin accessibility, and instead promotes chromatin accessibility just at its highest-occupancy sites. Overall, our results support a model where synergy between the global increases in accessibility promoted by CLAMP and the local effects of MSL complex create a specialized chromatin domain on the male X-chromosome.

overall_design: Drosophila S2 and Kc cells were evaluated using MNase-sequencing following a 6-day RNAi treatment of gfp (control), clamp, or msl2 (S2 cells only). Two biologigal replicates were performed for each treatment.

first: Jennifer

last: Urban

first: Guray

last: Kuzu

first: Sarah

last: Bowman

first: Benjamin

last: Scruggs

first: Telmo

last: Henriques

first: Robert

last: Kingston

first: Karen

last: Adelman

first: Erica

last: Larschan


title: Changes in mature mouse primary motor cortex transcriptome after conditional Fezf2 knockdown

city: Dunedin

first: Alison

middle: Jane

last: Clare

state: Otago

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

summary: RNA-seq analysis of mature mouse primary motor cortex in response to conditional knockdown of Fezf2. Analysis of M1 transcriptomes identifies significant changes to gene expression with the knockdown of Fezf2 in mature tissue.

overall_design: Lentiviral delivery of a control (non-silencing) or Fezf2 shRNA to mouse primary motor cortex in mature animals (P21-P25; n=4 of each) was used to conditionally reduce Fezf2 expression. Paired-end sequencing was used to generate transcriptome profiles of Fezf2-reduced and control samples.

first: Hollie

last: Wicky

first: Ruth

middle: M

last: Empson

first: Steph

last: Hughes


title: Genome-wide identification of microRNAs responsive to Ectropis oblique feeding in the tea plant (Camellia sinensis L.)

city: Hefei

first: chaoling

last: Wei

state: Anhui

address: 130 West Changjiang Road

institute: Anhui Agricultural University

summary: micro RNA identification of tea plant

overall_design: Tea leaves

first: Jeyaraj

last: Anburaj

first: C

middle: L


title: Rem2 promotes synapse formation by regulating the expression of genes encoding synaptogenic molecules

city: Waltham

first: Suzanne

last: Paradis

address: 415 South Street

department: Department of Biology

institute: Brandeis University

summary: Purpose: Determination of whether knockout of the GTPase Rem2 results in changes in gene expression

overall_design: 2 biological replicates of RNA harvested from cultured cortical neurons from 4 conditions (Control, Control_KCl, Rem2 KO, Rem2 KO_KCl)

first: Katelyn

last: Kenny


title: Expression profiling of differentiating emerin-null myogenic progenitor identifies molecular pathways implicated in their impaired differentiation

city: Bethlehem

first: Ashvin

last: Iyer

state: Pennsylvania

address: 1325B Johnston Drive

department: Pharmaceutical Sciences

institute: University of the Sciences

summary: RNA sequencing was performed on proliferating and differentiating wildtype and emerin-null myogenic progenitors to identify molecular pathways implicated in Emery-Dreifuss Muscular Dystrophy.

overall_design: Total RNA was isolated from 2 million wildtype or emerin-null H2Ks during proliferation and at each day of differentiation using the miRNeasy Mini Kit (Qiagen, product #217004) and processed according to manufacturer’s protocol. RNA was isolated from three independent cell culture plates for each sample.

first: Adam

last: Koch

first: James

last: Holaska


title: The immunosuppressive effect of the tick salivary protein, Salp15, is persistent and has long-term effects in a murine model of hematopoietic transplant

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

summary: Salp15, a salivary protein of Ixodes ticks, inhibits the activation of naïve CD4 T cells. Treatment with Salp15 results in immunomodulation in different murine models in which these cells participate.  The fate of the CD4 T cells activated in the presence of the immunosuppressor or its long-term effects on these cells are however, unknown. We now show that Salp15 binding to CD4 is persistent and induces a long-lasting immunomodulatory effect. The activity of Salp15 results in sustained diminished antibody production against specific and unrelated antigens. Transcriptionally, the salivary protein provokes a sharp acute effect that includes known activation factors, such as Il2, Cd44, or Il2ra, and that fades over time. The long-term effects exerted by Salp15 do not involve the induction of either anergy traits nor increased populations of regulatory T cells. Similarly, the treatment with the immunomodulatory protein does not result in B cell anergy or the generation of myeloid suppressor cells. However, the immunomodulatory protein induces the increased expression of the ectoenzyme, CD73, in regulatory T cells. Our results suggest that the specific regulation of CD73, a known modulator of adenosine levels, by Salp15 results in long-term cross-antigenic immunomodulatory effects.

overall_design: Genome-wide changes in gene Expression in mouse CD4 T cells activated with anti-CD3/CD28 in the presence of 25 ug/mL of the tick salivary protein, Salp15 or its inactive control (Salp15deltaP11) were generated by RNAseq.

first: Juan

last: Anguita


title: Effects of acute maximal exercise and high-fat feeding on the mouse skeletal muscle transcriptome

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

summary: Physical inactivity and over-nutrition are key risk factors for metabolic diseases, with impaired skeletal muscle gene transcription and metabolic function proposed as key etiological factors. Here, we have used RNA-seq to assessed the skeletal muscle transcriptome from mice fed a control or high fat diet (HFD), both pre- and 3h post-exercise. HFD up-regulated genes involved in lipid catabolism in skeletal muscle (quadriceps), while decreasing 241 exercise-responsive genes related to skeletal muscle plasticity. Collectively, this experimental approach provides a suitable resource to study transcriptional and metabolic networks in skeletal muscle in the context of health and disease.

