title: K. lactis Ste12-myc ChIP-Seq in pheromone-responding a cells

city: San Francisco

first: Trevor

last: Sorrells

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary: The purpose of this experiment was to determine the genes directly regulated by Ste12 in K. lactis. The experiment was performed in a cells to determine if the a-specific genes were bound by Ste12. Ste12 was tagged with c-myc and was immunoprecipitated with a c-myc antibody. Cells were starved in SD media lacking phosphate for 2 hours, then treated with 10µg/mL K. lactis alpha factor for 2 hours before harvesting.  A control untagged strain was processed in parallel. The experiment was repeated 3 times, and sequenced on an Illumina HiSeq 2500.

overall_design: K. lactis Ste12-myc vs. untagged control under pheromone response condition with 3 technical replicates done on different days


title: RNA-seq influenza infected B6 & D2 mice

status: Public on Jul 06 2015

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

type: Expression profiling by high throughput sequencing

summary: The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suitable to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilizing a dual RNAseq approach that allowed us to investigate both viral and host gene expression in the same individual from a single expression assay after H1N1 infection. We performed a comparative expression analysis to identify (i) correlations between host genes and the viral gene expression, (ii) host genes involved in viral replication, and (iii) genes showing differential expression between the two mouse strains after infection. These genes may be key players involved in regulating the differences in pathogenesis and host defense mechanisms after influenza A infections. Expression levels of influenza segments correlated well with the viral load and may thus be used as surrogates for conventional viral load measurements. Furthermore, we investigated the functional role of two genes, Reg3g and Irf7, in knock-out mice and found that deletion of the Irf7 gene renders the host highly susceptible to H1N1 infection.

overall_design: Female, 10-12 weeks old mice were anesthetized by intra-peritoneal injection with Ketamine/Xylazine (85% NaCl (0.9%), 10% Ketamine, 5% Xylazine) with doses adjusted to the individual body weight. Mice were then intra-nasally infected with 20µl virus solution (2x10³ FFU PR8M) or mock-treated with PBS.

first: Klaus

last: Schughart

first: Ashutosh

middle: K

last: Pandey


title: Tissue-specific changes in Tcrb conformation

status: Public on Jul 08 2015

city: Saint Louis

first: Eugene

middle: M

last: Oltz

state: Missouri

address: 660 Euclid Ave, Campus Box 8118

department: Pathology & Immumonolgy

country: USA

institute: Washington University in St Louis

summary: We report the changes in Tcrb interactome upon transitioning from DN to DP stage of thymocyte development

overall_design: Examination of the interactomes of Eb and Trbv5 viewpoints in RAG-deficient DN and DP thymocytes

first: Olivia

middle: I

last: Koues

first: Kinjal

last: Majumder


title: A CRISPR-based screen identifies genes essential for West Nile virus-induced cell death

status: Public on Jul 05 2015

city: El Paso

first: Haoquan

last: wu

state: Texas

address: 5001 El Paso Dr

department: Biomedical Scienes

institute: Texas Tech Health Sciences Center El Paso

summary: West Nile virus (WNV) causes an acute neurological infection attended by massive neuronal cell death. However, the mechanism(s) behind the virus-induced cell death is poorly understood. Using a library containing 77,406 sgRNAs targeting 20,121 genes, we performed a genome-wide screen using CRISPR/Cas9. HEK 293FT cells were infected with lentivirus expressing sgRNAs and then transfected with a Cas9 expressing construct. WNV infection killed most cells during a 12d selection. Survivor cells were harvested, from which DNA was isolated. The sgRNAs integrated in genome of survivor cells were amplified with PCR. The PCR product was sequenced with Illumina MiSeq to profile the sgRNA population in the survivor cells. Three replicates were conducted. Similarly, a second round of screen was conducted.  Among the genes identified, seven genes, EMC2, EMC3, SEL1L, DERL2, UBE2G2, UBE2J2, and HRD1, stood out as having the strongest phenotype, whose knockout conferred strong protection against WNV-induced cell death with two different WNV strains and in three cell lines. Interestingly, knockout of these genes did not block WNV replication. Thus, these appear to be essential genes that link WNV replication to downstream cell death pathway(s). In addition, the fact that all of these genes belong to the endoplasmic reticulum-associated protein degradation (ERAD) pathway suggests that this might be the primary driver of WNV-induced cell death.

overall_design: Examination of sgRNA populations in survival 293FT cells

last: Wu

first: Hongming

last: Ma


title: Genome-wide mapping of promoter-enhancer interactions with HiCap

city: Stockholm

first: Ilgar

last: Abdullayev

address: Nobels väg 3

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

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

overall_design: Refer to individual Series


title: Genome-wide mapping of promoter-enhancer interactions with HiCap [RNA-seq]

summary: Although the locations of promoters and enhancers have been identified in several cell types, we have yet limited information on their connectivity. We developed HiCap, which combines Hi-C with promoter sequence capture, to enable genome-wide identification of regulatory interactions with single-enhancer resolution. HiCap analyses of mouse embryonic stem cells (mESC) identified promoter-enhancer interactions predictive of gene expression change upon perturbation, opening up for genomic analyses of long-range gene regulation.

overall_design: HiCap was designed by combining Hi-C with with sequence capture (for all promoters) and carried out in mouse embryonic stem cells (mESC)

first: Daniel

last: Ramsköld

first: Pelin

last: Sahlen

first: Rickard

last: Sandberg


title: Expression data from RDI treated T-ALL cells

status: Public on Jul 03 2015

city: Philadelphia

first: Nancy

middle: Asmussen

last: Speck

state: Pennsylvania

address: 421 Curie Blvd, 554 BRB II/III

department: Cell and Developmental Biology

institute: University of Pennsylvania Perelman School of Medicine

summary:
RUNX1 and CBFB, which encode subunits of the core binding factor, are frequent targets of chromosomal aberrations in hematological malignancies. We previously determined that CBFβ  (encoded by CBFB) is important for the transforming activity of the chimeric protein AML1-ETO (RUNX1-RUNX1T1) generated by the t(8;21), and other studies showed that normal Runx1 functions are essential for survival and maintenance of some leukemias lacking RUNX1 or CBFB mutations. Thus, we hypothesized that we could achieve therapeutic efficacy in multiple leukemias by targeting the Runx1:CBFβ interaction with small molecule inhibitors. Using the structure of the DNA binding Runt domain (RD) of Runx1 and its interface with CBFβ, we employed a computational screen of a library of 78,000 drug-like compounds, and further optimized our initial hits. The Runt domain inhibitors (RDIs) bind directly to the RD and disrupt its interaction with CBFβ. These tool compounds reduced growth and induced apoptosis of t(8;21) acute myeloid leukemia (AML) cell lines, and reduced the progenitor activity of mouse and human leukemia cells harboring the t(8;21), but not normal bone marrow cells. The RDIs had similar effects on murine and human T cell acute lymphocytic leukemia (T-ALL) cell lines that did not harbor the t(8;21)
A murine T-ALL cell line 720, derived from Tcf12+/- mouse expressing a Tal1 transgene under the control of the Lck promoter, was especially sensitive to the inhibitors. To gain a better understanding of the mechanism of action of the Runt Domain Inhibitors (RDIs) we performed global gene expression analysis of the highly responsive 720 T-ALL cells following treatment. 720 T-ALL cells were treated with RDIs and harvested 8 hours later, before they underwent apoptosis, and expression was analyzed using microarrays.

overall_design: 720 T-ALL cells were cultured in the presence of Runt Domain Inhibitors for 8 hours, total RNA was then purified and gene expression was analyzed by microarray.

middle: A

first: Zaw

last: Oo


title: Reversal of persistent wound-induced retinal pigmented epithelial-to-mesenchymal transition by the TGFb pathway inhibitor, A-83-01.

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

state: CA

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

summary: Age-related macular degeneration (AMD) is a leading cause of blindness. Most vision loss occurs following the transition from a disease of deposit formation and inflammation to a disease of neovascular fibrosis and/or cell death. Here, we investigate how repeated wound stimulus leads to seminal changes in gene expression and the onset of a perpetual state of stimulus-independent wound response in retinal pigmented epithelial (RPE) cells, a cell-type central to the etiology of AMD. Using a human fetal RPE cell culture model that considers monolayer disruption and subconfluent culture as a proxy for wound stimulus, we have shown that prolonged wound stimulus leads to terminal acquisition of a mesenchymal phenotype post-confluence and altered expression of more than 40% of the transcriptome (see GEO:GSE62224). In contrast, at subconfluence fewer than 5% of expressed transcripts have 2-fold or greater expression differences after repeated passage. Protein-protein and pathway interaction analysis of the genes with passage-dependent expression levels in subconfluent cultures reveals a 158-node interactome comprised of two interconnected modules with functions pertaining to wound response and cell division.  Among the wound response genes are the TGFb pathway activators: TGFB1, TGFB2, INHBA, INHBB, GDF6, CTGF, and THBS1. Significantly, inhibition of TGFBR1/ACVR1B mediated signaling using receptor kinase inhibitors both forestalls and reverses the passage-dependent loss of epithelial potential. In this RNA-Seq based transcriptome analysis we show that the TGFb receptor kinase inhibitor, A-83-01, largely reverses the effects of passage and restores the transcriptome profile of Passage 4 RPE highly similar to that seen in differentiated Passage 0 RPE.

overall_design: Examination of mRNA expression in three different primary fetal RPE donor lines in 32 day old  passage 0, passage 3, and passage 3 treated with 500 nM A-83-01 culutres

middle: J

first: Carolyn

first: Ying-Hsuan

last: Shih

first: Pete

last: Coffey


title: Gene expression profiles in the embryonic midgut of Id2 knockout and wild-type mice

status: Public on Jul 04 2015

city: Shimoaizuki, Matsuoka

first: Kentaro

last: Mori

state: Fukui

country: Japan

institute: University of Fukui

summary: Id2 knockout mice develop heterotopic gastric tissues in the small intestine during development. To gain a mechanistic insight into the cell fate conversion in the Id2 knockout midgut endoderm, we performed microarray analysis using RNA samples extracted from midgut tissues at E13.5.

overall_design: We analyzed the gene expression patterns in the midgut of E13.5 Id2KO embryos compared to that of wild-type by microarrays.

first: Yoshifumi

last: Yokota


title: Genome-wide mapping of promoter-enhancer interactions with HiCap [HiCap]


title: Rapid pairing and subsequent resegregation of distant homologous loci enables double-strand break repair in bacteria

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

summary: Double-strand breaks (DSBs) can lead to the loss of genetic information and cell death. Consequently, cells in all domains of life have evolved mechanisms to repair DSBs, including through homologous recombination. Although recombination has been well characterized, the spatial organization of this process in living cells remains poorly understood. Here, we introduced site-specific DSBs in Caulobacter crescentus, and then used time-lapse microscopy to visualize the homology search, DSB repair, and the resegregation of chromosomal DNA. Even loci tethered to opposite cell poles can efficiently release, pair to enable recombination-based repair, and then resegregate to their original locations. Resegregation occurs independent of DNA replication and without disrupting global chromosome organization. Origin-proximal regions are resegregated by the same machinery, ParABS, used to segregate undamaged chromosomes following DNA replication. In contrast, origin-distal regions efficiently resegregate after a DSB independent of ParABS, and likely without dedicated segregation proteins. Instead, we propose that a physical, spring-like force drives the resegregation of origin-distal loci after DSB repair.

