title: EOMES-expressing CD4+ T cells are increased in PTPN22 (1858T) risk allele carriers

city: Stockholm

first: Karine

last: Chemin

address: 4th floor

department: Medicine

country: Sweden

institute: CMM, KI

summary: The presence of the PTPN22 risk variant (1858T) is associated to several autoimmune diseases including rheumatoid arthritis (RA). Despite a number of studies exploring the function of PTPN22 in T cells, the exact impact of the PTPN22 risk variant on T cell function in humans is still unclear. In this study, using RNA sequencing, we show that, upon TCR-activation, naïve CD4+ T cells carrying two PTPN22 risk alleles overexpress a limited number of genes including CFLAR and 4-1BB important for cytotoxic T cell differentiation. Moreover, an increased number of cytotoxic EOMES+ CD4+ T cells were observed in PTPN22 risk allele carriers, which negatively correlated with a decreased number of naïve T cells in older individuals. No difference in the frequency of other CD4+ T cell subsets (Th1, Th17, Tfh, Treg) was observed in PTPN22 risk allele carriers and Treg suppressive capacity was not altered. Finally, in synovial fluids of RA patients, an accumulation of EOMES+ CD4+ T cells was observed with a more pronounced production of Perforin-1 in PTPN22 risk allele carriers. Altogether, our data provide a novel mechanism of action of PTPN22 risk variant on CD4+ T-cell differentiation and identify EOMES+ CD4+ T cell as a relevant T cell subset in RA.

overall_design: Healthy blood donors were selected based PTPN22 genotype, and RNA-sequencing was done on CD4 T cells

first: Daniel

last: Ramsköld

first: Vivianne

last: Malmström


title: In vivo analysis of injury sites presenting full or attenuated pericyte-derived scarring after spinal cord injury (SCI)

status: Public on Feb 27 2018

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

institute: KTH-Science for Life Laboratory

type: Expression profiling by high throughput sequencing

summary: A subpopulation of pericytes expressing the Glast-CreERT2 transgene (Type A pericytes) has recently been identified as the main source of stromal scar tissue that forms after SCI. Identification of molecules associated with pericyte-derived scarring may offer new therapeutic targets to facilitate axon regeneration following central nervous system (CNS) injury. We conducted genome-wide RNA sequencing of (i) uninjured spinal cord segments and (ii) lesion sites presenting full or attenuated pericyte-derived scarring 14 days after SCI.

overall_design: Adult Glast-Rasless-YFP (Glast-CreERT2 x R26R-YFP x Rasless) mice receiving vehicle (Veh) or tamoxifen (Tam) underwent dorsal hemisection at high thoracic level. Fourteen days after SCI, injury sites were dissected out, homogenized and total RNA was isolated from lesions presenting (i) dense (Veh, n=4) and (ii) attenuated (Tam, n=4) pericyte-derived scarring. Age-matched Glast-Rasless-YFP mice served as uninjured controls (n=4).

first: Beata

middle: W

last: Solnestam

first: David

middle: O

last: Dias

first: Christian

last: Göritz

first: Jonas

last: Frisén


title: Transcriptome landscape of a bacterial pathogen under plant immunity

status: Public on Feb 26 2018

city: Cologne

first: Tatsuya

last: Nobori

address: Carl-von-Linne Weg 10, Max-Planck Institute for Plant Breeding Research

country: Germany

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

sample_organism: Pseudomonas syringae pv. tomato str. DC3000

overall_design: Refer to individual Series


title: Argonaute2 and LaminB modulate gene expression by controlling chromatin topology (neuRNA-seq)

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

country: USA

institute: National Institutes of Health

summary: Drosophila Argonaute2 (AGO2) is known to regulate expression of certain loci in an RNA interference-independent manner, but its genome-wide function on chromatin remains unknown.  In order to elucidate the mechanism by which AGO2 regulates transcription, we performed mass spec analysis of factors that interact with AGO2 in nuclear extracts and identified RNA Polymerase II (Pol II) and LaminB among the top-associated proteins. We found that AGO2 and LaminB attenuate transcription genome-wide, including borders between both LaminB-associated domains (LADs) and topologically-associated domains (TADs). Furthermore, we identified a somatic target of AGO2 transcriptional repression, nht, which is immersed in a LAD located within a repressive TAD. Null mutation of AGO2 leads to ectopic expression of spermatogenesis genes dependent on nht. Finally, depletion of either AGO2 or LaminB results in reduced looping interactions within the TAD as well as ectopic inter-TAD interactions, as detected by 4C-seq analysis. Overall, our findings reveal coordination of AGO2 and LaminB to dictate overall genome architecture and thereby regulate gene expression.

overall_design:
Nascent RNA-seq (neuRNA-seq) in mock, AGO2, LaminB, and Dcr-2 knockdowns. In addition, AGO2 was depleted using an alternative siRNA designed against its 5'UTR (si5UTRAGO2) and rescue with a wild type version of AGO2 (pwahf_ago2) or catalytic mutant AGO2V966M (pwahf_v966m). Three separate experiments are included here, and each experiment has between 2 and 3 biological replicates as indicated.