overall_design: Skeletal muscle (quadriceps) mRNA from wild type mice (C57BL/6NTac) fed a control (CON) or high fat diet (HFD) under basal pre-exercise condition (CON-pre & HFD-pre) and 3h post-exercise (CON-post & HFD-post). Each experimental group comprised 4 biological replicates (total of 16 samples), with RNA-seq performed with HiSeq2500 (Illumina).

first: Joaquin

last: Perez-Schindler


title: RNA-seq of HDAC2-disrupted 293FT cells by CRISPR-Cas9

city: Davis

first: Paul

last: Knoepfler

address: 1 Shields Ave

department: Cell Biology and Human Anatomy

institute: UC Davis School of Medicine

summary: The transcriptional functions of HDAC1 and HDAC2 are largely viewed as repressive through their association in corepressor complexes, however, the unique functions and targets of HDAC2 are less well understood. We have utilized HDAC2-null cells to distinguish the role of HDAC2 in human cells and identify uniqye HDAC2 targets.

overall_design: HDAC2-null 293FT cells were created via CRISPR-Cas9 targeting and analyzed by RNA-seq for differential expression.

first: Priyanka

last: Somanath

first: Rachel

middle: H

last: Klein


title: Coupling transcriptional activation of CRISPR-Cas and DNA repair systems by Csa3a in Sulfolobus islandicus

city: Wuhan

first: Tao

last: Liu

state: Hubei

address: Shizishang Street No.1

institute: State Key Laboratory of Agricultural Microbiology

summary: Transcriptome sequencing was carried out on an Illumina HiSeq platform to investigate the activation of CRISPR-Cas and DNA repair systems by Csa3a in Sulfolobus islandicus Rey15A. We compared the differently expressed genes in Sulfolobus islandicus Rey15A strain with csa3a overexpression vs. Sulfolobus islandicus Rey15A strain carrying an empty expression vector, cas1 deletion strain with csa3a overexpression vs. cas1 deletion strain carrying an empty expression vector, as well as interference-deficient strain with csa3a overexpression vs. interference-deficient strain carrying an empty expression vector. We find that cas genes (SiRe_0760, SiRe_0761, SiRe_0762, SiRe_0763), nucleotidyltransferase domain of DNA polymerase beta (SiRe_0459), chromosome segregation protein (SMC)-related ATPase (SiRe_0649), SMC-related protein (SiRe_1142) and three HerA helicases involved in DNA double break repair (encoded by SiRe_0064 and SiRe_0095 of nurA-herA operons, and SiRe_1857) were significantly up-regulated. Our data indicated that the Csa3a regulator couples transcriptional activation of spacer acquisition genes, CRISPR RNA transcription, DNA repair and genome stability genes.

overall_design: Examination of different gene expression in 6 cell types.

last: Peng


title: RNA-sequencing based analysis of Listeria monocytogenes 10403S::ΔBCHL Prha-sigB and ΔBCHL Prha

city: Ithaca

first: Martin

last: Wiedmann

address: 341 Stocking Hall

department: Food Science

institute: Cornell University

summary: In this study, RNA-seq was used to compare the transcriptomes of Listeria monocytogenes 10403S::ΔBCHL Prha-sigB and ΔBCHL Prha. RNA-seq was performed on ΔBCHL Prha-sigB and ΔBCHL Prha RNA samples representing three independent biological replicates at log phase in Brain Heart Infusion (BHI) broth under rhamnose induction. Indexed and purified cDNA libraries (6 libraries including 3 replicates for 2 strains) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2500 (single-end, 150-bp per read). Reads alignment was carried out using the Burrows-Wheeler Aligner (BWA). Differential expression of genes in different strains was statistically assessed using the BaySeq method. To identify sigB-dependent promoters, a method of moving sliding windows of 50 nt along the whole genome was used to compare the normalized RNA-seq coverage (NRC) between the two strains. Using the standard whole gene differential expression analysis, significant upregulation of 255 genes was found in the sigB overexpressing strain. While with the sliding windiow analysis, 18 σB-dependent promoters were newly identified.

overall_design: Transcriptome profiles of L. monocytogenes 10403S::ΔBCHL Prha-sigB and ΔBCHL Prha were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

first: Yichang

first: Renato

last: Orsi


title: FUS mutant human motoneurons transcriptome analysis reveals altered pathways and impairment of microRNA function

city: Rome

first: Alessandro

last: Rosa

address: P.le Aldo Moro 5

department: Biology and Biotechnology Charles Darwin

country: Italy

institute: Sapienza University of Rome

summary: Mutations in the RNA-binding protein FUS have been genetically linked to Amyotrophic Lateral Sclerosis (ALS), a neurodegenerative disease caused by the death of motoneurons (MNs). FUS is a ubiquitous protein and the mechanisms leading to selective MN loss downstream of FUS mutations are still largely unknown.   We report the first transcriptome analysis of human purified MNs, obtained from isogenic induced Pluripotent Stem Cells (iPSCs) with a FUS wild-type or mutant genetic background. Gene ontology analysis of differentially expressed genes identified significant enrichment of pathways previously associated to other neurological diseases and non-FUS ALS, suggesting a common pathological mechanism. We also found several microRNAs deregulated in FUS mutant MNs and focused on miR-375 and miR-125b. Notably, miR-125b is a neural-enriched microRNA with multiple functions in the nervous system and miR-375 had been previously associated to MN survival. We report that relevant targets of both microRNAs, including the neural RNA-binding protein ELAVL4 and apoptosis factors such as p53, are aberrantly increased in FUS mutant MNs. Characterization of FUS RNA targets in the cell type primarily affected by the disease contributes to the definition of the pathogenic mechanisms of FUS-linked ALS.