overall_design: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) and double-strand breaks were induced for 1 h by the addition of 500 μM vanillate. For control sample, no vanillate was added. Formadehyde (Sigma) was then added to the final concentration of 1%. Formadehyde crosslinks protein-DNA and DNA-DNA together, thereby capturing the structure of the chromosome at the time of fixation. Fixation was performed at the cell density of OD600 = 0.2. The crosslinking reactions were allowed to proceed for 30 minutes at 25 °C before quenching with 2.5 M glycine at a final concentration of 0.125 M. Fixed cells were then pelleted by centrifugation and subsequently washed twice with 1x M2 buffer (6.1 mM Na2HPO4, 3.9 mM KH2PO4, 9.3 mM NH4Cl, 0.5 mM MgSO4, 10 μM FeSO4, 0.5 mM CaCl2) before resuspending in 1x TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA) to a final concentration of 107 cells per µl. Resuspended cells were then divided into 25 µl aliquots and stored at -80 °C for no more than 2 weeks. Each Hi-C experiment was performed using two of the 25 µL aliquots. Chromosome conformation capture with next-generation seqeuncing (Hi-C) was carried out exactly as described previously (Le et al., 2013 PMID: 24158908)

first: A

last: Badrinarayanan

first: T

middle: B

first: M

middle: T

last: Laub


title: Parent-of-Origin Allelic Expression in the Mouse Cerebellum

status: Public on Jul 07 2015

city: Cambridge

first: Nimrod

middle: Daniel

last: Rubinstein

state: MA

address: 16 Divinity Avenue

department: Molecular and Cellular Biology

institute: Harvard University

summary: The maternal and paternal genomes play different roles in mammalian brains as a result of genomic imprinting, an epigenetic regulation leading to differential expression of the parental alleles of some genes. Here we investigate genomic imprinting in the cerebellum using a newly developed Bayesian statistical model that provides unprecedented transcript-level resolution. We uncover 160 imprinted transcripts, including 41 novel and independently validated imprinted genes. Strikingly, many genes exhibit parentally biased -rather than monoallelic- expression, with different magnitudes according to age, organ, and brain region. Developmental changes in parental bias and overall gene expression are strongly correlated, suggesting combined roles in regulating gene dosage. These findings reveal the remarkable complexity of genomic imprinting, with important implications for understanding the normal and diseased brain.

overall_design: 48 samples of F1 mouse hybrids produced by crossing C57Bl/6J males with Cast/EiJ females (denoted as F1i) and reciprocally crossing Cast/EiJ males and C57Bl/6J famales (denoted as F1r).

first: Julio

middle: D

last: Perez

middle: E

last: Fernandez

first: Catherine

last: Dulac


title: SETDB1 Represses Endogenous and Exogenous Retroviruses in B Lymphocytes [RNA-Seq]

first: Patrick

last: Collins

state: MO

address: 1217 Oakleaf dr

department: Pathology and Immunology

institute: Washington University

summary: Genome stability relies on epigenetic mechanisms that enforce repression of endogenous retroviruses (ERVs). Current evidence suggests that distinct chromatin-based mechanisms repress ERVs in cells of embryonic origin (histone methylation-dominant) versus more differentiated cells (DNA methylation-dominant). However, the latter aspect of this model has not been tested. Remarkably, and in contrast to the prevailing model, we find that repressive histone methylation catalyzed by the enzyme SETDB1 is critical for suppression of specific ERV families and exogenous retroviruses in committed B-lineage cells from adult mice. The profile of ERV activation in SETDB1-deficient B cells is distinct from that observed in corresponding embryonic tissues, despite the loss of repressive chromatin modifications at all ERVs. We provide evidence that, upon loss of SETDB1, ERVs are activated in a lineage-specific manner depending on the set of transcription factors available to target proviral regulatory elements. These findings have important implications for genome stability in somatic cells, as well as the interface between epigenetic repression and viral latency.

overall_design: Expression profiling and bisulfite PCR sequencing in Setdb1 C/C and Setdb1 D/D pro-B cells

middle: L

first: Katherine

last: Kyle

first: Takeshi

last: Egawa

first: Yoichi

last: Shinkai

first: Eugene

last: Oltz


title: IL-10 production and metabolic regulation in macrophages are linked by a TLR-driven CREB-mediated mechanism

city: Freiburg im Breisgau

first: David

last: Sanin

address: Stübeweg 51

department: Immunometabolism

institute: Max-Planck-Institute für Immunbiologie und Epigenetik

type: Genome binding/occupancy profiling by high throughput sequencing

summary: IL-10 is produced by macrophages in diverse immune settings and is critical in limiting immune-mediated pathology. In helminth infections macrophages are an important source of IL-10, however the molecular mechanism underpinning production of IL-10 by these cells is poorly characterized. Here, bone marrow derived macrophages exposed to Excretory/Secretory (E/S) products released by Schistosoma mansoni cercariae rapidly produce IL-10 as a result of MyD88-mediated activation of MEK/ERK/RSK and p38. The phosphorylation of these kinases was triggered by TLR2 and TLR4 and converged on activation of the transcription factor CREB. Uptake of cercarial E/S products by phagocytosis was critical for the production of IL-10 and the activation of MAPKs and CREB, which indicates that interactions between E/S products with TLR2 and TLR4, may be occurring in endosomes. Following phosphorylation, CREB is recruited to a novel regulatory element in the Il10 promoter and is also responsible for regulating a network of genes involved in metabolic processes, such as glycolysis, the tricarboxylic acid cycle and oxidative phosphorylation. Moreover, skin resident tissue macrophages, which encounter S. mansoni E/S products during infection, are the first monocytes to produce IL-10 in vivo early after infection with S. mansoni cercariae. The early and rapid release of IL-10 by these cells has the potential to condition the dermal microenvironment encountered by immune cells recruited to this infection site. To conclude, we propose a mechanism by which CREB regulates the production of IL-10 by macrophages in the skin, but also has a major effect on their metabolic state.

overall_design: CREB binding sites 3 pooled samples of stimulated bone marrow macrophages

first: Catriona

last: Prendergast

first: Adrian

middle: P

last: Mountford


title: Molecular mechanism behind the hematopoiesis-enhancing effect of SRT3025

city: Portland

first: Qingshuo

last: Zhang

state: OR

address: 3181 SW Sam Jackson Park Road

department: Department of Pediatrics

institute: Oregon Health & Science University

summary: We used wild-type 129 mice to understand the mechanism of action behind SRT3025’s hematopoiesis-enhancing effect. Transcriptome analysis of cKit+ Sca1+ Lin- cells (KSL) cells discovered that a list of genes changed their expression levels significantly after SRT3025 administration in wild-type mice. Most notably, the cell cycle regulator p21 was down-regulated by 2.1 fold after SRT3025 administration. It is possible that the transcriptional suppression of p21 by SRT3025 might contribute to the compound’s beneficial effects on hematopoiesis.  It has to be pointed out that, since our transcriptome analysis was limited to hematopoietic stem and progenitor cell population, we cannot rule out the possibility that SRT3025 works through the regulation of other cells such as certain important HSC niche components. The HSC niche is known to regulate stem cell pool size. Among the other genes suppressed by SRT3025, Thbs1 and Fosl2 encode thrombospondin 1 and Fos-like antigen 2, respectively. Both proteins are components of the HSC niche.

overall_design: The goal of this study is to investigate gene expression changes in wild-type 129 mice in response to SRT3025 treatment. The study focuses on bone marrow cKit+ Sca1+ Lin- cells (representing hematopoietic stem and progenitor cells). These cells were sorted twice by FACS to ensure the purity. Cells of interest were collected in Trizol. RNA were isolated using RNAeasy mini prep kit and mRNAs were positively selected using oligo(dT)- Dynobeads. Then RNAseq libraries were then made using Illumina TruSeq RNA Sample Prep Kit and sequeced on an Illumina HiSeq 2000 genome analyzer.

first: Zhang

last: Qingshuo

first: Grompe

last: Markus


title: Chronic growth factor signaling in Acute Myeloid Leukemia is connected to a specific chromatin signature [DNAse-Seq]

city: Freiburg

first: Pierre

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: We performed genome-wide DNaseI hypersensitive site in FLT3-ITD and WT patient samples. We report corresponding gene expression, promoter methylation patterns of differential DHSs as well as differentially occupied TF binding motifs using surrounding DNAseI cut profiles. We examined association patterns of FLT3 ITD and WT AMLs and found that FLT3-ITD signaling is associated with common gene expression and chromatin signature.

overall_design: Examination of genome-wide DNaseI hypersensitivite sites in  FLT3 ITD and WT AML.

first: Sally

last: James

first: Anetta

last: Ptasinska

first: Joaquin

last: Zacarias-Cabeza

first: Maria

middle: R

last: Imperato

first: Salam

last: Assi

first: Jason

last: Piper

first: Sascha

last: Ott

first: Constanze

last: Bonifer

first: Peter

last: Cockerill


title: Genomic Analysis Reveals Distinct Mechanisms and Functional Classes of SOX10-Regulated Genes in Melanocytes

city: Bethesda

first: Laura

last: Baxter

state: MD

address: 35A Convent Drive

department: NHGRI

institute: NIH


title: Integrative ‘omic analysis of experimental bacteremia identifies a metabolic signature that distinguishes human sepsis from SIRS

city: Albuquerque

first: Raymond

last: Langley

state: New Mexico

address: 2425 Ridgecrest Dr

department: immunology

institute: LRRI

summary: Rationale: Sepsis is a leading cause of morbidity and mortality; early diagnosis and prediction of progression is difficult to determine. The integration of metabolomic and transcriptomic data in an experimental model of sepsis may be a novel method to identify molecular signatures of clinical sepsis. Objectives: Develop a biomarker panel for earlier diagnosis and prognostic characterization of sepsis patients to inform personalized clinical management and improve understanding of the pathophysiology of sepsis progression. Methods: Mild to severe sepsis, lung injury and death was recapitulated in Macaca fascicularis by intravenous inoculation of Escherichia coli. Plasma samples were obtained at time of challenge and at one, three, and five days later or time of euthanasia. Necropsy was performed and blood, lung, kidney and spleen samples were obtained. An integrative analysis of comprehensive metabolomic and transcriptomic datasets was performed to identify and parameterize a biomarker panel. Measurements and Main Results: Pathogen invasion, respiratory distress, lethargy and mortality was dose dependent. Severe infection and death were associated with metabolomic and transcriptomic changes indicative of mitochondrial, peroxisomal and liver dysfunction.  Analysis of reciprocal pulmonary transcriptome and plasma metabolome data revealed an integrated host response that suggested dysregulated fatty acid catabolism resulting from peroxisome-proliferator activated receptor signaling. A representative 4-metabolite model effectively diagnosed sepsis in primates (AUC 0.966) and in two human sepsis cohorts (AUC=0.78 and 0.82).  Conclusion: A model to guide early management of patients with sepsis was developed by analysis of reciprocal metabolomic and transcriptomic data in primates that diagnosed sepsis in humans.