The supplemental counts table contains raw read counts in genes in each sample, and the supplemental_sample_lookup table describes the experimental design. The "experiment" column of the supplemental_sample_lookup table indicates the experiment from which each sample came from. When performing differential expression analysis with these counts, only samples that came from the same experiment should be compared; in particular note that each experiment has its own set of mock control samples.

first: Ezequiel

last: Nazer

first: Elissa

last: Lei


title: Expression data from mouse colon tissue in activated T cell transfer colitis model treated with MEK inhibitor or anti-TNFa antibody

status: Public on Feb 25 2018

city: Fujisawa

first: Kanae

last: Gamo

state: Kanagawa

address: 26-1, Muraoka-higashi 2-chome

department: Immunology Unit, Research

country: Japan

institute: Takeda Pharmaceutical Company Limited

summary: We analyzed publicly available mucosal gene expression data from Crohn's disease (CD) patients pre- and post-infliximab therapy and found that a series of gene expression signature that remains abnormal even if patients achieve clinical remission. Using CMap approach to discover novel therapeutic target for untreatable mechanism of anti-TNFa mAb therapy, we have identified MEK inhibitor exhibiting negatively-correlated effects on reference signature match infliximab therapy untreatable signature. Our findings provide the rationale for testing MEK inhibitor to identify a novel mechanism of action for CD. Using an activated T cell trasnfer colitis model, a highly selective MEK inhibitor showed therapeutic efficacy and improved the histological changes. To dissect molecular mechanisms, we performed global gene expression profile by RNA-sequencing on the Ion Torrent platform to identify broad scale changes in gene expression treated with MEK inhibitor compared to anti-TNFa mAb.

overall_design:
Splenocytes from BALB/c female mice were activated with Concanavalin A (4 μg/mL), and recombinant human IL-2 (10 ng/mL, R&D systems) for 3 days. CD4+ T cells were isolated by MACS separation systems, and then 2 x105 activated CD4+ T cells were intravenously injected into female SCID mice (day 0). At day 17, diarrhea score for stool consistency was graded and equally divided into 5 groups as follows: vehicle control, enteric MEK inhibitor microparticles (MPs) at 0.3 mg/kg and at 1 mg/kg, isotype antibody (Isotype mAb) and anti-TNFa antibody (Anti-TNFa mAb). Enteric MEK inhibitor MPs were orally administered once a day from day 17 to day 27. Isotype mAb and anti-TNFa mAb were intraperitoneally injected every 4 days from day 17 at 0.1 mg/mouse. Total RNA from individual cohorts were extracted from the distal part of the colon at day 28, and whole transcriptome sequencing was performed on the Ion Torrent platform.
MEK inhibitor (compound 33 in Bioorg. Med. Chem. Lett. 22 (2012) 2411   2414))

first: Hiroki

last: Hayashi

first: Yoshiki

last: Katou

first: Kuniko

last: Kikuchi

first: Hirokazu

last: Tozaki

first: Yuumi

last: Okuzono


title: Whole Exome-seq profiles of prostate cancer cell lines for copy number and PARADIGM analysis

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute

summary: Genomic studies using paired enzalutamide-sensitive and resistant cell models were performed. After transcriptional and copy number profiling, we used PARADIGM to compare the genomic alterations between the parental V16D and resistant MR49F cell models to identify critically deregulated networks to demonstrate the utility of integrative genomic analysis for therapy selection. There were 607 genes and pathway entities that had PARADIGM scores that fell outside the normally distributed range in the MR49F cell line. The top 64 genes were selected for RNAi validation. The most biologically relevant genes between the V16D and MR49F cell line models under enzalutamide treatment conditions were identified as significant by siRNA analysis and deemed biologically relelvant by network and enrichment analyses.

overall_design: Whole Exome-seq profiles of prostate cancer cell lines for copy number analysis

first: Josha

last: Woodward

first: Carly

middle: J

last: King

first: Jacob

last: Schwartzman

first: Daniel

last: Coleman

first: Robert

last: Lisac

first: Nicholas

last: Wang

first: Katy

last: Van Hook

first: Lina

last: Gao

first: Joshua

last: Urrutia

first: Mark

last: Dane

first: Laura

middle: M

last: Heiser


title: Argonaute2 and LaminB repress transcription by controlling RNA Pol II recruitment and chromatin topology in Drosophila melanogaster (mRNA)

first: Ryan

last: Dale

summary: Although best known as core components of RNA silencing pathways in the cytoplasm, Argonautes have been shown to regulate gene expression by functioning in the nucleus. Previous work showed that Drosophila AGO2 is preferentially associated with active promoters and can activate gene expression by promoting looping to an enhancer. In order to elucidate the genome-wide role of AGO2 in regulating transcription, we performed mass spec analysis of factors that interact with AGO2 in nuclear extracts and found RNA Pol II and LaminB among the top-associated proteins. Using nascent RNA sequencing, we showed that AGO2 and LaminB co-repress transcription at borders between both LaminB-associated domains (LAD) and topologically-associated domains (TADs). Furthermore, LaminB and AGO2 specifically prevent RNA Pol II recruitment at repressed genes, and AGO2 additionally impairs the ability of RNA Pol II to extend into active elongation. Using mRNA-seq profiling, we identified a somatic target of AGO2 repression, nht, which leads to ectopic expression of spermatogenesis genes in AGO2 null mutants. Interestingly, nht is immersed in a LAD located within a repressive TAD flanked by AGO2 binding sites. 4C-seq analysis showed that depletion of either AGO2 or LaminB results in a significant decrease in frequency of interactions within the TAD as well as ectopic inter-TAD interactions. Overall, our findings reveal a coordinated function for AGO2 and LaminB in dictating the overall architecture of the genome to control the recruitment of RNA Pol II and thereby regulate gene expression.

overall_design: mRNA-seq from female whole larvae in different AGO2 mutant strains. Two biological replicates were analyzed.

first: Madoka

last: Chinen

first: Elissa

last: Lei


title: Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

country: China

institute: Peking University

summary:
Background:
Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive.
Results:
We perform single-cell RNA sequencing analysis of 1,916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, namely, the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine. Based on the regulatory activities rather than the expression patterns, all cells analyzed can be well classified into four major groups with epithelial, mesodermal, hematopoietic and neuronal identities. For different organs within the same group, the similarities and differences of their features and developmental paths are revealed and reconstructed.
Conclusions:
We identify mutual interactions between epithelial and mesenchymal cells and detect epithelial cells with prevalent mesenchymal features during organogenesis, which are similar to the features of intermediate epithelial/mesenchymal cells during tumorigenesis. The comprehensive transcriptome at single-cell resolution profiled in our study paves the way for future mechanistic studies of the gene- regulatory networks governing mammalian organogenesis.