overall_design: High-throughput sequencing of total RNA from human iPSC-derived motoneurons Hb9::GFP-positive (day12), 2 replicates; human iPSC-derived neural cells Hb9::GFP-negative (depleted of motoneurons, day12), 2 replicates; human iPSC-derived motoneurons FUS-WT (day12+7), 3 replicates;  human iPSC-derived motoneurons FUS-P525L/P525L mutant (day 12+7), 3 replicates. High-throughput sequencing of small RNA from human iPSC-derived motoneurons FUS-WT (day12+7), 3 replicates;  human iPSC-derived motoneurons FUS-P525L/P525L mutant (day 12+7), 3 replicates.

first: Riccardo

last: De Santis

first: Alessio

last: Colantoni

first: Laura

last: Santini

first: Giovanna

last: Peruzzi

first: Valeria

last: de Turris

first: Irene

last: Bozzoni


title: A blood RNA signature for predicting the treatment outcome in the Tuberculosis Treatment Response Cohort

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

summary: Identification of blood biomarkers that prospectively predict Mycobacterium tuberculosis treatment response.

overall_design: There are a total of 914 samples used in this design. This involves samples from 100 cases and 38 controls. Most of the samples have 2 technical replicates where as 2 samples have 4. Samples from the TB cases have been collected on the start day of TB treatment and on 1,4 and 24 weeks after treatment as well. For some subjects we also have samples after the subject has been cured. The case or TB Subjects have been categorized by the nature of their response as definite,probable or possible cure. The day of cure is presented in the time to negativity column. Also provided in the metadata are the MGIT -Mycobacteria Growth Indicator Tube and XPERT (cartridge based nucleic acid amplification test, automated diagnostic test that can identify Mycobacterium tuberculosis (MTB)) values at the various times of sample collection for all TB Subjects.

first: D

middle: E

first: Ethan

last: Thompson

first: Smitha

last: Shankar


title: Agonistic targeting of TLR1/TLR2 induces p38 MAPK-dependent apoptosis and NfkB-dependent differentiation of AML cells

first: Pablo

last: Peña-Martínez

address: Klinikgatan 28

department: Clinical Genetics

summary: Acute myeloid leukemia (AML) is associated with poor survival and there is a strong need to identify disease vulnerabilities that might reveal new treatment opportunities. Here, we found that Toll-like receptor 1 (TLR1) and TLR2 are upregulated on primary AML CD34+CD38- cells relative to corresponding normal bone marrow cells. Activating the TLR1/TLR2 complex by the agonist Pam3CSK4 in MLL-AF9 driven human AML, resulted in induction of apoptosis by p38 MAPK-dependent activation of Caspase 3 and myeloid differentiation in a NFκB-dependent manner. By using murine Trp53-/- MLL-AF9 AML cells, we demonstrate that p53 is dispensable for Pam3CSK4-induced apoptosis and differentiation. Moreover, also murine AML1-ETO9a driven AML cells were forced into apoptosis and differentiation upon TLR1/TLR2 activation, demonstrating that the antileukemic effects observed were not confined to MLL-rearranged AML. We further evaluated whether Pam3CSK4 would exhibit selective antileukemic effects. Ex vivo Pam3CSK4 treatment inhibited murine and human leukemia-initiating cells, whereas murine normal hematopoietic stem and progenitor cells (HSPCs) were relatively less affected. Consistent with these findings, primary human AML cells across several genetic subtypes of AML were more vulnerable for TLR1/TLR2 activation relative to normal human HSPCs. In the MLL-AF9 AML mouse model, treatment with Pam3CSK4 provided proof of concept for in vivo therapeutic efficacy. Our results demonstrate that TLR1 and TLR2 are upregulated on primitive AML cells and that agonistic targeting of TLR1/TLR2 forces AML cells into apoptosis by p38 MAPK-dependent activation of Caspase 3, and differentiation by activating NFκB, thus revealing a new putative strategy for therapeutically targeting AML cells.

overall_design: MA9 cells were grown in media containing baseline cytokines with or without Pam3CSK4 (1 ug/mL) for 3 or 24 hours

first: Mia

last: Eriksson


title: Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm

city: Penang

first: Jason

last: Chin

state: Penang

address: Jalan Inovasi

department: INFORMM

country: Malaysia

institute: Universiti Sains Malaysia

summary: Six sequencing libraries was prepared from S. Typhi planktonic cells and biofilm cells using Illumina HiSeq 2500 sequencing to investigate differential gene expression between the two conditions. The transcriptome was processed using Cufflinks and there were a total of 35 up-regulated genes and 29 down-regulated genes log2-fold change values of greater than 2 and less than negative 2. The differentially expressed genes were identified using BLAST and the functions was analysed. This study provides an overview of the genes that are differentially expressed in S. Typhi when it transitions from the planktonic to the biofilm phenotype. The data will provide a basis for further study is necessary to uncover the mechanisms of biofilm formation in S. Typhi and discovery of novel gene functions or pathways associated with the development of the typhoid carrier state. This data may also be used to elucidate the effect of biofilm on the virulence and pathogenicity of S. Typhi in chronic carriers.