overall_design: Transcriptomic analysis of lungs from Cynomolgus macaques challenged with E. coli

first: Shannon

last: Bruse


title: Genetic Variation Determines PPARγ Function and Antidiabetic Drug Response In Vivo [RNA-seq]

status: Public on Jul 02 2015

first: Mitchell

last: Lazar

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: SNPs affecting disease risk often reside in non-coding genomic regions. Here we show that SNPs are highly enriched at mouse strain-selective adipose tissue binding sites for PPARγ, a nuclear receptor for antidiabetic drugs. Many such SNPs alter binding motifs for PPARγ or cooperating factors, and functionally regulate nearby genes whose expression is strain-selective and imbalanced in heterozygous F1 mice. Moreover, genetically-determined binding of PPARγ accounts for mouse strain-specific transcriptional effects of TZD drugs, providing proof-of- concept for personalized medicine related to nuclear receptor genomic occupancy. In human fat, motif-altering SNPs cause differential PPARγ binding, provide a molecular mechanism for some expression quantitative trait loci, and are risk factors for dysmetabolic traits in genome- wide association studies. One PPARγ motif-altering SNP is associated with HDL levels and other metabolic syndrome parameters. Thus, natural genetic variation in PPARγ genomic occupancy determines individual disease risk and drug response.

overall_design:
Comparison of 5 RNA-seq experiments between 2 strains of mice differing in diet and fat depot. One of the experiments was evaluation of the response to a drug Rosiglitazone.
Our RNA-seq data comprises primarily of 4 main experiments:
The first experiment consists of samples taken from 2 strains of mice and their F1 progeny
The samples are all taken from the same depot and when the mice were fed the same chow diet
The second experiment has 2 parts, the first one involves samples taken from the 2 strains from the same eWAT depot when they were kept on a Low Fat Diet (LFD)
This first part serves as a control for the second one in which the mice were treated with a drug, rosiglitazone in conjunction with a LFD
The third experiment consists of samples taken from mice being fed on LFD. The samples are taken from the  eWAT depot for both the strains.
The fourth experiment consists of samples taken from mice being fed on LFD. The samples are taken from the  iWAT depot for both the strains.
We also have a solitary sample from a GRO-seq experiment which was done on eWAT in a B6 strain of mice being fed a LFD
eWAT: epididymal White Adipose Tissue
iWAT: inguinal White Adipose Tissue
LFD-12w: mice were fed a control low fat diet (Research Diet D12450B)
chow: mice were fed standard rodent chow Diet
LFD w/rosiglitazone: Drug rosiglitazone (Cayman Chemicals) was incorporated into low fat diet D12450B by Research Diets at 36mg/kg of diet. Mice received control low fat diet for 10 weeks (age 6-16 weeks), and the rosiglitazone-containing diet versus control diet for the final 2 weeks (until sacrifice at 18 weeks)
LFD control for rosi: mice were fed a control low fat diet (Research Diet D12450B)

last: Soccio

first: Eric

last: Chen

first: Satyajit

last: Rajapurkar

first: Pegah

last: Safabakhsh

first: Jill

last: Marinis

first: Joanna

last: Dispirito

first: Matthew

last: Emmett

first: Erika

last: Briggs

first: Bin

last: Fang

first: Logan

last: Everett

first: Hee-Wong

last: Lim

first: Kyong

last: Won

first: David

last: Steger

first: Ying

last: Wu

first: Mete

last: Civelek

first: Benjamin

middle: F

last: Voight


title: Analysis of wildtype and Xbp1-deficient hematopoietic progenitor cell transcriptomes

city: New York

first: Sarah

last: Bettigole

state: NY

address: 1300 York Avenue, E907

institute: Weill Cornell Medical College

summary:
Purpose:  The goals of this study are to assess the transcriptional networks governed by the transcription factor XBP1 in lineage-uncommitted myeloid progenitors and in eosinophil-committed myeloid progenitors.
Methods:  mRNA profiles of FACS-purified granulocyte-macrophage progenitors (GMPs) from XBP1 flox/flox or XBP1 flox/flox Vav1-Cre mice were generated by sequencing, in biological triplicates, using an Illumina HiSeq2000 sequencer. The Illumina HiSeq2000 sequencer was also used to obtain mRNA profiles of FACS-purified GMPs transduced with the transcription factor GATA2, resorted 36 hours post-transduction, and cultured for 48 hours, again in biological triplicates per genotype.  Sequence data from Illumina's HiSeq2000 sequencer were demuxed to generate FASTQ files for each sample using Illumina's CASAVA pipeline (version 1.8.2). The reads that passed illumina's quality/purity filter were aligned to the mouse genome (Illumina iGenomes mm9 build) using STAR aligner (version 2.3.0) with default parameters. The resulting SAM alignment files were then converted to the BAM file format, sorted and indexed using SAMtools (version 0.1.14).  Mapped reads were counted with the python module HTSeq, and differential expression analyzed with the Bioconductor package DESeq.
Results and conclusions:  By monitoring XBP1-dependent transcriptional changes at different stages of eosinophil development, we demonstrated that classical XBP1-dependent networks such as glycosylation, chaperone production, and ERAD were downregulated in GMPs prior to eosinophil commitment, though there were no major defects in differentiation or survival.  However, mRNA profiling clearly demonstrated that XBP1 deficiency causes a state of cellular stress upon eosinophil commitment.  The eosinophil transcriptome was largely intact, and most dysregulated genes were associated with ER stress.  However key granule protein genes required for eosinophil development such as Prg2 and Epx were selectively downregulated only after eosinophil commitment, but not in pre-committed myeloid progenitors, and this correlated with Ingenuity Pathway Analysis predictions that GATA1 function was impaired.  This study documents the interplay between cellular stress and the ability to maintain key facets of cellular differentiation.

overall_design: Analyses of XBP1-dependent transcriptional networks at two stages of eosinophil development.

first: Laurie

middle: H

last: Glimcher


title: The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: In many developmental systems, morphogenesis is coupled with dramatic changes in spatiotemporal gene expression, often orchestrated by the coordinated action of transcription factors. Development of the social soil amoebae Dictyostelium discoideum proceeds through a sequence of morphological and transcriptional changes, but the role of transcription factors in development is not well understood. GtaC, a GATA-type zinc-finger transcription factor, is essential for Dictyostelium development. It decodes pulsatile extracellular cAMP signals during early development and mediates cell-type differentiation at later stages. Here, we studied the developmental regulatory roles of GtaC through the concerted analysis of temporal ChIP- and RNA-sequencing data from strains that carry different alleles of gtaC. We show that GtaC exhibits temporally distinctive DNA-binding patterns throughout early development, accompanied by largely cotemporaneous expression of its target genes. We also show that GtaC binds DNA in two modes. One of these modes exhibits binding preferences for canonical GATA-like sequences, the regulatory consequences accompanying which is predominantly up-regulation of target gene expression. The other binding mode is mostly associated with down-regulation. Among its targets we find transcription factors that are essential for development as well as genes involved in cAMP signaling and cell-type specification. Our results suggest that GtaC is a master regulator that regulates multiple physiological processes during early development, when Dictyostelium transitions from a group of unicellular amoebae to an integrated multicellular organism.

overall_design: Cotemporaneous transcriptional profiling and ChIP sequencing during early Dictyostelium development

first: Balaji

last: Santhanam

first: Huaqing

last: Cai

first: Peter

middle: N

last: Devreotes

first: Mariko

last: Katoh-Kurasawa


title: Genomic Analysis Reveals Distinct Mechanisms and Functional Classes of SOX10-Regulated Genes in Melanocytes [ChIP-Seq]

first: Laura

last: Baxter

summary: We performed ChIP-Seq analysis of SOX10, histone H3 lysine 27 acetylation (H3K27ac) and H3K27 trimethylation (H3K27me3) in melanocytes to profile the genomic binding sites of SOX10 and the chromatin landscape. In parallel, we generated Sox10 haploinsufficient cell lines using gene knockout approaches and conducted microarray gene expression analysis to identify functional gene targets of SOX10 transcriptional regulation in melanocytes. We demonstrate that SOX10 predominantly engages “open” chromatin, binds to melanocyte enhancer elements and plays a central role in transcriptional activation and repression of functionally distinct classes of genes. Furthermore, we identified cis-regulatory sequence motifs of putative co-regulatory transcription factors that define SOX10-activated and SOX10-repressed target genes. Our results uncover novel mechanisms and roles of SOX10 in global transcriptional regulation of diverse regulatory pathways in the melanocyte lineage.

overall_design: ChIP-seq profiling of SOX10, H3K27ac, and H3K27me3 in the mouse melanocyte cell line melan-Ink4a-Arf-1 (melan-a).

first: Temesgen

last: Fufa

first: Melissa

last: Harris

first: Dawn

last: Watkins-Chow

first: Denise

last: Levy

middle: U

last: Gorkin

first: Lingyun

last: Song

first: Alexias

last: Safi

first: Gregory

last: Crawford

first: Elena

middle: V

last: Sviderskaya

first: Dorothy

middle: C

last: Bennett

first: Andrew

middle: S

last: McCallion

first: Stacie

middle: K

last: Loftus

first: William

last: Pavan


title: ncRNA (non-coding RNA) signature in endothelial cells during hypoxia [RNA-seq]

status: Public on Jul 01 2015

city: Hannover

first: Jan

last: Fiedler

address: Carl-Neuberg-Str. 1

department: Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx

institute: Hannover Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary: To define ncRNA expression in hypoxic endothelial cells, we applied pro-angiogenic hypoxia to cultured endothelial cells. Afterwards, total RNA was isolated and underwent RNA-seq analysis.

overall_design: HUVECs were subjected to normoxic or hypoxic (0.1-0.2% O2) cell culture conditions.

first: Christian

last: Remmele


title: Transcriptomic profiles of M. barkeri Fusaro DSMZ804 and Pyr+ strains

city: Urbana

last: Metcalf

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois at Urbana Champaign

summary: The goal of this work was to elucidate the mechanism by which pyruvate is utilized as a substrate in a mutant strain of Methanosarcina barkeri Fusaro. In this study, using RNAseq we gained insight into how the mutant strain modulate its transcriptional profile in order to use pyruvate as a substrate. In addition, we obtained information on how methanogens respond to pyruvate at the transcriptional level.