overall_design: Here, we performed single-cell RNA sequencing (RNA-Seq) analysis of 1,916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, including the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine.

first: Yuqiong

last: Hu

first: Xiaoying

last: Fan

first: Xinglong

last: Wu

first: Fuchou

last: Tang


title: Expression data in LoVo cells treated with MEK inhibitor

first: Kanae

last: Gamo

summary: We analyzed publicly available mucosal gene expression data from Crohn's disease (CD) patients pre- and post-infliximab therapy and found that a series of gene expression signature that remains abnormal even if patients achieve clinical remission. Using CMap approach to discover novel therapeutic target for untreatable mechanism of anti-TNFa mAb therapy, we have identified MEK inhibitor exhibiting negatively-correlated effects on reference signature match infliximab therapy untreatable signature. Our findings provide the rationale for testing MEK inhibitor to identify a novel mechanism of action for CD. Gene expression profile was performed to analyze the gene modulation induced by a highly selective MEK inhibitor, and to evaluate whether it normalized reference residual CD signature in vitro.

overall_design:
LoVo, a human colorectal cancer cell line, was treated with MEK inhibitor for 24 hours across ten dose response conditions (0.03–1,000 nM), and amplicon sequencing was performed on the Ion Torrent platform. Effects of MEK inhibitor were compared with that of DMSO-treated control.
MEK inhibitor (compound 33 in Bioorg. Med. Chem. Lett. 22 (2012) 2411   2414))

first: Yoshiki

last: Katou

first: Kuniko

last: Kikuchi

first: Hirokazu

last: Tozaki

first: Yuumi

last: Okuzono


title: RNA-seq of hiPSCs-derived NPCs from 3 pairs of dizygotic discordant twins for Congenital Zika syndrome

city: São Paulo

first: Murilo

last: Sena Amaral

state: SP

address: Avenida Prof Lineu Prestes

country: Brazil

institute: Universidade de São Paulo

summary: Congenital Zika syndrome (CZS), caused by Zika virus (ZIKV) infection, has been associated to impairment of early brain development, particularly related to neural progenitor cells (NPCs) survival and growth. In this work we report in a high-throughput manner (RNA-Seq) the differences in the transcriptomes of hiPSCs(human induced pluripotent stem cells)-derived NPCs from 3 pairs of discordant twins for Congenital Zika syndrome (CZS). We found significant differences in the expression levels of genes relevant to the regulation of neural development between the NPCs from CZS-affected and non-affected twins, suggesting that epigenetic differences may contribute to the different susceptibilities of NPCs to ZIKV infection.

overall_design: hiPSCs were generated from CD71+-cells, which were isolated from peripheral blood samples from three pairs of dizygotic/discordant twins. Then,  NPCs were obtained after hiPSCs differentiation and cultivated for 4 days before the RNA was extracted and deep sequenced using Illumina HiSeq4000.

first: Lucas

middle: F

last: daSilva

first: Sergio

last: Verjovski-Almeida

first: Mayana

last: Zatz


title: 5-Hydroxymethylcytosine profiling of aging hippocampi

city: San Francisco

first: Jeremy

middle: Michael

last: Shea

state: CA

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California, San Francisco

type: Methylation profiling by high throughput sequencing

summary: We profiled 5-hydroxymethylcytosine patterns in hippocampi using hydroxymethylated DNA immunoprecipitation followed by Illumina deep sequencing (hMeDIP-Seq). We profiled the hippocampi of 4 young (3 month old) and 4 aged (18 month old) C57BL/6 mice. Additionally, we profiled the 5-hmC patterns of hippocampi that were stereotactically injected with lentiviral constructs that overexpressed Tet2 or luciferase.

overall_design: Examination of 5-hydroxymethylcytosine in hippocampi of two ages (3 months and 18 months) and Tet2 overexpression and control hippocampi

first: Saul

middle: A

last: Villeda


title: Plant development on ISS differes from the development on the ground and is influenced by the genetic background.

status: Public on Feb 24 2018

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary: The development of Col-0 and WS plants on orbit differs from that on the ground as demonstrated by the comparison of the gene expression profiles between 4 days old to 8 days old plant in the two environments. The Col-0 plants used different genes reflecting different physiological processes than WS plants, suggesting the role of the genetic background in the developmental decisions. The 4 days old Col-0 plant in orbit showed deficit in wax and suberin production relatively to the 8 days old plants, the difference unregistered on the ground. There was more dramatic difference in the overexpression of the root system development and anatomical structure development genes in 8 days old plants than in 4 days old plant in both genotypes on the ground than in flight, implying smaller root developmental gap between 4 days and 8 days old roots in orbit. The WS plant uniquely showed overexpression of the photosynthesis related genes in the 4 days old roots relative to 8 days old root in the spaceflight environment but not on the ground.  The seeds germinated in the novel growth environment of ISS implemented different developmental strategies as captured by the genes expression patterns, than seeds developing on the ground.

overall_design: APEX03-2 (Advanced Plant Experiment 03-2) also identified as TAGES-Isa (Transgenic Arabidopsis Gene Expression System—Intracellular Signaling Architecture) was launched on SpaceX mission CRS-5 on 10 January 2015. Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates and remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station). The plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS with the overhead LED lighting of the VPS. At four or for the second experimental set at eight days, seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Upon return to Earth, the harvested material was used to compare the transcriptomes of each genotype and each age using RNAseq technology. The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment. For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis.

first: Anna-Lisa

last: Paul

first: Agata

middle: K

last: Zupanska


title: Knockout human reveal an essential role for Paternally Expressed 10 (PEG10) in JEG3 cell line development

city: Los Angeles

first: Yu-Ting

last: Tseng

state: California

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

summary: Tissue- and cell-type specific regulators of alternative splicing (AS) are an essential layer of posttranscriptional gene regulation necessary for normal cellular function, patterning, and development. Here we report the Paternally Expressed 10 (PEG10) are required for patterning of multiple organs, with loss of PEG10, resulting in increasingly severe phenotypes.