sample_organism: Salmonella enterica subsp. enterica serovar Typhi

overall_design: Examination of two sequencing libraries from planktonic and biofilm cells of S. Typhi

first: Phua

middle: K

last: Kien

first: Todd

middle: D

last: Taylor


title: RNA sequencing  quantitative analysis of exosome miRNAs in plasma in Metastatic renal cell carcinoma (mRCC)

city: Milwaukee

first: Liang

last: Wang

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary:
Purpose: Since clinical characteristics are often inaccurate and subjective, we evaluated the prognostic value of plasma exosomal miRNAs to predict survival in metastatic renal cell cancer (mRCC).
Methods: RNA sequencing was performed to identify candidate exosomal miRNAs associated with overall survival in a screening cohort of 41 mRCC patients.Candidate miRNAs were further evaluated for prognosis by TaqMan quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) in a follow-up cohort of 65 mRCC patients.
Results: RNA sequencing in screening cohort generated 3.75 million mappable reads per patient, of those with normalized read counts>8 RPM (reads per million), 93.8% were mapped to miRNAs for a total of 322 unique miRNAs. Cox regression analysis identified 20 miRNAs that were associated with overall survival (OS, FDR< 0.05). Among these 20 significant miRNAs, three were validated in a separate independent cohort of 65 patients with mRCC.Patients with lower expression of miR-26a1-3p, miR-let-7i-5p and miR-615-3p had a significantly poorer OS than those with higher expression. Multivariate model by combining miR-let-7i-5p and the Memorial Sloan-Kettering Cancer Center (MSKCC) score significantly improved survival prediction.
Conclusions: Our study identifies multiple plasma exosomal miRNAs showing association with survival in mRCC stage patients. Multivariate model by combining miR-let-7i-5p and the Memorial Sloan-Kettering Cancer Center (MSKCC) score significantly improved survival prediction.

overall_design: exosomal miRNAs profiles of 41 mRCC patients were generated by 50 bp single read sequencing using Illumina HiSeq2000 DNA sequence analyzer.

first: Meijun

last: Du


title: Development of zebrafish medulloblastoma model by TALENs induced somatic gene inactivation methods

city: Goyang

first: Young-Ki

last: Bae

state: Gyeonggi

address: 323 Ilsan-ro

department: Research Institute

institute: National Cancer Center

summary: we developed the zebrafish cancer models by TALENs mediated somatic inactivation of tumor suppressor genes, rb1, induced brain tumors in tp53 mutation background. Using RNA sequencing analysis in addition to histopathology and immunohistochemistry, we demonstrated that the brain tumors induced by rb1 gene somatic inactivation have a molecular feature of MB-like PNETs

overall_design: QuantSeq 3’ mRNA sequencing with whole brain tissue wild type (WT) zebrafish and tumors induced by rb1 TALENs injected zebrafish at 5 month post fertilization


title: Role of 14-3-3 in the transcriptional response of Saccharomyces cerevisiae to potassium starvation.

city: Leiden

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

institute: Leiden University

summary: We investigated the transcriptional response of yeast Saccharomyces cerevisiae bmh1 and bmh2 deletion mutants to potassium starvation. To this end yeast strains were grown for 60 min in media without potassium or in media with a standard potassium concentration (50 mM KCl).  Using Serial Analysis of Gene Expression (SAGE)-tag sequencing the effect of potassium starvation on the transcriptome was determined. This study is a follow-up of our previous study (Anemaet IG and van Heusden GPH. 2014. BMC Genomics:1040)( GEO accession number GSE57093).

overall_design: 3 samples of cells grown in media without potassium and 3 samples of cells grown in the presence of potassium were analyzed.

first: G

middle: P


title: Impact of HGFL-Ron signaling on breast cancer stem cell transcriptomic profiles.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Introduction: HGFL-Ron signaling is augmented in human breast cancer and is associated with poor overall prognosis.  Here, we investigate the role of HGFL-Ron signaling in murine breast cancer stem cells (BCSC) through characterization of BCSC transcriptomes through RNA-sequencing, focusing on the impact of Ron knockdown through a short hairpin construct.
Methods:R7 breas cancer cell lines were drived from mammary tumors in transgenic MMTV_Ron mice.  They were sorted based on expression of cell surface markers indicative of lineage negative, CD29hi and CD24+ cells.  Bulk R7, sorted cells, and sorted cells treated with shRon were submitted for transcriptomic characterization on the Illumina HiSeq 2500.  High quality reads were aligned to the mm9 genome and quantified to generate RPKM.
Results: Approximately 30 million reads were aligned to the mouse genome in each sample which corresponded to over 36000 transcripts.  Of these, ~16000 were included in analysis.
Conclusions: Differential expression analysis indicated that depletion of Ron markely reduces mammosphere formation and self-renewal, and highlighted by the decrease in B-catenin and NFKB pathways.

overall_design: Transcriptome profiles of bulk and sorted R7 BCSCs with Ron knockdown through RNA-sequencing.

first: Susan

last: Waltz

first: Sasha

last: Ruiz-Torres


title: Transcriptomic comparison of aerial and root cells of a wild yeast biofilm colony

city: Vestec

first: Derek

last: Wilkinson

address: Prumyslova 595

department: Genetics and Microbiology

country: Czech Republic

institute: Charles University

summary: Wild yeast and many clinical strains form complex, biofilm colonies, providing protection from desiccation, drugs and other stresses. Few transcriptomic studies have focused on sub-surface invasive “roots” due to the challenges of cell isolation from agar and subpopulation cross-contamination. Here we present, a first transcriptomic analysis via RNA sequencing of root and aerial cells, separated by a novel method. We identified 719 coding genes with upregulated root expression, mainly involved in ribosome structure/biogenesis, biosynthesis and translation and 529 loci/genes with upregulated aerial expression, mainly involved in meiosis/sporulation, stress defense and protein degradation; all indicating that aerial cells are resting and root cells are metabolically active cells. On the basis of 172 root-upregulated and 233 aerial-upregulated non-coding loci detected, anti-regulated gene/lncRNA pairs have been identified that may contribute to negative regulation of gene expression. Importantly, cells showing typical markers of “roots” correspond with cells embedded in extracellular matrix and cells showing typical markers of “aerial” parts with ECM-free cells.