overall_design: The mRNA from of Methanosarcina barkeri Fusaro DSMZ804 and Pyr+ strains grown on a variety of substrates (methanol, acetate, methanol-acetate, methanol-pyruvate, methanol-pyruvate-acetate) were harvested sequenced and mapped to M. barkeri genome. Pairwise comparisons between two cell lines of the Pyr+ strain and the DSMZ 804 strain were performed in all substrates tested.

first: Madeline

middle: M

last: López Muñoz

middle: W


title: Exosome-mediated microRNA signaling from breast cancer cells is altered by the anti-angiogenesis agent docosahexaenoic acid (DHA)

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

summary: Background: Docosahexaenoic acid (DHA) is a natural compound with anticancer and anti-angiogenesis activity that is currently under investigation as both a preventative agent and an adjuvant to breast cancer therapy. However, the precise mechanisms of DHA’s anticancer activities are unclear. It is understood that the intercommunication between cancer cells and their microenvironment is essential to tumor angiogenesis. Exosomes are extracellular vesicles that are important mediators of intercellular communication and play a role in promoting angiogenesis. However, very little is known about the contribution of breast cancer exosomes to tumor angiogenesis or whether exosomes can mediate DHA’s anticancer action. Results: Exosomes were collected from MCF7 and MDA-MB-231 breast cancer cells after treatment with DHA. We observed an increase in exosome secretion and exosome microRNA contents from the DHA-treated cells. The expression of 83 microRNAs in the MCF7 exosomes was altered by DHA (>2-fold). The most abundant exosome microRNAs (let-7a, miR-23b, miR-27a/b, miR-21, let-7, and miR-320b) are known to have anti-cancer and/or anti-angiogenic activity. These microRNAs were also increased by DHA treatment in the exosomes from other breast cancer lines (MDA-MB-231, ZR751 and BT20), but not in exosomes from normal breast cells (MCF10A). When DHA-treated MCF7 cells were co-cultured with or their exosomes were directly applied to endothelial cell cultures, we observed an increase in the expression of these microRNAs in the endothelial cells. Furthermore, overexpression of miR-23b and miR-320b in endothelial cells decreased the expression of their pro-angiogenic target genes (PLAU, AMOTL1, NRP1 and ETS2) and significantly inhibited tube formation by endothelial cells, suggesting that the microRNAs transferred by exosomes mediate DHA’s anti-angiogenic action. These effects could be reversed by knockdown of the Rab GTPase, Rab27A, which controls exosome release. Conclusions: We conclude that DHA alters breast cancer exosome secretion and microRNA contents, which leads to the inhibition of angiogenesis. Our data demonstrate that breast cancer exosome signaling can be targeted to inhibit tumor angiogenesis and provide new insight into DHA’s anticancer action, further supporting its use in cancer therapy.

overall_design: Examination of small RNA populations in MCF7 cells and exosomes after DHA treatment.

first: Karla

middle: J

last: Carpenter

last: Berry

first: Ralf

last: Janknecht

last: Dooley

first: Wei-Qun

last: Ding


title: Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte [RNA-seq]

city: Los Angeles

first: Xinjun

last: He

address: 1425 San Pablo St

department: BROAD CIRM Center

institute: University of Southern California

summary: We compared Sox9-association at chondrocyte targets to a broad catalogue of regulatory indicators of chromatin organization and transcriptional activity to determine Sox9’s direct regulatory actions in normal developing chondrocytes. Sox9-associated regions resolve into two distinct regulatory categories. Class I regions closely associate with transcriptional start sites (TSSs). Their targets reflect general regulators of basal cell activities that Sox9 engages indirectly through a likely association with the basal transcriptional complex. In contrast, Class II regions outside of the local TSS domains highlight evolutionarily conserved, active enhancers directing expression of chondrocyte specific target genes, though DNA binding of Sox9-dimers at target sites with sub-optimal binding affinity. The level of associated chondrocyte gene expression correlates with the number of enhancer modules around the target gene and grouping into super-enhancer clusters. Comparison of Sox9 programs between neural crest and mesoderm-derived chondrocytes points to similar modes of chondrocyte specification in distinct chondrocyte lineages. These data provide the first insight into mammalian Sox family actions at the genome scale in the vivo setting. The resulting enhancer sets provide a key resource for further dissection of the regulatory programs of mammalian chondrogenesis.

overall_design: Incorportation of ChIP-seq data of Sox9 and histone modification marks for chromatin status together with micorarray gene expression profiling in neonatal mice chondrocytes to uncover Sox9 regulatory system. Overexpression of Sox9 with a control of EGFP in human fibroblasts to identify the direct targets of Sox9 regulatory system

first: Shinsuke

last: Ohba

first: Hironori

last: Hojo

last: McMahon


title: Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte [ChIP-seq]

summary: We compared Sox9-association at chondrocyte targets to a broad catalogue of regulatory indicators of chromatin organization and transcriptional activity to determine Sox9’s direct regulatory actions in normal developing chondrocytes. Sox9-associated regions resolve into two distinct regulatory categories. Class I regions closely associate with transcriptional start sites (TSSs). Their targets reflect general regulators of basal cell activities that Sox9 engages indirectly though a likely association with the basal transcriptional complex. In contrast, Class II regions outside of the local TSS domains highlight evolutionarily conserved, active enhancers directing expression of chondrocyte specific target genes, though DNA binding of Sox9-dimers at target sites with sub-optimal binding affinity. The level of associated chondrocyte gene expression correlates with the number of enhancer modules around the target gene and grouping into super-enhancer clusters. Comparison of Sox9 programs between neural crest and mesoderm-derived chondrocytes points to similar modes of chondrocyte specification in distinct chondrocyte lineages. These data provide the first insight into mammalian Sox family actions at the genome scale in the vivo setting. The resulting enhancer sets provide a key resource for further dissection of the regulatory programs of mammalian chondrogenesis.


title: Variable glutamine-rich repeats modulate the function of the transcriptional regulator SSN6

city: Leuven

first: Kevin

last: Verstrepen

address: Gaston Geenslaan 1

country: Belgium

institute: VIB/KULeuven

summary: Excessive expansions of glutamine (Q)-rich repeats in various human proteins are known to result in severe neurodegenerative disorders such as Huntington’s disease and several ataxias. However, the physiological role of these repeats and the consequences of more moderate repeat variation, remain unknown. Here, we demonstrate that Q-rich repeats are highly enriched in eukaryotic transcription factors where they act as functional modulators. Incremental changes in the number of repeats in the yeast transcriptional regulator Ssn6p (Cyc8p) result in systematic, repeat-length dependent variation in expression of target genes that result in direct phenotypic changes. The function of Ssn6p increases with its repeat number, until a certain threshold where further expansion leads to aggregation. Quantitative proteomic analysis reveals that the Ssn6p repeats affect its solubility and interactions with Tup1 and other regulators. Thus, Q-rich repeats are dynamic functional domains that modulate a regulator’s innate function, with the inherent risk of pathogenic repeat expansions.

overall_design: Transcriptome profiles of two biological replicates of each SSN6 tandem repeat number variant and the WT grown in a glucose-rich medium (4% glucose - glu4) or in a glucose-starved medium (0 % glucose - glu0)

first: Rita

last: Gemayel


title: Specificity quantification of Glucocorticoid receptor binding using high-throughput sequencing

city: Palo Alto

first: Zheng

last: Zuo

address: Stanford

department: Genetics

institute: Stanford university

summary: In this work, we used our recently developed method Spec-seq to characterize the binding specificity of Glucocorticoid receptor in vitro.

overall_design: This GR Spec-seq experiment has been run twice separately (Dec 2014 and Mar 2015) with different library compositions. The basic workflow is the same as our previous work for lac repressor published in  Genetics 198.3 (2014): 1329-1343. Recombinant human GR protein was used to facilitate in vitro DNA-binding and separation experiments. Bound and Unbound DNA fragments were separated in EMSA gels, purified, barcoded for further Illumina sequencing.  An initial experiment was performed using the putative consensus sequence: AGAACA GGG TGTTCT; randomized library 1: AGAACN NSN NGTTCT [diversity =512]; randomized library 2: AGAANN GGG NNNTCT [diversity = 1024]; randomized library 3: AGAACA GGG TGNNNN [diversity =256]; randomized library 4: AGAACA GGGC NNNTCT [diversity = 64]. The initial total library diversity was ~1853 with a library composition of 10% positive control sequence + randomized libraries 1-4 + 5% negative control sequence. A 5th library containing 2304 sequences based on DDNACW KKN KGTTCT, where D="not C", N="any base", W="A or T" and K="G or T" was subsequently prepared and analyzed using similar ratios of control sequences. Binding conditions for EMSA were 100ng FAM-labelled dsDNA+ 0/0.5/1/2/4uM GR DBD protein for each lane, 1X NEB buffer 4. GR DBD was prepared as previously described. The EMSA was performed using a 9% 33:1 acrylamide gel and TB buffer, and was run at 200V for 30mins @ 0 degrees C. The 2uM protein lane used for final sequencing. Bound/unbound fractions resulting from EMSA of these libraries and conditions were used to generate PWMs as described. The GR PWM that was generated through this analysis was used to define relative binding energies using the patser program (35), which can be accessed online at (http://stormo.wustl.edu/consensus/cgi-bin/Server/Interface/patser.cgi ). Derived binding affinities are proportional to the inverse of the natural log of the calculated energies.

first: Gary

last: Stormo


title: High-throughput sequencing of Moringa oleifera microRNAs: a bioinformatics and functional approach for cross-kingdom regulation

city: Rome

first: Stefano

last: Pirro'

address: Via della Ricerca Scientifica

department: Biology

country: Italy

institute: University of Rome "Tor Vergata"

summary: MicroRNAs (miRNAs) are endogenous, noncoding, smallRNAs that regulate gene expression at the post-transcriptional level during plant development, growth and seed germination. Among all medicinal plants, Moringa oleifera is one of the most useful trees for which, despite its diffusion, no information about its miRNAs and their respective target genes is available. In this research, we report results obtained from a high-throughput sequencing analysis performed with the Illumina platform. A total of 31,290,964 raw reads were produced from M. oleifera seed smallRNA library. First, we found 99 conserved miRNAs and 43 novel ones that we partially validated by qRT- PCR. Second, by comparing their expression abundances with those of other common plants, we identified 20 conserved M. oleifera miRNAs. For both these results an in silico analysis allowed us to predict some of their targets which in turn allowed us to link them to a wide range of physiological processes. Based on qRT-PCR expression analyses, we reported the expression profile of some selected conserved miRNAs in different M. oleifera tissues (roots, stems and leafs). We compared the most conserved miRNAs found in Moringa with those of other edible plants, such as Olea europaea and Brassica rapa. Furthermore, by taking advantage of a recently developed web- application based on an algorithm that compares plants and mammalian miRNAs, we identify a few possible plant miRNAs with functional homologies with mammalian ones. We used the 20 most abundant M. oleifera miRNAs to conduct a preliminary analysis to investigate potential cross-kingdom gene regulation. To our knowledge, this is the first report of M. oleifera miRNAs that uses high-throughput sequencing analysis. Our analysis increases the amount of information about plant miRNAs currently available and it can help us understanding the molecular mechanism of this medical plant.