overall_design: RNA from purified total placenta of human uterus were harvested by Trizol extraction. 1 ug of total RNA was used for  for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample Prep Kit (Illumina). 100x2 bp paired-end RNA-seq reads were generated on a HiSeq 2000 sequencer.

first: Yi

last: Xing

first: Russ

last: Carstens


title: Consequences of Ribosomal Protein Haploinsufficiency in Human Hematopoiesis

city: Cambridge

first: Vijay

middle: G

last: Sankaran

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: Ribosomal protein haploinsufficiency (RPH) underlies diverse human diseases with distinct and specific phenotypes, including Diamond-Blackfan anemia (DBA). Although multiple mechanisms have been proposed for the erythroid-specific hematopoietic defects observed in DBA, only recently has the role of selectively impaired translation been highlighted in these phenotypes. Exactly how and to what extent this impairment of translation occurs is currently unknown. Here, by identifying a novel DBA gene affecting ribosome biogenesis, we show that both RPH and impaired ribosome biogenesis (IRB) limit the availability of actively translating ribosomes, resulting in the hematopoietic and translational defects observed in DBA. Our results show that the selective impairment of translation is due to a quantitative defect, where ribosomes of invariant protein composition have a reduced abundance, rather than a qualitative defect, where a subset of ribosomes lack specific ribosomal proteins (RPs) and thus may have altered translational capacity. In RPH, we find that cellular RP homeostasis is largely maintained through translational co-regulation, and we identify a selective subset of transcripts that have impaired association with the ribosome. Surprisingly, these transcripts have short and unstructured 5’ UTRs and are highly abundant and efficiently translated in healthy human erythroid progenitors, suggesting that the impaired translation of a number of key transcripts, including GATA1, may underlie DBA. Overall, our study identifies mechanisms by which RPH and IRB affect mRNA translation, illuminating how these alterations can result in cell-type specific defects and cause human disease.

overall_design: (mRNA-seq) RNA-seq for control (shLuc), RPL5 knockdown (shRPL5), RPS19 knockdown (shRPS19), and TSR2 knockdown (shTSR2) was performed for two biological replicates of primary human erythroid cells at Day 7 of in vitro culture. (RPF-seq) Ribosome profiling was similarly performed for shLuc, shRPL5, and shRPS19 in the matching biological replicates.

first: Jacob

middle: C

last: Ulirsch


title: RNAseq of hypnozoites and schizonts in the MPCC system

status: Public on Feb 23 2018

first: Sangeeta

middle: N.

last: Bhatia

state: Massachusetts

address: 500 Main Street Cambridge MA 02142

department: HST

institute: Massachusetts Institute of Technology

summary: Upon P. vivax infection, dormant liver stage forms, hypnozoites, linger for weeks to months and then relapse to cause recurrent blood stage infection. Very little is known about the hypnozoite: Definitive biomarkers are lacking and in vitro platforms that support phenotypic studies have not been available. Here, we recapitulate the entire liver stage life cycle of P. vivax in vitro in a multiwell format and assay the hypnozoite transcriptome

overall_design: Determination of differentially expressed genes between hypnozoite enriched and mixed populations

last: Gural

middle: N


title: Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

city: Geneva

first: Mirco

last: Schmolke

address: Rue Michel Servet 1

department: Department of Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

summary: The impact of viral infections, on host microbiota composition and dynamics is poorly understood. Influenza A viruses (IAV) are common respiratory pathogens causing acute infections. In this study, we show dynamic changes in respiratory and intestinal microbiota over the course of a sublethal IAV infection in a mouse model. Using a combination of 16S rRNA gene specific next generation sequencing and qPCR as well as culturing of bacterial organ content, we found body site specific and transient microbiota responses to influenza infection. In the lower respiratory tract, we observed only minor qualitative changes in microbiota composition. In the small intestine, IAV induced robust depletion of bacterial content, disruption of mucus layer integrity and higher levels of antimicrobial peptides in Paneth cells. By RNAseq approach, we tried to analyze changes in transcriptomics of lung, and small intestine on the day of maximum changes to dissect possible causal players leading to the phentype observed.

overall_design: mock treated (n=3) or influenza A virus infected (n=4) animals are weighted daily, and sacrifised to collect corresponding tissues on 7 days post infection.

first: Soner

last: Yildiz

first: Beryl

last: Mazel-Sanchez


title: In-nodule transcriptome analysis of Paraburkholderia phymatum during symbiosis with Phaseolus vulgaris

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

institute: University of Zürich

summary: Paraburkholderia phymatum belongs to the β-subclass of proteobacteria. It has recently been shown to be able to nodulate and fix nitrogen in symbiosis with several mimosoid and papillionoid legumes. In contrast to symbiosis of legumes with α-proteobacteria, very little is known about the molecular determinants underlying the successful establishment of this mutualistic relationship with β-proteobacteria. In this study, we analyzed RNA-seq data of free-living P. phymatum growing under nitrogen replete and limited conditions, the latter partially mimicking the situation in nitrogen deprived soils. Among the genes up-regulated under nitrogen limitation, we found genes involved in exopolysaccharide production and motility, two traits relevant for plant root infection. Next, RNA-seq data of P. phymatum grown under free-living conditions and from symbiotic root nodules of Phaseolus vulgaris (common bean) were generated and compared. Among the genes highly up-regulated during symbiosis, we identified an operon encoding a potential cytochrome o ubiquinol oxidase (Bphy_3646-49). Bean root nodules induced by a cyoB mutant strain showed reduced nitrogenase and nitrogen fixation abilities suggesting an important role of the cytochrome for respiration inside the nodule. Analysis of mutant strains for RNA polymerase transcription factor rpoN (σ54) and its activator NifA indicated that – similar to the situation in α-rhizobia – P. phymatum RpoN and NifA are key regulators during symbiosis with P. vulgaris.