overall_design: Identification of differences in gene expression and potential regulation by lncRNA between aerial and root cell subpopulations of differentiated yeast biofilm colonies

first: Jana

last: Marsikova

first: Otakar

last: Hlavacek

first: Gregor

last: Gilfillan

first: Alexandru

last: Mizeranschi

first: Timothy

last: Hughes

first: Marketa

last: Begany

first: Stanislava

last: Resetarova

first: Libuse

last: Vachova

first: Zdena

last: Palkova


title: Transcriptome analysis of extracellular matrix (ECM)-induced changes in mammary epithelial cell gene expression

city: Parkville

first: christophe

last: lefevre

state: VIC

address: 1 G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter Eliza Hall Institute of Medical Research

summary: We report transcriptome analysis of wallaby mammary epithelial cells (WallMEC) following treatment with mammary ECM from two distinct stages of lactation

overall_design: Wallaby mammary epithelial cells (WallMEC) following treatment with mammary ECM from two distinct stages of lactation

first: Stephen

middle: S

last: Wanyonyi

first: Christophe

last: Lefevre


title: Viral and Cellular N6-methyladenosine (m6A) Epitranscriptomes in KSHV Life Cycle

city: Xuzhou

first: Hui

last: Liu

state: Jiangsu

address: #1 Daxue Road

institute: China University of Mining and Technology

summary: Tan et al. discovered abundant conserved N6-methyladenosine (m6A) modifications on KSHV transcripts during latent and productive infection in different cell types. They also show that m6A readers YTHDF2 and YTHDF3 mediate KSHV replication, and KSHV optimizes both phases of viral replication by reprograming cellular epitranscriptome to regulate distinct signaling pathways.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: m6A epitranscriptome profiles of four uninfected cell types, five latently infected cell types, and three lytic cell types. Each cell type has an immunoprecipitated (IP) and input sample.

first: Brandon

last: Tan

first: Suzane

middle: R

last: Silva

first: Lin

last: Zhang

first: Jia

last: Meng

first: Xiaodong

last: Cui

first: Hongfeng

last: Yuan

first: Océane

last: Sorel

first: Yufei

last: Huang

first: Shou

middle: J

last: Gao


title: RNA profiling of testis from wild-type and tamoxifen-induced NIPP1 knockout mice

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: This study aimed to explore the role of NIPP1 in adult germline cell proliferation and differentiation, using a ubiquitous inducible NIPP1 knockout (TKO) mouse model. To gain unbiased insight into the molecular mechanism that underly the sertoli-only phenotype in TKO, we performed a comparative RNA sequencing profiling of control and TKO, in which NIPP1 was  tamoxifin-induced depleted.

overall_design: Two genotypes are compared after treatment with tamoxifen. The control genotype (UBC CRE-ERT2+/- Ppp1r8 fl/+) looses the floxed allele of PPP1R8 (aka NIPP1) as a consequence of the treatment with tamoxifen and becomes heterozygous for PPP1R8. The KO genotype (UBC CRE-ERT2+/- Ppp1r8 fl/-) also looses the floxed allele of PPP1R8 as a consequence of the tamoxifen treatment and becomes homozygous KO. For each genotype, 4 replicates are profiled.

first: Monica

last: Ferreira

first: Shannah

last: Boens

first: Kathelijne

last: Szekér

first: Iris

last: Verbinnen

first: Aleyde

last: Van Eynde

first: Margarida

last: Fardilha

first: Mathieu

last: Bollen


title: Molecular profiling of rhabdoid tumors in a Smarcb1-deficient mouse model

city: Los Angeles

first: Jeremie

last: Vitte

state: California

address: 675 Charles E Young Dr. S

country: USA

institute: UCLA

summary: Germline mutations of the SMARCB1 gene predispose to two distinct tumor syndromes: rhabdoid tumor predisposition syndrome, with malignant pediatric tumors mostly developing in brain and kidney, and familial schwannomatosis, with adulthood benign tumors involving cranial and peripheral nerves. The mechanisms by which SMARCB1 germline mutations predispose to rhabdoid tumors versus schwannomas are still unknown. Here, to understand the origin of these two types of SMARCB1-associated tumors, we generated different tissue- and developmental stage-specific conditional knockout mice carrying Smarcb1 and/or Nf2 deletion. Smarcb1 loss in early neural crest was necessary to initiate tumorigenesis in the cranial nerves and meninges with typical histological features and molecular profiles of human rhabdoid tumors. By inducing Smarcb1 loss at later developmental stage in the Schwann cell lineage, in addition to biallelic Nf2 gene inactivation, we generated the first mouse model developing schwannomas with the same underlying gene mutations found in schwannomatosis patients.

overall_design: RNA-sequencing of 12 Smarcb1-deficient mouse cranial nerves and meninges tumors

first: Fuying

first: Giovanni

last: Coppola

first: Alezander

last: Judkins

first: Marco

last: Giovannini


title: Syndecan-1 controls lung tumorigenesis by regulating microRNAs packaged in exosomes [EKVX]

status: Public on Oct 30 2017

first: Tanyalak

last: Parimon

state: CA

address: 127 San Vicente

department: Medicine

institute: Cedars-Sinai Medical Center

summary: We evaluated the effect of syndecan-1 in various cell-based and animal models of lung cancer and found that lung tumorigenesis was promoted when cells lose syndecan-1 expression. We also demonstrate that syndecan-1 (or lack thereof) alters the microRNA (miRNA) cargo carried within exosomes exported from lung cancer cells. Analysis of the changes in miRNA expression identifies a distinct shift toward augmented pro-cancerous signaling, which are consistent with the changes found in lung adenocarcinoma. In all, our work identifies syndecan-1 as an important factor on lung cancer cells that control its ability to shape the lung tumor microenvironment through alterations in miRNA packaging within exosomes.