overall_design: microRNA profile of M. oleifera seed, germinated on paper soaked in sterile water.

last: Pirro

first: Andrea

last: Galgani


title: Histone variant H2A.Z.2 mediates proliferation and drug sensitivity of malignant melanoma [ChIP-seq]

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: Here we report a novel role for H2A.Z.2 (H2AFV) as a mediator of cell proliferation and sensitivity to targeted therapies in malignant melanoma. While both H2A.Z.1 and H2A.Z.2 are highly expressed in metastatic melanoma and correlate with decreased patient survival, only H2A.Z.2 deficiency results in impaired cellular proliferation of melanoma cells, which occurs via a G1/S arrest. Integrated gene expression and ChIP-seq analyses revealed that H2A.Z.2 positively regulates E2F target genes, and that such genes acquire a distinct H2A.Z occupancy signature over the promoter and gene body in metastatic melanoma cells. We further identified the BET family member BRD2 as an H2A.Z-interacting protein in melanoma cells, and demonstrate that H2A.Z.2 silencing cooperates with BET inhibition to induce cell death.

overall_design: Cross-linked ChIP in SKmel147 melamoma cell line for E2F1 and BRD2

first: Chiara

last: Vardabasso

first: Alexandre

last: Gaspar-Maia

first: Dan

last: Hasson

first: Sebastian

last: Pünzeler

first: David

last: Valle-Garcia

first: Tobias

last: Straub

first: Eva

last: Keilhauer

first: Thomas

last: Strub

first: Joanna

last: Dong

first: Taniya

last: Panda

first: Chi-Yeh

last: Chung

first: Jonathan

last: Yao

first: Rajendra

last: Singh

first: Miguel

last: Segura

first: Barbara

last: Fontanals-Cirera

first: Amit

last: Verma

first: Matthias

last: Mann

last: Hernando

first: Sandra

middle: B

last: Hake


title: Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte

first: Xinjun

last: He

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Recruitment of RNA Polymerase II by the pioneer transcription factor PHA-4

first: Erel

last: Levine

address: 52 Oxford St

institute: Harvard University

summary: Using staged embryos, we find many more genes with poised RNA polymerase than had been observed previously in C. elegans embryos, suggesting that early embryos accumulate poised PolII, and that poising is dynamic.

overall_design: Embryos were staged at the 8E and Bean stages of development prior to ChIP-seq

first: Hui

middle: T

last: Hsu

first: Susan

last: Mango


title: Histone variant H2A.Z.2 mediates proliferation and drug sensitivity of malignant melanoma [native ChIP-seq]

first: Emily

last: Bernstein

overall_design: Mononucleosomes from SK-mel147 (wt and stably expressing eGFP-H2A. eGFP-H2A.Z.1 and eGFP-H2A.Z.2) and melanocytes were isolated for ChIP with H2A.Z antibody or GFP trap beads (Chromotek).

first: Chiara

last: Vardabasso

first: Alexandre

last: Gaspar-Maia

first: Dan

last: Hasson

first: Sebastian

last: Pünzeler

first: David

last: Valle-Garcia

first: Tobias

last: Straub

last: Keilhauer


title: Genetic Variation Determines PPARγ Function and Antidiabetic Drug Response In Vivo

city: Philadelphia

first: Mitchell

last: Lazar


title: ChIP-seq analysis of SREB during yeast phase growth of Blastomyces dermatitidis at 37oC

city: Madison

first: Gregory

last: Gauthier

state: WI

address: 1550 Linden Drive

department: Medicine

institute: University of Wisconsin - Madison

summary: ChIP-seq analysis was used to identify B. dermatitidis genes bound by the GATA transcription factor encoded by SREB during growth as yeast at 37oC

overall_design: SREB was engineered to contain an in-frame 3x-hemagglutinin (HA) epitope tag at the C-terminus. The SREB-3xHA construct was under control of its native promoter and contained the 3-untranslated region.  Using Agrobacterium tumefaciens, B. dermatitidis ATCC 26199 was transformed with the SREB-3xHA construct (referred to a SREB-3xHA strain in this document).  The SREB-3xHA construct was functional because retransformation of SREBΔ with the construct complented the null mutant. Chromatin was extracted and sheared from ATCC 26199 and SREB-3xHA yeast grown in liquid Histoplasma macrophage medium (HMM) containing 10 μM iron sulfate (FeSO4) at 37oC.  ATCC 26199 was the untagged control strain.

first: Amber

last: Mary

first: Sunduz

last: Keles


title: Genetic Variation Determines PPARγ Function and Antidiabetic Drug Response In Vivo [ChIP-seq]

overall_design:
6 ChIP-seq experiments conducted in mice and 5 in human subjects. Deep sequencing carried out using Illumina HiSeq2000 and the Solexa Analysis Pipeline
eWAT; epididymal White Adipose Tissue
iWAT; inguinal White Adipose Tissue
12wLFD; mice were fed a control low fat diet (Research Diet D12450B)
chow; mice were fed standard rodent chow Diet
GR; Glucocorticoid receptor

first: Raymond

last: Soccio

first: Eric

last: Chen

first: Satyajit

last: Rajapurkar

first: Pegah

last: Safabakhsh

first: Jill

last: Marinis

first: Joanna

last: Dispirito

first: Matthew

last: Emmett

first: Erika

last: Briggs

first: Bin

last: Fang

first: Logan

last: Everett

first: Hee-Wong

last: Lim

first: Kyong

last: Won

last: Steger

first: Ying

last: Wu

first: Mete

last: Civelek

first: Benjamin

last: Voight


title: laryngo-pharyngeal tumor RNA-seq study for both mRNA and miRNA

city: new delhi

first: binay

last: panda

address: 1649A vasant kunj

country: India

institute: ganit labs foundation

summary:
Cancers of the upper aero-digestive tracts (oral cavity, pharynx and larynx) are the sixth most common cancer worldwide. Laryngo-pharyngeal squamous cell carcinomas are one of the most common cancers in this category. Despite recent advances in the field of cancer research using high-throughput tools, the information, especially on tumors of hypopharynx, is relatively scarce. We have used next-generation sequencing and computational biology to study both the genes and miRNA from laryngo-pharyngeal tumors.
Laryngo-pharyngeal squamous cell carcinomas are one of the most common head and neck cancers. Despite the presence of a large body of information, molecular biomarkers are not currently used in the diagnosis, treatment and management of patients for this group of cancer. Here, we have profiled expression of genes and microRNAs of larynx and hypopharynx tumors using high-throughput sequencing experiments. We found that matrix metalloproteinases along with SCEL, CRNN, KRT4, SPINK5, and TGM3 among others have significantly altered expression in these tumors. Alongside gene expression, the microRNAs hsa-miR-139, hsa-miR-203 and the hsa-miR-424/503 cluster have aberrant expression in these cancers. Using target genes for these microRNAs, we found the involvement of pathways linked to cell cycle, p53 signaling, and viral carcinogenesis significant ( *P*-values 10-13, 10-9 and 10-7 respectively). Finally, using an ensemble machine-learning tool, we discovered a unique 8-gene signature for this group of cancers that differentiates the group from the other subsites of head and neck. We investigated the role of promoter methylation in one of these genes, WIF1, and found no correlation between DNA methylation and down-regulation of WIF1. We validated our findings of gene expression, 8-gene signature and promoter methylation using q-PCR, data from TCGA and q-MSP respectively.

overall_design:
RNA-seq experiments in tumors of larynx and hypopharynx for discovery of gene and miRNA expression

Please note that processed data files were not provided since they are available through the journal's website. However a brief description of each processed data is provided in the 'readme.txt'.


title: Omic Personality: Implications of Stable Transcript and Methylation Profiles for Personalized Medicine [miRNA-Seq]

city: Atlanta

first: Greg

last: Gibson

state: Georgia

address: North Ave NW

department: School of Biology

institute: Georgia Institute of Technology

summary:
Background:   Personalized medicine is predicated on the notion that individual biochemical and genomic profiles are relatively constant in times of good health and to some extent predictive of disease or therapeutic response.  We report a pilot study quantifying gene expression and methylation profile consistency over time, addressing the reasons for individual uniqueness, and its relation to N=1 phenotypes.
Methods:  Whole blood samples from 4 African American women, 4 Caucasian women, and 4 Caucasian men drawn from the Atlanta Center for Health Discovery and Well Being study at three successive 6-month intervals were profiled by RNASeq, miRNASeq, and Illumina Methyl-450 arrays.  Standard regression approaches were used to evaluate the proportion of variance for each type of omic measure that is among individuals, and to quantify correlations among measures and with clinical attributes related to wellness.
Results:  Longitudinal omic profiles are in general highly consistent over time, with an average of 67% of the variance in transcript abundance, 42% of CpG methylation level (but 88% for the most differentiated CpG per gene), and 50% of miRNA abundance among individuals, which are all comparable to 74% of the variance among individuals for 74 clinical traits.  One third of the variance can be attributed to differential blood cell type abundance, which is also fairly stable over time, and a lesser amount to eQTL effects, whereas seven conserved axes of covariance that capture diverse aspects of immune function explain over half of the variance.  These axes also explain a considerable proportion of individually extreme transcript abundance, namely approximately 100 genes that are significantly up- or down-regulated in each person and are in some cases enriched for relevant gene activities that plausibly associate with clinical attributes.  A similar fraction of genes have individually divergent methylation levels, but these do not overlap with the transcripts, and fewer than 20% of genes have significantly correlated methylation and gene expression.
Conclusions:  People express an “omic personality” consisting of peripheral blood transcriptional and epigenetic profiles that are constant over the course of a year and reflect various types of immune activity.  Baseline genomic profiles can provide a window into the molecular basis of traits that might be useful for explaining medical conditions or guiding personalized health decisions.

overall_design: Whole blood samples from 12 subjects drawn from the Atlanta Center for Health Discovery and Well Being study at three successive 6-month intervals were profiled by RNASeq, miRNASeq, and Illumina Methyl-450 arrays.