overall_design: Unraveling the molecular basis of the nitrogen-fixing symbiosis between P. vulgaris and P. phymatum.

first: Martina

last: Lardi

first: Yilei

last: Liu

first: Gabriela

last: Purtschert

first: Samanta

last: Bolzan de Campos


title: Peptidomimetic blockade of MYB in acute myeloid leukemia [H3K27ac ChIP-seq]

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Aberrant gene expression is a hallmark of acute leukemias. However, therapeutic strategies for its blockade are generally lacking, in large part due to the pharmacologic challenges of drugging transcription factors. MYB-driven gene trans-activation with CREB-binding protein (CBP) is required for the initiation and maintenance of a variety of acute lymphoblastic and myeloid leukemias, including refractory MLL-rearranged leukemias. Using structure-guided molecular design, we developed a prototypical peptidomimetic inhibitor MYBMIM that interferes with the assembly of the molecular MYB:CBP complex at ¼M concentrations and rapidly accumulates in the nuclei of AML cells. We found that treatment of AML cells with MYBMIM, but not with its inactive near-isosteric analogue TG3, led to the displacement and dissociation of MYB:CBP complex in cells, displacement of MYB from oncogenic enhancers and promoters enriched for MYB binding sites, and rapid downregulation of MYB-dependent gene expression, including of MYC and BCL2 oncogenes. Both human MLL-rearranged and non-rearranged AML cells, but not normal CD34+ umbilical cord blood progenitor cells, underwent sustained mitochondrial apoptosis in response to MYBMIM treatment, an effect that could be partially rescued by ectopic expression of BCL2. We observed that MYBMIM treatment impeded leukemia growth and extended survival of immunodeficient mice engrafted with primary patient-derived MLL-rearranged leukemia cells. These findings emphasize the exquisite dependence of human AML on MYB:CBP transcriptional dysregulation, and establish a pharmacologic approach for its therapeutic blockade.

overall_design: ChIP-sequencing of H3K27ac in human leukemia cell line with MYB peptide mimic and controls.

middle: P

first: Kavitha

last: Ramaswamy

first: Alex

last: Kentsis


title: H-STS NET cell line perturbed with small molecule compounds

first: Mariano

middle: Javier

last: Alvarez

state: NY

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

summary: Expression profile of H-STS NET cell line at 6h and 24h after perturbation with small molecule compounds.

overall_design: H-STS cells were perturbed with small molecule compounds at isopotent concentrations, corresponding to ED20 and 1/10 of it, as measured by cell viability assays at 60h, or vehicle control (DMSO, ethanol and methanol). The cells were lysed at 6h and 24h after perturbation and total RNA isolated. Libraries for RNA-seq were generated with the TruSeq protocol (Illumina) and sequenced in a Hi-Seq 2500 instrument (Illumina).


title: Expression data and genome-wide maps of chromatin in Phf8 knock out and wild type mice

city: Shanghai

first: Xuemei

last: Chen

address: 320 Yueyang Road

department: State Key Laboratory of Molecular Biology

institute: Chinese Academy of Sciences

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

overall_design: Refer to individual Series


title: Genome-wide maps of chromatin in Phf8 knock out and wild type mice [ChIP-seq]

summary: we found the difference binding of H3K20me1 between Phf8 knock out and wild type mice

overall_design: Examination of H3K20me1 modification in hippocampus of  Phf8 knock out and wild type mice, in triplicate, using Illumina  HiSeq 2500.

first: Wang

last: shuai

first: Chen

last: Xuemei

first: Yu

last: lu


title: A transcriptomic study of myogenic differentiation under the overexpression of PPARγ by RNA-Seq

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

institute: Anhui University

summary: To study the cellular and molecular function of PPARγ in skeletal muscle differentiation, we have generated inducible gain-of-function to overexpress PPARγ in C2C12 skeletal muscle cells. In order to identify PPARγ targets, RNA sequencing (RNA-seq) was used to evaluate and quantify of transcriptomes and expression patterns during myogenic differentiation under the overexpression of PPARγ. The formation of myotubes and the expression of muscle-specific myogenic genes such as MyoD and MyoG may be inhibited by any altered expression of PPARγ. Multiple genes and pathways were significantly involved in this process, including 11 genes such as Fndc9 and Slc14a1 with fundamental change of regulation modes, 9 genes of which were validated by the data of qRT-PCR. Our studies demonstrate that PPARγ would play critical roles on the skeletal muscle cells differentiation, mediating crosstalk among several pathways and transcription factors.

overall_design: Inducible PPARγ C2C12 cells were differentiated for 5 days. Uninduced cells were used as controls. Experiments were performed in triplicate. Gene expression profiling analyses by high throughput sequencing were performed on mRNA samples isolated from the sense PPARγ C2C12 cells (PPARγ/+) and the wildtype cells on 0d and 5d.

first: Guoying

last: Wu


title: Transcriptome analysis of C. elegans embryos lacking ADARs and the 26G pathway

city: Salt Lake City

first: Brenda

middle: L

last: Bass

state: Utah

address: 15 N Medical Drive East, Rm 4800

department: Biochemistry

institute: University of Utah

summary: Adenosine deaminases that act on RNA (ADARs) catalyze the conversion of adenosine to inosine in dsRNA. C. elegans ADARs, ADR-1 and ADR-2, promote the expression of genes containing dsRNA structures by preventing their processing into siRNAs and silencing by RNAi. The 26G endogenous siRNA (endo-siRNA) pathway generates a subset of siRNAs distinct from those made in adr-1;adr-2 mutants, but using many of the same factors. We found that adr-1;adr-2;rrf-3 mutants, lacking both ADARs and the RNA-dependent RNA polymerase RRF-3 required for the 26G pathway, display a bursting phenotype rescued by the RNAi factors RDE-1 and RDE-4. To determine what gene expression changes underlie the synthetic phenotype of adr-1;adr-2;rrf-3 mutants, we sequenced poly(A)+ RNA from adr-1;adr-2;rrf-3 embryos, their parent strains, and strains rescued with mutations in rde-1 and rde-4. We found that genes associated with edited structures were robustly downregulated in adr-1;adr-2;rrf-3 mutants in a manner partially dependent on rde-1 and rde-4. Additionally, genes induced during Orsay virus infections were induced in rrf-3 mutants and further upregulated in adr-1;adr-2;rrf-3 mutants, again dependent in part on rde-1 and rde-4.