overall_design: Examiniation of exosomal microRNA profile in 2 sets of human non-small cell lung cancer cell lines (EKVX cell line); The first set is scramble (wild-type; EKVX.Scrb) cells and syndecan-1 knock-down (EKVX.1735) cells

first: Peter

last: Chen


title: A network-based strategy for prioritizing hits from chemical screening data by leveraging genetic, epigenetic and transcriptional datasets

city: Boston

first: Oana

last: Ursu

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Small molecule screens are widely used to prioritize compounds for development of pharmaceuticals and to reveal pathways altered in biological processes.  However, interpreting the results of these screens is very challenging since in almost all cases, the compounds are highly promiscuous.  Here we present a network-based strategy for analyzing molecular screening data.  We report a screen for kinase inhibitors that synergize with gemcitabine, the first-line chemotherapy treatment for pancreatic cancer.  The eight kinase inhibitors that emerge from the screen target a total of 140 kinases, and these kinases show little overlap with previously detected genetic modifiers of gemcitabine toxicity.  Using the SAMNet algorithm, we link the chemical and genetic modifiers of gemcitabine toxicity to transcriptional and epigenetic changes induced by gemcitabine that we measure using DNaseI-Seq and RNA-Seq. SAMNet uses a constrained optimization algorithm to connect genes from these complementary datasets through  a small set of protein-protein and protein-DNA interactions.  The resulting network is able to recapitulate known gemcitabine response pathways including DNA damage repair, control of cellular growth and the EMT pathway. We query the network downstream of putative kinase inhibitor targets and in addition to identifying known gemcitabine synergizers STAT3, NFKB2 and AKT1, we propose novel candidate targets for gemcitabine chemoresistance, including ETS transcription factors (ELK1, ELK3) and the adaptor protein NCK1. Our work suggests that a subset of the “off-target kinases” are directly involved in the cellular response to gemcitabine by modulating the activity of known and proposed chemosensitizing genes.

overall_design: 4 RNAseq samples and 2 DNaseI-hypersensitivity samples in the PANC1 human cell line

first: Sara

last: Gosline

first: Neil

last: Beeharry

first: Lauren

last: Fink

first: Vikram

last: Bhattacharjee

first: Yan

last: Zhou

first: Shao-shan

middle: C

first: Tim

last: Yen

first: Ernest

last: Fraenkel


title: Syndecan-1 controls lung tumorigenesis by regulating microRNAs packaged in exosomes

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

overall_design: Refer to individual Series


title: Transcriptome analysis of PC9 cells with gefitinib or/and hypoxia treatment and comparison with gefitinib resistant PC9 cells and ALDH positive PC9 cells

city: Shanghai

first: Shimin

last: AN

address: 280, South Chongqing Road

department: Department of Pharmacology and Chemical Biology

institute: Shanghai Jiao Tong University School of Medicine

summary: Inevitable gefitinib resistance and relapse of the disease was the biggest hurdle to NSCLC treatment. Importantly, the role of hypoxia in solid tumor tissues in vivo in gefitinib acquired resistance and its relationship to lung cancer stem cells (LCSCs) has not been fully elucidated. Here, the PC9 cells were treated with short term gefitinib or/and hypoxia, also, PC9 gefitnib resistant (PC9-GR) cell line was established and ALDH positive PC9 cells were sorted by FACs. Transcriptome analysis among those PC9 cell groups revealed the important role of hypoxia in gefitinib acquired resistance and signaling transduction change, which may critical for NSCLC disease progression and recurrence.

overall_design: The PC9 cells were treated with 0.1 uM gefitinib or/and hypoxia for 1 week, also, PC9 geifitnib resistant (PC9-GR) cells and ALDH positive PC9 cells were anlyzed by RNA-seq technology.


title: Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive, ASRC 164

department: Animal Sciences

institute: University of Missouri, Columbia

summary: Assisted reproductive therapies (ART) have become increasingly common worldwide and up to ~6% of children currently born in developed countries were conceived employing these technologies.  Numerous retrospective studies have suggested that ART-conceived children are more likely to develop the overgrowth syndrome Beckwith-Wiedemann (BWS).  In bovine, the use of ART can induce a similar overgrown condition, which is referred to as large offspring syndrome (LOS).  Both BWS and LOS involve dysregulation of imprinted genes.  However, it remains largely unknown whether aberrant gene expression and DNA methylation occur at non-imprinted loci and to what extent these molecular alterations can contribute to these syndromes.  Here we examined the transcriptome of skeletal muscle, liver, kidney, and brain of control and LOS bovine fetuses and found that different LOS fetuses exhibit different severity of the transcriptome alterations and different tissues have distinct gene pathways disturbed in LOS fetuses.  Particularly for skeletal muscle, multiple pathways involved in myoblast proliferation and fusion into myotubes are misregulated in LOS fetuses.  Further, characterization of the methylome of skeletal muscle demonstrates numerous local methylation differences; however, global DNA methylation is comparable between all individuals regardless of bodyweight.  Importantly, only a small percent of differentially expressed genes (DEGs) including the imprinted gene IGF2R can be linked to the neighboring differentially methylated regions (DMRs).  In summary, we not only show that misregulation of non-imprinted genes in addition to loss-of-imprinting contributes to the ART-induced overgrowth syndrome but also demonstrate that most of the aberrant gene expression is  not associated with DNA methylome epimutations.

overall_design:
Comparison of DNA methylome of fetal skeletal muscle between control and overgrown bovine fetuses; Comparison of transcriptome of skeletal muscle, brain, kidney, and liver of control and overgrown bovine fetuses
This Series represents the DNA methylome dataset. The RNA-seq data of brain, kidney, liver, and skeletal muscle have been deposited in GEO database under accession number: GSE63509.