first: Rubina

last: Tabassum

first: Ambily

last: Sivadas

first: Vartika

last: Agrawal

first: Haozheng

last: Tian

first: Dalia

last: Arafat


title: Omic Personality: Implications of Stable Transcript and Methylation Profiles for Personalized Medicine

type: Methylation profiling by genome tiling array


title: Histone variant H2A.Z.2 mediates proliferation and drug sensitivity of malignant melanoma [RNA-seq]

first: Emily

last: Bernstein

overall_design: Expression levels for non tumorigenic (Melanocytes) and human melanoma cell line SKmel147, before and after JQ1 treatement

first: Chiara

last: Vardabasso

first: Alexandre

last: Gaspar-Maia

first: Dan

last: Hasson

first: Sebastian

last: Pünzeler

first: David

last: Valle-Garcia

first: Tobias

last: Straub

first: Eva

last: Keilhauer

first: Thomas

last: Strub

first: Joanna

last: Dong

first: Taniya

last: Panda

first: Chi-Yeh

last: Chung

first: Jonathan

last: Yao

first: Rajendra

last: Singh

first: Miguel

last: Segura

first: Barbara

last: Fontanals-Cirera

first: Amit

last: Verma

first: Matthias

last: Mann

last: Hernando

first: Sandra

last: Hake


title: Methods comparison for ribosome profiling

city: Durham

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

summary: Assessment of the effecacy of direction extraction of ribosome-protected mRNA fragments for ribosome profiling

overall_design: Immortalized human lymphocytes were analyzed by ribosome profiling protocols with or without ribosome purification


title: Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori

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: In this study transcriptional start sites (TSS) for H. pylori 26695 were determined

overall_design: To detect the complement of transcripts expressed from H. pylori, we collected three independent biological replicates (B1 – B3) from 26695 wild type strain grown to mid-exponential (OD 600 ~0.6) phase under microaerophilic conditions at 37°C in BHI medium. For all three samples, total RNA was extracted and subjected to differential RNA-seq (dRNA-seq) library preparation for primary transcriptome analysis as described previously (Sharma et al., 2010). Specifically, prior to cDNA library construction half of each RNA sample was treated with 5’ terminator exonuclease (+TEX samples), which degrades RNAs containing a 5’-monophosphate (5’-P) and, thus, enriches for primary transcripts containing 5’-triphosphates (5’-PPP). The other half of each sample was left untreated (-TEX samples) and thus contains both primary transcripts (5’-PPP) and processed RNAs (5’-P).

first: Thorsten

last: Bischler

first: Hock Siew

last: Tan

first: Kay

last: Nieselt

first: Cynthia

last: Sharma


title: The MEF2B Regulatory Network - RNA-seq data

city: Vancouver

first: Patrick

last: Plettner

state: BC

address: 100-570 West 7th Avenue

country: Canada

institute: BC Cancer Agency GSC

summary: Myocyte enhancer factor 2B (MEF2B) is a transcription factor with somatic mutation hotspots at K4, Y69 and D83 in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). The recurrence of these mutations indicates that they may drive lymphoma development. However, inferring the mechanisms by which they may drive lymphoma development was complicated by our limited understanding of MEF2B’s normal functions. To expand our understanding of the cellular activities of wildtype (WT) and mutant MEF2B, I developed and addressed two hypotheses: (1) identifying genes regulated by WT MEF2B will allow identification of cellular phenotypes affected by MEF2B activity and (2) contrasting the DNA binding sites, effects on gene expression and effects on cellular phenotypes of mutant and WT MEF2B will help refine hypotheses about how MEF2B mutations may contribute to lymphoma development. To address these hypotheses, I first identified genome-wide WT MEF2B binding sites and transcriptome-wide gene expression changes mediated by WT MEF2B. Using these data I identified and validated novel MEF2B target genes.  I found that target genes of MEF2B included the cancer genes MYC, TGFB1, CARD11, NDRG1, RHOB, BCL2 and JUN.  Identification of target genes led to findings that WT MEF2B promotes expression of mesenchymal markers, promotes HEK293A cell migration, and inhibits DLBCL cell chemotaxis. I then investigated how K4E, Y69H and D83V mutations change MEF2B’s activity. I found that K4E, Y69H and D83V mutations decreased MEF2B DNA binding and decreased MEF2B’s capacity to promote gene expression in both HEK293A and DLBCL cells. These mutations also reduced MEF2B’s capacity to alter HEK293A and DLBCL cell movement. From these data, I hypothesize that MEF2B mutations may promote DLBCL and FL development by reducing expression of MEF2B target genes that would otherwise function to help confine germinal centre B-cells to germinal centres. Overall, my research demonstrates how observations from genome-scale data can be used to identify cellular effects of candidate driver mutations. Moreover, my work provides a unique resource for exploring the role of MEF2B in cell biology: I map for the first time the MEF2B ‘regulome’, demonstrating connections between a relatively understudied transcription factor and genes significant to oncogenesis.

overall_design: RNA-seq was performed on cells expressing V5 tagged WT or mutant MEF2B and on empty vector control cells. One biological replicates was performed on cell treated with either ionomycin or a solvent-only control.

first: Julia

last: Pon

first: Marco

middle: A

last: Marra


title: Bacteria differently regulate mRNA abundance to specifically respond to various stresses

city: Potsdam

first: Alexander

last: Bartholomaeus

address: Telegrafenberg C

department: Department 3 Geochemie

institute: Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences

summary: Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational level. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up- and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly-translated transcripts with high copy numbers, allowing reallocation of translation resources to undegraded and newly synthesised mRNAs

sample_organism: Escherichia coli str. K-12 substr. MC4100

overall_design: Comparing global transcriptional and translational control by mRNA-Seq and Ribosome Profiling (mRNA-Seq of ribosome protected fragments – RPF)

last: Bartholomäus

first: Ivan

last: Fedyunin

first: Peter

last: Feist

first: Celine

last: Sin

first: Gong

last: Zhang

first: Angelo

last: Valleriani

first: Zoya

last: Ignatova


title: The MEF2B Regulatory Network


title: Molecular phenotyping of a test compound (small-molecule neurotransmitter receptor antagonist) in primary human hepatocytes

city: Basel

first: Jitao David

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

summary: Expression profiles of 917 pathway repoter genes were determined by AmpliSeq-RNA in primary human hepatocytes treated with Diclofenac and a test compound 3 hours after treatment.

overall_design: Vehicle control, diclofenac, and three doses of the test compound (small-molecule neurotransmitter receptor antagonist) were applied to three primary cell lines, with three biological replicates in each group. In some treatment groups read-outs were only available for two samples. All together 41 samples were profiled.

first: Jitao

middle: D

first: Erich

last: Kueng

first: Franziska

last: Boess

first: Ulrich

last: Certa

first: Martin

last: Ebeling


title: Omic Personality: Implications of Stable Transcript and Methylation Profiles for Personalized Medicine [RNA-Seq]

first: Greg

last: Gibson

first: Rubina

last: Tabassum

first: Ambily

last: Sivadas

first: Vartika

last: Agrawal

first: Haozheng

last: Tian

first: Dalia

last: Arafat


title: Analysis of the honey bee brain transcriptome from nurses and forager bees

city: Jeddah

first: Vladimir

last: Bajic

state: Jeddah

address: Thuwal

department: CEMSE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology (KAUST)

summary: New insights into the transcriptional regulation of behavioral plasticity in honey bees gained by analyzing brain genes expression with the CAGEscan technique that involves identification of specific transcription factors, cis regulatory motifs and alternate transcriptional start sites

overall_design: Examination of 2 different types of Honey Bee Apis Mellifera samples (Nurse and Foragers)

first: Abdullah

last: Khamis

first: Adam

middle: R

last: Hamilton

first: Yulia

last: Medvedeva

first: Tanvir

last: Alam

first: Intikhab

first: Magbubah

last: Essack

first: Boris

last: Umilny

last: Jankovic

first: Nicholas

middle: L

last: Naeger

first: Makoto

last: Suzuki

first: Matthias

last: Harbers

first: Gene

middle: E

last: Robinson


title: Pre-ovulatory follicle size modulates the periovulatory endocrine environment and endometrial tissue phenotype in cattle

city: Pirassununga

first: Mario

last: Binelli

state: SP

address: Rua Duque de Caxias Norte, 255

department: department of animal reproduction

country: Brazil

institute: University of Sao Paulo (USP)

summary:
Purpouse: Aims of this study were (1) to characterize the endometrial transcriptome, (2) to identify functional pathways, and (3) to molecularly characterize selected pathways overrepresented in the endometrium of day 7 post-ovulation induction of cows treated to ovulate larger versus smaller follicles
Methods: Seventy-four multiparous, nonlactating, presynchronized Nelore cows received a progesterone-releasing device and estradiol benzoate on Day–10 (D−10). Animals received cloprostenol (large follicle-large CL group; LF-LCL; N = 35) or not (small follicle-small CL group; SF-SCL; N = 39) on D−10. Progesterone devices were withdrawn and cloprostenol administered 42 to 54 hours (LF-LCL) or 30 to 36 hours (SF-SCL) before GnRH treatment (D0). Tissues were collected at slaughter on D7. Transcriptional profiling of the endometrial tissue was performed by RNA-seq and protein markers for proliferation and apoptosis were identified by immunohistochemistry.
Results: Functional enrichment data indicated that LF-LCL endometrium expressed greater abundance of genes associated with biosynthetic and metabolic processes, whereas SF-SCL endometrium .gene expression profile was biased towards cell proliferation. Extracellular matrix-related genes were also upregulated in the SF-SCL endometrium suggesting reorganization of the ECM towards a proliferation permissive phenotype. Immunohistochemistry data confirmed the greater proliferative activity observed in SF-SCL endometrium I comparison to LF-LCL counterparts, and indicated a time-related transition within experimental group. In conclusion, the periovulatory endocrine milieu regulates bovine endometrial gene expression. Furthermore, timing and amplitude of ovarian steroid secretion pattern seem to determine the transition from a proliferation permissive to a biosynthetic and metabolically active endometrial phenotype, which may be associated with the preparation of an optimally receptive uterine environment.
Conclusion: the periovulatory endocrine milieu affected D7 endometrial molecular signature. Main pathways affected were related to cell proliferation, ECM composition and remodeling, biosynthetic and metabolic processes. Reported data further suggest that the endometrial tissue from LF-LCL cows experienced an early proliferative phase (D4), whereas the SF-SCL endometrium, exposed to a distinct periovulatory endocrine environment, expressed a delayed onset of the proliferative activity (D7).

overall_design: endometrial mRNA profiles of endocrine manipulated cows were generated by deep sequencing using Illumina HiScanSQ platform

first: Fernando

last: Mesquita

first: Roney

last: Ramos

first: Sonia

last: Andrade

first: Gustavo

last: Gasparin

first: Angela

last: Gonella

first: Luiz

last: Lehmann Coutinho


title: Opposing Roles of STAT1 and STAT3 in IL-21 Function in CD4+ T cells

city: Bethesda

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Interleukin-21 (IL-21) is a type 1 cytokine essential for immune cell differentiation and function. Although IL-21 can activate several STAT family transcription factors, previous studies focused mainly on the role of STAT3 in IL-21 signaling. Here, we investigated the role of STAT1 and show that STAT1 and STAT3 have at least partially opposing roles in IL-21 signaling in CD4+ T cells. IL-21 induced STAT1 phosphorylation, and this was augmented in Stat3-deficient CD4+ T cells. RNA-Seq analysis of CD4+ T cells from Stat1- and Stat3-deficient mice revealed that both STAT1 and STAT3 are critical for IL-21-mediated gene regulation. Expression of some genes, including Tbx21 and Ifng, was differentially regulated by STAT1 and STAT3, and interestingly, ChIP-Seq analysis showed that STAT3 binding at Tbx21 and Ifng loci was attenuated in Stat1-deficient cells. Moreover, opposing actions of STAT1 and STAT3 on IFN- expression in CD4+ T cells were demonstrated in vivo during chronic lymphocytic choriomeningitis (LCMV) infection. Finally, IL-21-mediated induction of STAT1 phosphorylation, as well as IFNG and TBX21 expression, were higher in CD4+ T cells from patients with autosomal dominant hyper-IgE syndrome (AD-HIES), which is caused by STAT3 deficiency. These data indicate an interplay between STAT1 and STAT3 in fine-tuning IL-21 actions.