overall_design: RNAseq of poly(A)+ RNA from C.elegans mixed-stage embryos, four biological replicates per genotype, six genotypes: wildtype (Bristol N2), adr-1(uu49);adr-2(uu28), rrf-3(uu56), adr-1(uu49);adr-2(uu28);rrf-3(uu56), adr-1(uu49);adr-2(uu28);rrf-3(uu56);rde-1(uu51), and adr-1(uu49);adr-2(uu28);rrf-3(uu56);rde-4(uu53).

first: Daniel

last: Reich

first: Katarzyna

last: Tyc


title: Changes in chromatin state reveal a central role for the transcription factor ARNT2, in the control of glioblastoma stem cell tumorigenicity

city: Paris

first: Alexandra

last: Bogeas

address: 7 quai St Bernard

country: France

institute: Inserm U1130, CNRS UMR 8246,University P. & M. Curie

summary: Although a growing body of evidence indicates that the phenotypic plasticity exhibited by glioblastoma cells plays a central role in tumor development and post-therapy recurrence, the master drivers of their aggressiveness remain elusive. Here we mapped the changes in the transcriptionally permissive (H3K4me3) and repressive (H3K27me3) epigenetic histone marks accompanying the repression of glioblastoma stem cells (GSC) tumorigenicity. Genes with changing marks delineated a network of transcription factors related to cancerous behavior, stem state, and neural development, which highlighted a previously unsuspected association between repression of ARNT2 and loss of cell tumorigenicity. Immunohistochemistry confirmed ARNT2 expression in cell sub-populations of patients’ glioblastoma. Its transcriptional repression was consistently found in non-tumorigenic glioblastoma cells, compared to tumorigenic cells. Moreover, ARNT2 expression correlated with a stem signature at both the tissue level within the tumor core and at the single cell level in the patients’ tumors. ARNT2 knockdown decreased expression of the transcription factors SOX9, POU3F2 and OLIG2 known promoters of glioblastoma cell tumorigenicity, and repressed GSC tumorigenic properties in vivo. Our results unveil ARNT2 as a master gene of the glioblastoma tumorigenic cell signature, located at a node of the transcription factor network controlling glioblastoma cell aggressiveness.

overall_design: Histone modification profiling for two different marks by ChIP-Seq in glioblastoma stem-like cells and glioblastoma stem-like cells transduced with miR-302-367

first: Hugues

last: Parinello

first: Stephanie

last: Rialle

first: Matthieu

last: Defrance

first: François-Xavier

last: Lejeune

first: Marie-Pierre

last: Junier

first: Herve

last: Chneiweiss


title: Early events during the interaction between wheat and cereal cyst nematode as revealed by transcriptomic analysis

first: Changlong

address: Haidian District, No. 12 Zhongguancun South Street

department: Institute of Crop Sciences

institute: Chinese Academy of Agricultural Sciences

summary: Cereal cyst nematode (Heterodera avenae) can be attracted by wheat roots before infestation, while largely is unknown underlying this phenomenon. Here, we examined the transcriptional responses of both wheat roots and nematodes during the attraction stage by mRNA sequencing analysis (with and without reference genome, respectively). We found that consistent with their respective mobility, the immobile host wheat root only had 93 DEGs (27 up-regulated and 66 down-regulated), while the mobile plant parasitic nematode H. avenae reacted much more actively with 879 DEGs (867 up-regulated and 12 down-regulated). Among the DEGs, a number of wheat DEGs (most down-regulated) were involved in biotic stress pathways, while several putative effector genes (up-regulated) were found in the nematode DEGs. Results of the experiments demonstrated that nematode responds more actively than wheat during the attraction stage of parasitism, and the parasite responses mainly involved up-regulation whereas the host responses mainly involved down-regulation.

sample_organism:
Triticum aestivum
Heterodera avenae

platform_organism:
Triticum aestivum
Heterodera avenae

overall_design: mRNA profiles of wheat roots gathered aroud by cereal cyst nematodes (treated wheat roots), wheat roots untreated with nematodes (control of wheat roots), nematodes gathering around wheat roots (treated nematodes) and nematodes untreated with wheat roots (control of nematodes); five to six wheat seedlings in each pool of wheat treatment or wheat control and 25,000~30,000 nematodes in each pool of nematode treatment and nematode control; in triplicate for each treatment or control.

first: Hongjie

last: Li


title: Genome wide identification of chromatin modifications in the hypothalamus during pubertal development

city: Beaverton

first: Hollis

last: Wright

address: 505 NW 185th Avenue

department: DIvision of Neuroscience

institute: ONPRC/OHSU

summary: Histone modification analysis of hypothalami from female animals at different juvenile developmental reproductive stages. Results provide insight into the role of the hypothalamus in controlling the onset of puberty.

overall_design: SD rats were housed (8/cage) in a controlled environment and euthanized at different ages ( PND=14, Early Juvenile: 21 days and Late Juvenile: 28 days) Rats were anesthetized and brains were rapidly removed. The medial basal hypothalamus (MBH) was dissected away from the rest of the brain and flash frozen. Chromatin was prepared and ChIP assays performed to detect H3K27me3, H3K27Ac and H3K4me1. After immunoprecipitation, DNA samples were amplified using LinDA whole genome amplification before sending them to the OSU Center for genome Research and Biocomputing for library preparation and sequencing.