first: Zhiyuan

first: Darren

last: Hagen

first: Tieming

last: Ji

first: Christine

middle: G

last: Elsik


title: Nuclear Export Factor 3 Regulates Localization of Small Nucleolar RNAs

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: Small nucleolar RNAs (snoRNAs) guide chemical modifications of ribosomal and small nuclear RNAs, functions that are carried out in the nucleus. While most snoRNAs reside in the nucleolus, a growing body of evidence indicates that snoRNAs are also present in the cytoplasm and that snoRNAs move between the nucleus and cytoplasm by a mechanism that is regulated by lipotoxic and oxidative stress. Here, in a genome-wide shRNA-based screen, we identified nuclear export factor 3 (NXF3) as a transporter that alters the nucleocytoplasmic distribution of box C/D snoRNAs from the ribosomal protein L13a (Rpl13a) locus. Using RNA-sequencing analysis, we show that NXF3 associates not only with Rpl13a snoRNAs, but also with a broad range of box C/D and box H/ACA snoRNAs. Under homeostatic conditions, gain or loss of function of NXF3, but not related family member NXF1, decreases or increases cytosolic Rpl13a snoRNAs, respectively. Furthermore, treatment with the adenylyl cyclase activator forskolin diminishes cytosolic localization of the Rpl13a snoRNAs through a mechanism that is dependent on NXF3, but not NXF1. Our results provide evidence of a new role for NXF3 in regulating the distribution of snoRNAs between the nuclear and cytoplasmic compartments.

overall_design: 3 input and 3 NXF3-immunoprecipitated RNA samples from NIH 3T3 mouse fibroblasts.  NIH 3T3 cells were transfected with pEGFP-NXF3 plasmid and NXF3-GFP was immunoprecipitated using anti-GFP antibody from Abcam (catalog #ab290) bound to protein A-Dynabeads (Invitrogen).

first: Melissa

middle: W

last: Li

first: Jean

last: Schaffer


title: Single-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of human glioblastoma

city: Stanford

first: Spyros

last: Darmanis

address: Clark Center, E300

department: Bioengineering

institute: Stanford University

summary: We used single-cell RNAseq to investigate the heterogeneity of glioblastoma tumors and assess differential expression between cells within and in proximity of the tumor.

overall_design: Examination of cell types in human primary glioblastoma samples.

first: Spyridon

first: Stephen

last: Quake


title: miRNAs analysis of Sika deer antler at different stages (15 d and 60 d)

city: Changchun

first: Yu

last: Zhao

address: No.1035 Boshuo Road, Jingyuetan tourism economic development district

institute: Changchun University of Chinese Medicine

summary: Deer antlers are amazing natural appendages that grow faster than any other known mammalian bone. Antler growth occurs at the tip and is initially cartilage, which is later replaced by bone tissue. However, little is known regarding the precise role of cooperation between cell lineages and functional genes in regulating antler growth, and molecular mechanisms responsible for rapid growth remain elusive. In this study, we use an RNA-Seq approach to identify miRNA expression patterns during antler growth.

overall_design: 2 samples

first: Baojin

last: Yao


title: RNA-Sequencing and proteomics approaches reveal multi-cellular deficits in the cortex of Rett syndrome mice

city: Blacksburg

first: Michelle

middle: L.

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Polytechnic and State University

summary: Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the transcriptional regulator MeCP2. RTT is characterized by having apparently normal development until 6-18 months, when a progressive decline in motor and language functions begins and breathing abnormalities and seizures present. Despite intense research, the molecular targets of MeCP2 and their contribution to the disease are unknown. Here we present the first comprehensive and comparative transcriptomic and proteomic analysis in a RTT mouse model. Examining whole cortex tissue in symptomatic males (Mecp2Jae/y) and wild-type littermates, we have identified 391 genes and 465 proteins considered to be significantly altered. We observed an overall poor correlation between global gene and protein expression (Pearson correlation 0.12), yet 35 hits were common to both data sets, with 12 hits not described elsewhere. These 35 hits indicate disrupted cellular metabolism, calcium signaling, protein stability, DNA binding and cytoskeletal cell structure in the RTT cortex. Pathway analysis in both data sets identified biological pathways ubiquitous to multiple cell types as well as cell type specific pathways, underscoring the contributions of multiple central nervous system (CNS) cell populations to the disease pathogenesis. These findings prompted us to compare identified ‘hits’ to a publicly available database containing CNS cell type specific gene expression. This indicated approximately 32% of differentially expressed (DE) genes and 16% proteins were highly enriched in unique CNS cell types, while the remaining DE genes and proteins were ubiquitously expressed and not ascribable to any unique cell population. Our comparative transcriptome and proteome analysis in the cortex of RTT mice supports previous works indicating widespread CNS dysfunction.

overall_design: Wild-type (WT) males were bred with heterozygous Mecp2tm1.1Jae/+ (Jaenisch) female mice. The whole cortex of mutant male mice (Mecp2Jae/y) along with WT littermates were collected after postnatal day 60 (P60+). An n of 4 biological replicates per genotype were used, with WT animals serving as controls. For RNA-Sequencing, 2 technical replicates were run per biological replicate.

first: Natasha

last: Pacheco

first: Michael

last: Heaven

first: Leanne

last: Holt

first: David

last: Crossman

first: Kristin

last: Boggio

first: Scott

middle: A

last: Shaffer

first: Daniel

last: Flint


title: YEATS2 Links Histone Acetylation to Tumorigenesis of Non-small Cell Lung Cancer