overall_design: Genome-wide transcription factors mapping and binding of STAT3 in mouse CD4+ T cells in both WT and Stat1-deficient mice. RNA-Seq is performed in mouse CD4+ T cells in WT, Stat1-deficient and Stat3-deficient mice.

first: Chi-Keung

last: Wan

first: Allison

last: Andraski

first: Rosanne

last: Spolski

first: Majid

last: Kazemian

first: Jangsuk

last: Oh

first: Leigh

last: Samsel

first: Phillip

last: Swanson

first: Dorian

last: McGavern

first: Elizabeth

middle: P

last: Sampaio

first: Alexandra

middle: F

last: Freeman

first: Joshua

last: Milner

first: Steven

last: Holland

first: Warren

last: Leonard


title: The MEF2B Regulatory Network - H3K27ac and H3K4me3 ChIP-seq data

first: Patrick

last: Plettner

overall_design: ChIP-seq was performed using H3K27ac and H3K4me3 antibodies on cells expressing V5 tagged WT MEF2B and on empty vector control cells. Two biological replicates were performed.

first: Julia

last: Pon

first: Marco

last: Marra


title: transcriptome of Amycolatopsis mediterranei U32 in the Bennet medium with or without nitrate

city: Shanghai

first: shao

last: zhihui

address: Fenglin Road 300

country: China

institute: Institute of Plant Physiology & Ecology, SIBS, CAS

summary: We reported transcriptome profiles of rifamycin SV-produced strain Amycolatopsis mediterranei U32 in the Bennet medium with or without 80 mM nitrate in different cultivation stage. By comparative analysis of  genome-wide gene expression in these conditions, we found that the mechanism of high production of rifamycin SV induced by nitrate could be elucidated.

overall_design: Examination of 2 time-course transcription in 2 different nitrogen source conditions

first: Shao

last: Zhihui

first: Wang

last: Jin


title: The MEF2B Regulatory Network - MEF2B-V5 ChIP-seq data

overall_design: ChIP-seq was performed using a V5 antibody on cells expressing V5 tagged WT and mutant MEF2B. Two biological replicates were performed on WT, K4E, Y69H and D83V MEF2B-V5 cells.


title: MicroRNA-224 promotes tumor progression in non-small cell lung cancer

city: Columbus

first: wei

last: meng

state: Ohio

address: 400 W12 street

department: Radiation Oncology

institute: The Ohio State University

summary: Lung cancer is the leading cause of cancer-related deaths worldwide. Despite advancements and improvements in surgical and medical treatments, the survival rate of lung cancer patients remains frustratingly poor. Local control for early stage non-small cell lung cancer (NSCLC) has dramatically improved over the last decades for both operable and inoperable patients. However, the molecular mechanisms of NSCLC invasion leading to regional and distant disease spread remain poorly understood. Here we identify miR-224 to be significantly up-regulated in NSCLC tissues, in particular in resected NSCLC metastasis. Increased miR-224 expression promotes cell migration, invasion and proliferation by directly targeting the tumor suppressors, TNFAIP1 and SMAD4. In concordance with in vitro studies, mouse xenograft studies validated that miR-224 function as a potent oncomiR in NSCLC in vivo. Moreover, we found promoter hypomethylation and activated ERK signaling to be involved in the regulation of miR-224 expression in NSCLC. Up-regulated mir-224 thus facilitates tumor progression by shifting the equilibrium of the partially antagonist functions of SMAD4 and TNFAIP1 towards enhanced invasion and growth in NSCLC. Our findings indicate that targeting miR-224 could be effective in the treatment of certain lung cancer patients

overall_design: Oncogenic role of miR-224 in lung cancer

first: Ri

last: Cui

first: Wei

last: Meng

first: Hui-Lung

last: Sun

first: Taewan

last: Kim

first: Zhenqing

last: Ye

first: Matteo

last: Fassan

first: Young-Jun

last: Jeon

first: Bin

last: Li

first: Caterina

last: Vicentini

first: Yong

last: Peng

first: Tae

last: Lee

first: Zhenghua

last: Luo

first: Lan

last: Liu

first: Dongyuan

last: Xu

first: Esmerina

last: Tili

first: Victor

middle: X

first: Justin

last: Middleton

first: Arnab

last: Chakravarti

first: Tim

last: Lautenschlaeger

first: Carlo

last: Croce


title: FOXL2 and ESR1 binding sites in primary cells from mouse ovarian follicles

city: GIF SUR YVETTE

first: Adrien

last: Georges

address: CEA/SACLAY

country: France

institute: CNRS

summary: It has previously been shown that FOXL2 and ESR1 cooperate to repress the testis-determining gene Sox9 in murine granulosa cells, and suggested that FOXL2/ESR1 cooperation may be central to granulosa cell differentiation (Uhlenhaut et al., 2009). However, no study has so far compared the DNA-binding of FOXL2 and ESR1 at the genomic level or analyzed the impact of FOXL2 on ESR1 binding to its regulatory elements. Here, we have analyzed and compared the genomic locations recognized by ESR1 and FOXL2 in E2-treated primary murine granulosa cells.

overall_design: Input DNA, FOXL2 and ESR1 ChIP

first: David

last: L'Hôte

first: Bérangère

last: Legois

first: Anne

last: Todeschini

first: Reiner

last: Veitia


title: Efficient and quantitative high-throughput tRNA sequencing

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced due to the abundant presence of post-transcriptional modifications and extensive structure that interfere with cDNA synthesis and adapter ligation. We achieve efficient and quantitative tRNA sequencing by removing base methylations using engineered demethylases and using a highly processive thermo-stable reverse transcriptase without the need for adapter ligation (DMTRT-tRNA-seq). Our method should be applicable for biological investigations of tRNA in all organisms.

overall_design: Development of tRNA-Seq method

first: Guanqun

last: Zheng

first: Wesley

middle: C

last: Clark


title: Haemophilus influenzae 86-028NP

first: Alistair

last: Harrison

state: OH

address: 700 Children's Drive

department: Center for Microbial Pathogenesis

institute: The Research Institute at Nationwide Children's Hospital

summary:
Transcriptome analysis of NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, and NTHi 86-028NPrpsL∆fur(pT-fur) strains

Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the normal human nasopharyngeal flora, yet also an opportunistic pathogen of the upper and lower respiratory tracts. Changes in gene expression patterns in response to host microenvironments are likely critical for survival. One such system of gene regulation is the ability to carefully regulate iron uptake. A central regulatory system that controls iron uptake, mediated by the ferric uptake regulator Fur, is present in multiple bacteria, including NTHi. To understand the regulation of iron homeostasis in NTHi, fur was deleted in the NTHi strain 86-028NPrpsL. Using RNA-Seq, we identified both protein-encoding and small RNA genes whose expression was repressed or activated by Fur. Overall design: These data comprise transcriptional anaylses of an rpsL mutant of 86-028NP, an isogenic fur mutant of 86-028NPrpsL and a complemented fur mutant strain. All strains were grown in defined medium containing 10 µg/ml human hemoglobin to mid-log phase. Cells were then harvested and RNA extracted. A total of three biological replicates were generated for these analyses.

overall_design: Analysis of transcriptomes using the Illumina HiSeq 2000 of three strains of nontypeable Haemophilus influenzae which include NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, and NTHi 86-028NPrpsL∆fur(pT-fur) strains. For each strain three biological replicates were analyzed

first: Robert

middle: S

last: Munson Jr

first: Estevan

last: Santana


title: Comparative Genome-Wide Profiling of Transposon and Retrovirus Integration Sites in Primary Human CD4+ T Cells

city: Gießen

first: Andreas

last: Gogol-Döring

address: Wiesenstraße 14

department: MNI

institute: Technische Hochschule MIttelhessen

summary: We mapped Sleeping Beauty (SB) and piggyBac (PB) insertions in primary human CD4+ T cells and compared their insertion profiles with those of the MLV retrovirus and the HIV lentivirus with respect to proximity to genes, TSSs, CpG islands, DNase I hypersensitive sites, repetitive elements, chromatin marks and transcriptional status of genes.

overall_design: Examination of two transposon systems in one cell type.

first: Ismahen

last: Ammar

first: Csaba

last: Miskey

first: Mario

last: Bunse

first: Wei

last: Chen

first: Wolfgang

last: Uckert

first: Zsuzsanna

last: Izsvák

first: Zoltán

last: Ivics


title: Effects of selection for ethanol preference on gene expression (RNA-Seq) in the nucleus accumbens shell of HS-CC mice

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

summary: Nucleus accumbens shell gene expression was assessed by RNA-Seq to determine effects of bidirectional selection for ethanol preference from a highly genetically diverse founder population.  We analyzed the data with both standard methodologies to detect differential expression, and coexpression network changes, and with novel methodologies to detect alternative exon usage, and coordinated splicing pattern changes due to selection.

overall_design: 48 samples of HSCC animals selected for high and low ethanol preference were analyzed (selection generation 4): 24 females (12 High, 12 Low) 24 males (12 High, 12 Low).

first: Alexandre

last: Colville

first: Ovidiu

last: Iancu

first: Denesa

last: Oberbeck

last: Hitzemann


title: RNA sequencing of cultured mouse wild-type E10.25 forelimbs in control or cyclopmaine containing media [SOLiD]

city: Cambridge

first: Jordan

last: Lewandowski

state: MA

address: 7 Divinity Ave

institute: Harvard University

summary: We wanted to identify differentially expressed genes in wild-type forelimbs and forelimbs briefly exposed to Shh signaling.  E10.25 forelimbs were cultured in control media and media containing cyclopmaine (inhibits the Hedgehog pathway)

overall_design:
Generated two wild-type (control) and two cyclopmaine biological replicates for RNA-seq
UT-Genome and Analysis Facility

first: Fang

last: Du


title: Optimized siRNAs with a minimal off-target effect facilitate the screening of essential genes in cancer cells

city: Beijing

first: Zhenzhen

last: Liu

state: Beijing

address: NO.1 Beichen West Road, Chaoyang Distric

department: Beijing Institute of Genomics

institute: Chinese Academy of Sciences

summary: siRNAs with dN are a promising and easy approach to characterize essential genes by minimizing the off-target effect in cancer cells.