first: Alejandro

last: Lomniczi

first: Carlos

last: Toro

first: Sergio

middle: R

last: Ojeda


title: TRIM24 is an oncogenic transcriptional co-activator of STAT3 in glioblastoma

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

summary: Aberrant amplication and mutations of epidermal growth factor receptor (EGFR) are the most common oncogenic events in glioblastoma (GBM), but the mechanisms by which they promote aggressive pathogenesis are not well understood. Here, we determined that non-canonical histone signature acetylated H3 lysine 23 (H3K23ac)-binding protein tripartite motif-containing 24 (TRIM24) is upregulated in clinical specimens of glioblastoma and is required for EGFR-driven tumorigenesis.

overall_design: Examination of effects of TRIM24 knockdown or EGFRvIII on differential gene expression in glioma cells.


title: Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with signatures from post mortem adult brains

first: Gabriel

middle: E

last: Hofman

address: 1 Gustave L Levy Plaza

department: Department of Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Whereas highly penetrant variants have proven well-suited to human induced pluripotent stem cell (hiPSC)-based models, the power of hiPSC-based studies to resolve the much smaller effects of common variants within the size of cohorts that can be realistically assembled remains uncertain. In developing a large case/control schizophrenia (SZ) hiPSC-derived cohort of neural progenitor cells and neurons, we identified and accounted for a variety of technical and biological sources of variation. Reducing the stochastic effects of the differentiation process by correcting for cell type composition boosted the SZ signal in hiPSC-based models and increased the concordance with post mortem datasets. Because this concordance was strongest in hiPSC-neurons, it suggests that this cell type may better model genetic risk for SZ. We predict a growing convergence between hiPSC and post mortem studies as both approaches expand to larger cohort sizes. For studies of complex genetic disorders, to maximize the power of hiPSC cohorts currently feasible, in most cases and whenever possible, we recommend expanding the number of individuals even at the expense of the number of replicate hiPSC clones.

overall_design: RNA-seq from hiPSC-derived neural progenitor cells and neurons

last: Hoffman

first: Kristen

last: Brennand


title: Characterizing the epigenome of glioma stem cells (RRBS)

first: Dan

last: Zhou

address: 131 Dong 'an Road, Xuhui District

institute: Fudan University

summary: Glioma initiating cells/stem cells exist in the bulk tumor of glioblastoma. This cell population contributes to the frequent resistances toward radiation/chemotherapy, aggressiveness of adult brain cancer and increased recurrence rate. Targeting stem cell population becomes one the most promising and permissive therapeutic strategies. We isolated glioma stem cells from patient-derived xenografts and profiled their epigenomic features, including 4 different DNA marks and 2 enhancer marks, and transcriptome in these in vitro cultured cell lines. Three fetal brain-derived neural stem/progenitors cells were used for comparing the unique and common molecular features in these glioma cancer stem cells.

overall_design: A core set of 12 glioma stem cell lines and 3 neural stem/progenitor cell lines were mapped for 5mC, 5hmC, 5fC/caC, H3K4me1, H3K27ac, and transcriptome using next generation sequencing technique.

first: Keith

middle: D

last: Robertson


title: Peptidomimetic blockade of MYB in acute myeloid leukemia

first: Richard

last: Koche


title: Characterizing the epigenome of glioma stem cells (ChIP-Seq)

summary: Glioma initiating cells/stem cells exist in the bulk tumor of glioblastoma. This cell population contributes to the frequent resistances toward radiation/chemotherapy, aggressiveness of adult brain cancer and increased recurrence rate. Targeting stem cell


title: Characterizing the epigenome of glioma stem cells (RNA-Seq)


title: Peptidomimetic blockade of MYB in acute myeloid leukemia [MYB ChIP-seq]

overall_design: ChIP-sequencing of MYB in human leukemia cell line with MYB peptide mimic and controls.

first: Kavitha

last: Ramaswamy

first: Alex

last: Kentsis


title: Ribosomal protein S6 phospho-deficient mice display altered novelty-induced locomotion, synaptic plasticity, and specific mRNA translation

city: Montpellier

first: Emmanuel

last: Valjent

address: 141, rue de la cardonille

department: Neurobiology

institute: INSERM

summary: By high-throughput RNA-seq of heavy polysomal fractions, we report that rpS6 knockin mice, in which the 5 phosphorylatable serines have been replaced by alanines, show an alteration in the translation, but not transcription, of a subset of mRNAs in the nucleus accumbens (NAc) but not in the dorsal striatum (DStr). Gene Ontology analysis revealed that multiple dysregulated mRNAs are related to the mitochondria. Moreover, we described that rpS6 knockin mice also display an alteration in novelty-induced locomotion and synaptic plasticity.

overall_design: mRNAs from heavy polysomal fractions (Heavy) and total RNA (Total) from both the nucleus accumbens (Nac) and dorsal striatum (DStr) were compared between rpS6 knockin mice and wildtype littermates. We sequenced triplicates per genotype and brain region.

first: Emma

last: Puighermanal

first: Anne

last: Biever

first: Vincent

last: Pascoli

first: Su

last: Melser

first: Stephanie

last: Rialle

first: Dany

last: Severac

first: Jihane

last: Boubaker-Vitre

first: Oded

last: Mehuyas

first: Giovanni

last: Marsicano

first: Christian

last: Lüscher


title: Characterizing the epigenome of glioma stem cells


title: Peptidomimetic blockade of MYB in acute myeloid leukemia [RNA-seq]

overall_design: RNA-sequencing of human leukemia cell line with MYB peptide mimic and controls.