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: Recognition of modified histones by “reader” proteins constitutes a key mechanism regulating diverse chromatin-associated processes important for normal and neoplastic development. For instance, bromodomain-containing proteins bind to acetylated histones and regulate chromatin dynamics and gene expression. We recently identified the YEATS domain as a novel acetyllysine-binding module; however, the functional importance of YEATS domain-containing proteins in human cancer remains largely unknown. Here we show that the YEATS2 gene is highly amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell growth and survival. Biochemical and crystal structural studies show that YEATS2 binds to acetylated histone H3, and the YEATS domain utilizes a serine-lined aromatic “sandwiching” cage for acetyllysine readout. ChIP-seq analyses in lung cancer cells reveal that the YEATS2-containing ATAC complex colocalizes with H3K27 acetylation (H3K27ac) on the promoters of actively transcribed genes. Depletion of YEATS2 or disruption of the interaction between its YEATS domain and acetylated histones reduces the ATAC complex-dependent promoter H3K9ac levels and deactivates the expression of essential genes, including the ribosomal protein-encoding genes, which are important for cancer cell growth and survival. Taken together, our study identifies YEATS2 as a histone H3K27ac specific reader that regulates a transcriptional program essential for NSCLC tumorigenesis.

overall_design: ZZZ3, H3K4me1, H3K4me3, H3K9ac and H3K27ac ChIP-seq in H1299 cells and H3K9ac ChIP-seq in control and shYEATS2 H1299 cells; mRNA-seq of shNT and shYEATS2 duplicates in H1299 cells.

first: Jie

last: Lyu

first: Wenyi

last: Mi

first: Xiaobing

last: Shi


title: RNAseq data on single dose KMO inhibitor (CHDI-00340246) treated R6/2 mice.

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: Dysregulation of the kynurenine (Kyn) pathway has been associated with the progression of Huntington's disease (HD). In particular, elevated levels of the kynurenine metabolites 3-hydroxy kynurenine (3-OH-Kyn) and quinolinic acid (Quin), have been reported in the brains of HD patients as well as in rodent models of HD. The production of these metabolites is controlled by the activity of kynurenine mono-oxygenase (KMO), a mitochondrial outer membrane enzyme which catalyzes the synthesis of 3-OH-Kyn from Kyn.  Thus inhibiting KMO is expected to produce a beneficial effect in Huntington's Disease (HD) patients, hopefully reversing their phenotype to match healthy subjects. To test this effect, we acutely treated a mouse model of HD (R6/2, a transgenic mouse model of HD which contains a human HTT gene containing 90 CAG repeats) and wild type mice with a KMO inhibitor, and separately used a mock treatment on both the transgenic mice and wild type mice. The goal of this project is to analyze the RNA-seq data and find gene expression changes associated with the KMO inhibitor

overall_design: 12 wk old R6/2 and WT mice were treated per os with a single dose of 10 mg/kg CHDI-00340246 or vehicle (10% (w/v) HP-β-CD in 50mM Citrate Buffer (pH 5.5)); striatum, cortex, cerebellum and liver tissues were collected 6 hrs following administration. N = 10 per group (5M/5F).

first: Jim

last: Rosinski


title: RNA-Seq data on KMO inhibitor (CHDI-00340246) subchronic treated R6/2 mice.

summary: Dysregulation of the kynurenine (Kyn) pathway has been associated with the progression of Huntington's disease (HD). In particular, elevated levels of the kynurenine metabolites 3-hydroxy kynurenine (3-OH-Kyn) and quinolinic acid (Quin), have been reported in the brains of HD patients as well as in rodent models of HD. The production of these metabolites is controlled by the activity of kynurenine mono-oxygenase (KMO), a mitochondrial outer membrane enzyme which catalyzes the synthesis of 3-OH-Kyn from Kyn.  Thus inhibiting KMO is expected to produce a beneficial effect in Huntington's Disease (HD) patients, hopefully reversing their phenotype to match healthy subjects. To test this effect, we chronically treated a mouse model of HD (R6/2, a transgenic mouse model of HD which contains a human HTT gene containing 90 CAG repeats) and wild type mice with a KMO inhibitor for 8 weeks, and separately used a mock treatment on both the transgenic mice and wild type mice. The goal of this project is to analyze the RNA-seq data and find gene expression changes associated with the KMO inhibitor.

overall_design: 12 wk old R6/2 and WT mice were treated per os twice-daily with 30 mg/kg CHDI-00340246 or vehicle (10% (w/v) HP-β-CD in 50mM Citrate Buffer (pH 5.5)) for 8 weeks (4-12 weeks of age). Cerebral cortex and striatum samples were taken from 23 mice, giving a total of 46 samples (half cortex and half striatum). RNA-seq data was collected on the three sets of mice. There were 8 HD+drug mice, 7 HD+mock mice, and 8 WT+mock mice. The mice were a mix of male and female.


title: A molecular roadmap of the aorta-gonad-mesonephros region reveals BMPER as a novel regulator of HSC maturation

city: Edinburgh

first: Alexander

last: Medvinsky

address: 5 Little France Drive

department: MRC Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh


title: A molecular roadmap of the aorta-gonad-mesonephros region reveals BMPER as a novel regulator of HSC maturation [AGM]

summary: In the developing embryo, haematopoietic stem cells (HSCs) emerge from the aorta-gonad-mesonephros (AGM) region but the molecular regulation of this process is poorly understood. Recently, the progression from E9.5 to E10.5 and polarity along the dorso-ventral axis have been identified as clear demarcations of the supportive HSC niche. To identify novel secreted regulators of HSC maturation, we performed RNA-sequencing over these spatio-temporal transitions in the AGM region, and supportive OP9 cell line.

overall_design: RNA-sequencing profiles of the aorta-gonad-mesonephros region from E9.5 embryos and E10.5 embryos sub-dissected into dorsal (AoD), ventral (AoV) and urogenital ridges (UGR) and pooled from between 15 and 34 embryos in three separate experiments.


title: A molecular roadmap of the aorta-gonad-mesonephros region reveals BMPER as a novel regulator of HSC maturation [OP9]

overall_design: RNA-sequencing profiles of OP9 cells grown in flat, submersed culture or reaggregate and cultured at the liquid-gas interface were compared.