overall_design: mRNA profiles of HCT 116 cells after the transfection of siRNAs or blank control by deep sequencing, using HiSeq 2000

first: Chunyan

last: Li

last: Yang

first: Wensheng

first: Di

last: Wang

first: Encheng

last: Dong

first: Yu

first: Chung-I

last: Wu

first: Xuemei

last: Lu


title: RNA-sequencing based analysis of transcriptomes of Listeria monocytogenes grown on cold smoked salmon and modified BHI broth

city: Ithaca

first: Silin

last: Tang

state: NY

address: Stocking Hall

department: Food Science

institute: Cornell University

summary: In this study, RNA-seq was used to compare the transcriptomes of L. monocytogenes strain H7858 grown on cold smoked salmon (CSS) and in modified brain heart infusion broth (MBHIB, water-phase salt 4.65%, pH 6.1) at 7oC.  RNA-seq was performed on H7858 RNA samples representing four independent biological replicates of growth experiments that involved growth of H7858 on CSS or in MBHIB. Samples for RNA preparation were collected when H7858 was grown to late log phase on these two matrices. Indexed and purified cDNA libraries (8 libraries including 4 replicates for each CSS and MBHIB) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2000 (single-end, 100-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. Significant differential transcription of 149 genes in H7858 was observed between these two treatments including 88 genes and 61 genes up- and downregulated, respectively, in H7858 grown on CSS compared to in MBHIB. Our results show that genes involved in cobalamin biosynthesis, ethanolamine and 1,2-propanediol utilization, and specific carbohydrate transport systems have significantly higher transcript level in H7858 grown on CSS compared to in MBHIB. PrfA-dependent gene enrichment analysis showed that, genes regulated by PrfA were overrepresented among L. monocytogenes genes with higher transcript level on CSS than in MBHIB.

overall_design: Transcriptome profiles of L. monocytogenes grown on cold smoked salmon and in modified BHI broth at 7oC were generated by deep sequencing, in quadruplicate, using Illumina Hiseq 2000 (100 bp per read, single-end).

first: Renato

middle: H

last: Orsi


title: Influence of Sulfur on Transcription of Genes Involved in Arsenic Accumulation in Rice Grains

city: Zhengzhou

first: Jing

last: Zhang

state: Henan

address: 95 Wenhua Road

institute: Henan Agricultural University

summary: Arsenic (As) contamination of rice grains affects millions of people worldwide. In this study, we found that sulfur application (20As+120S) decreased As concentration in rice grains by 44 % compared to grains without sulfur application (20As+0S). Importantly, sulfur application decreased arsenate [As(V)] and arsenite [As(III)] concentration in rice grains significantly, while there was no significant effect on dimethylarsenate (DMA) concentration. To elucidate the molecular basis of As accumulation in rice grains, we performed Illumina sequencing to acquire the differentially expressed genes induced by arsenate and sulfur treatments. By contrast with the control, the expression of 1,000 genes was found to be changed significantly, with 46 genes up-regulated and 954 genes down-regulated in grains grown in arsenate-contaminated soil (20As+0S). Between samples of control and arsenate together with sulfur treatment (20As+120S), 1,169 genes expressed significantly differently, with 16 genes up-regulated and 1,153 genes down-regulated. Sulfur application significantly changed the expression of genes involved in As metabolism in rice grains, significantly down-regulated phosphate transporter gene OsPT23 and aquaporin gene OsTIP4;2, while ABC transporter genes (OsABCG5, OsABCI7_2 and OsABC6) and phytochelatin synthase genes (OsPCS1, OsPCS3 and OsPCS13) were up-regulated. These results provide an insight into the molecular basis of how sulfur assimilation regulates As accumulation in rice grains.

overall_design: Arsenic (As) was artificially added to soil with 20 mg/kg As (Na2AsO4.12H2O, 20As), another treatment was 20As+120S, sulfur (S) were supplied artificially with 120 mg/kg (Na2S2O3•5H2O) to the As-added soil (20As+120S).

first: Quan-Zhi

last: Zhao


title: LMTK3 Represses Tumour Suppressor-Like Genes through Chromatin Remodeling in Breast Cancer

status: Public on Jun 30 2015

city: London

first: Yichen

last: Xu

address: Du Cane Rd

institute: Imperial College London

summary: LMTK3 is an oncogenic receptor tyrosine kinase (RTK) implicated in various types of cancer including breast, lung, gastric and colorectal. It is localized in different cellular compartments but its nuclear function has not been investigated thus far. We have mapped LMTK3 binding across the genome using ChIP-seq and found that LMTK3 binding events are correlated with repressive chromatin markers. We further identified KRAB associated protein-1 (KAP1) as a novel binding partner of LMTK3. The LMTK3/KAP1 interaction is stabilized by PP1_, which suppresses KAP1 phosphorylation specifically at LMTK3-associated chromatin regions, inducing chromatin condensation and resulting in transcriptional repression of LMTK3-bound tumour suppressor-like genes. Furthermore, LMTK3 functions at enhancer regions in tethering the chromatin to the nuclear periphery, resulting in H3K9me3 modification and gene silencing. In summary, we propose a new model where a scaffolding function of nuclear LMTK3 promotes cancer progression through chromatin remodeling, revealing a new mechanism of RTK activity.

overall_design: Examination of LMTK3 binding profile in 2 cell types.

first: Luca

last: Magnani

first: Justin

last: Stebbing

first: Georgios

last: Giamas


title: Changes in ovarian gene expression profiles in maturing European eel (Anguilla anguilla)

city: Leiden

first: Ron

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

summary: The goal of this study was to gain a better understanding of the genetic background of gonadal maturation of the European eel and to use gene expression profiles to identify predictive markers for broodstock selection that can be measured in blood samples. To find leads for maturation markers we performed a pilot deep-sequencing transcriptome analysis of ovarian tissue derived from a yellow eel, a prepubertal silver eel and a post-spawning matured eel. Among the best leads were two key players in steroidogenesis, namely pP450c17 and liver receptor homolog-1.

overall_design: Pilot deep-sequencing transcriptome analysis of ovary from a yellow, a prepubertal silver and a post-spawning matured eel

first: Hans

last: Jansen


title: Genome-wide ChIP-seq analysis of Nr4a1 binding sites in regulatory T (Treg) cells

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

institute: National Center for Global Health and Medicine

summary: We have revealed that Nr4a family nuclear orphan receptors broadly regulate a transcriptional program in Treg cells. In this study, to give an insight into Nr4a-mediated regulation of the transcriptional program in Treg cells, we performed ChIP-seq experiment using anti-Nr4a1 antibodies and a chromatin lysate from Treg cells.

overall_design: Examination of Nr4a1 binding sites in mouse Treg cells.

first: Akihiko

last: Yoshimura


title: Spatiotemporal regulation of GLI target genes in the mammalian limb bud

first: Jordan

last: Lewandowski

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

overall_design: Refer to individual Series


title: Patient Derived Xenograft for Delivery of Precision Medicine in Castrate Resistant Prostate Cancer

city: Rochester

first: Hugues

last: Sicotte

state: MN

address: 200 first street SW

department: Health Sciences Research

institute: Mayo Clinic

summary: Developing animal models representating the cancer biology of advanced prostate cancer patients is challenging but essential for delivering individualized medical therapies. In an effort to develop patient derived xenograft (PDX) models, we took the metastatic site tissue from the rib lesion twice (ie, before and after enzalutamide treatment) over a twelve week period  and implanted subcutaneously and under the renal capsule in immuno-deficient mice.  To characterize and compare the genome and transcriptome landscapes of patient tumor tissues and the corresponding PDX models, we performed whole exome and transcriptome sequencing for metastatic tumor tissue as well as its derived PDXs. We demonstrated the feasibility of developping PDX models from patient who developed castrate-resistant prostate cancer. Our data  suggested PDX models preserve the patient’s genomic and transcriptomic alterations in high fidelity, as illustrated by somatic mutation, copy number variation, gene fusion and gene expression.

overall_design: RNA sequencing of prostate cancer tumor tissue and derived xenograft using Illumina HiSeq 2000.

first: Manish

last: Kohli

first: Liewei

last: Wang

first: Liguo


title: Region-specific identity of small intestinal stem cells from the ileum and jejunum

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We report the expression profiles of three stem-cell varieties derived from the ileum and jejunum, focusing on gene signatures that are consistent in all stem cells of an intestinal location.  We find that intestinal stem cells establish and maintain a regional identity that is discernable through gene expression patterns consistent with intestinal function particular to that region.

overall_design: Small intestines of mice aged 6-12 weeks were extracted, proximal tissues (5-8cm from the pylorus) and distal tissues (5-8cm from the cecum) were obtained.  Crypt stem cells, LGR5 stem cells, and CD44+/CD24lo/CD166+ stem cells were obtained from intestinal tissues after mechanical and enzymatic digestion.  Sorted cells were directly collected in RNA lysis buffer.

first: Maxime

last: Mahe

first: Michael

last: Helmrath


title: Gata6 potently initiates reprogramming of pluripotent and differentiated cells to extraembryonic endoderm stem cells [ChIP-Seq & RNA-Seq]

first: Kathy

last: Niakan

address: Mill Hill

institute: The Francis Crick Institute

summary: Transcription factor-mediated reprogramming is a powerful method to study cell fate changes. In this work, we demonstrate that the transcription factor Gata6 can initiate reprograming of multiple cell types to induced extraembryonic endoderm (iXEN) cells. Intriguingly, Gata6 is sufficient to drive iXEN cells from mouse pluripotent cells and differentiated neural cells. Furthermore, GATA6 induction in human ES (hES) cells also downregulates pluripotency gene expression and upregulates extraembryonic endoderm genes, revealing a conserved function in mediating this cell fate switch. Profiling transcriptional changes following Gata6 induction in mES cells reveals step-wise pluripotency factor disengagement, with initial repression of Nanog and Esrrb, then Sox2 and finally Oct4, alongside step-wise activation of extraembryonic endoderm genes. Chromatin immunoprecipitation and subsequent high-throughput sequencing analysis shows Gata6 enrichment near both pluripotency and endoderm genes, suggesting that Gata6 functions as both a direct repressor and activator. Together this demonstrates that Gata6 is a versatile and potent reprogramming factor that can act alone to drive a cell fate switch from diverse cell types.

overall_design: (1) Microarray analysis of Gata6 overexpressing cells from 12 to 144 hours of doxycycline treatment in mouse embryonic stem (mES) cells compared to uninduced mES cells, embryo-derived XEN cells and Sox7 overexpressing mES cells after 144 hours of doxycycline treatment. (2) ChIP-seq analysis of Gata6 binding 36 hours following doxycycline treatment. (3) ChIP-seq analysis of Gata6 binding in embryo-derived XEN cells. (4) RNA-seq analysis of GATA6 overexpressing cells following 144 hours of induction in hES cells.

first: Sissy

last: Wamaitha

first: Ignacio

last: del Valle

first: Lily

last: Cho

first: Yingying

last: Wei

first: Norah

middle: M

last: Fogarty

first: Paul

last: Blakeley

first: Richard

middle: I

last: Sherwood

first: Hongkai

last: Ji

middle: K