title: RNA-sequencing of mouse knockout models for Cnp, Plp1, and Ugt8 in the frontal cortex and cerebellum

first: Yongzhong

last: Zhao

address: 1470 Madison Avenue btw. 101st and 102nd Streets

department: Genetics

institute: Mount Sinai Medical Center

summary: Oligodendrocytes (OLs) and myelin are critical for normal brain function and they have been implicated in neurodegeneration. Human neuroimaging studies have demonstrated that alterations in axons and myelin occur early in Alzheimer’s Disease (AD) course. However, the molecular mechanism underlying the role of OLs in AD remains largely unknown. In this study, we systematically interrogated OL-enriched gene networks constructed from large-scale genomic, transcriptomic, and proteomic data in human AD postmortem brain samples. These robust OL networks were highly enriched for genes associated with AD risk variants, including BIN1. We corroborated the structure of the AD OL coexpression and gene-gene interaction networks through ablation of genes identified as key drivers of the networks, including UGT8, CNP, MYRF, PLP1, NPC1, and NDGR1. Perturbations of these key drivers not only caused dysregulation in their associated network neighborhoods, but also mimicked pathways of gene expression dysregulation seen in human AD postmortem brain samples. In particular, the OL subnetwork controlled by the AD risk gene PSEN1 was strongly dysregulated in AD, suggesting a potential role of PSEN1 in disrupting the myelination pathway towards the onset of AD. In summary, this study built and systematically validated the first comprehensive molecular blueprint of OL dysregulation in AD, and identified key OL- and myelination-related genes and networks as potential candidate targets for the future development of AD therapies.

overall_design: The mouse knockout models have been previously described for each of Ugt8 (Coetzee et al., 1996), Cnp (Lappe-Siefke et al., 2003), and Plp1 (Klugmann et al., 1997). For each of the two conditions studied (control and homozygous knockout mice), five mice of either sex were sacrificed at postnatal day 20 and brains were flashed-frozen until analysis. The frontal cortex (FC) and cerebellum (CBM) were dissected out and individually processed. RNA was isolated using Trizol reagent and processed using Ribo-Zero rRNA removal. RNA-sequencing was performed using the Illumina HiSeq2000 with 100 nucleotide paired-end reads. RNA-sequencing reads were mapped to the mouse genome (mm10, UCSC assembly) using Bowtie (version 2.2.3.0), TopHat (version 2.0.11), and SamTools (version 0.1.19.0) using a read length of 100. Reads were converted to counts at the gene level using HTSeq on the BAM files from TopHat2 using the UCSC known genes data set.

first: Andrew

middle: T

last: McKenzie

first: Sarah

last: Moyon

first: Minghui

last: Wang

first: Igor

last: Katsyv

first: Won-Min

last: Song

first: Xianxiao

first: Eric

middle: B

last: Dammer

first: Duc

last: Duong

first: Joshua

last: Aaker

first: Jun

last: Zhu

first: James

middle: J

last: Lah

first: Nicholas

last: Seyfried

first: Allan

middle: I

last: Levey

first: Pavel

last: Katsel

first: Vahram

last: Haroutunian

last: Schadt

first: Brian

last: Popko

first: Klaus-Armin

last: Nave

first: Patrizia

last: Casaccia

first: Bin

last: Zhang


title: Gene regulation by small RNAs and ADAR RNA editing

first: Brenda

last: Bass

type: Non-coding RNA profiling by high throughput sequencing


title: Integrated microRNA-mRNA transcript analysis reveals microRNAs regulating therapy resistant diffuse large B-cell lymphoma

city: Helsinki

first: Suvi-Katri

last: Leivonen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma in adults. Although 60-70% of the patients can be cured with standard chemoimmunotherapy, a substantial number of patients die from the disease due to relapse or primary refractory disease. To better understand the biological processes behind the treatment resistance, we characterized the microRNA (miRNA) expression profiles of matched primary and relapsed DLBCL by next-generation sequencing. A total of 492 known miRNAs were expressed in the DLBCL samples (n=7 pairs). A majority of these showed similar expression at diagnosis and relapse; we identified 24 highly expressed and 177 lowly expressed miRNAs in the DLBCL samples as compared to a control set of non-malignant cells. Interestingly, only 13 miRNAs had differential expression between the primary–relapse pairs. MiRNA-mRNA target pair analysis combined with pathway enrichment analysis revealed the putative targets of differentially expressed miRNAs to be significantly enriched for several cancer-associated pathways that included phosphatidylinositol, MAPK and B-cell receptor signaling, suggesting activation of these pathways during progression. Additionally, Kaplan-Meier survival analyses indicated higher expression of genes from these pathways to be associated with shorter survival in immunochemotherapy-treated patients (n=92). Taken together, our data demonstrate that the miRNA expression profile remains relatively constant during the disease progression, but a small set of differentially expressed miRNAs may contribute to the relapse by regulating key cell survival pathways, thus representing potential novel therapeutic targets.

overall_design: Matched primary-relapse tumor sample pairs from seven patients with high-risk DLBCL.

first: Katherine

last: Icay

first: Ilari

last: Siren

first: Kirsi

last: Jäntti

first: Chengyu

last: Liu

first: Maja

last: Ludvigsen

first: Stephen

last: Hamilton-Dutoit

first: Francesco

last: d’Amore

first: Marja-Liisa

last: Karjalainen-Lindsberg

first: Jan

last: Delabie

first: Harald

last: Holte

first: Rainer

last: Lehtonen

first: Sampsa

last: Hautaniemi

first: Sirpa

last: Leppä


title: dsRNAs expressed in C. elegans development

summary: Cellular RNAs containing double-stranded RNA (dsRNA) structures are subject to A-to-I RNA editing by the adenosine deaminases that act on RNA (ADARs). While A-to-I editing can alter mRNA coding potential, most editing is observed in non-coding sequences, the function of which remains poorly characterized. Using a dsRNA immunoprecipitation and high-thoughput sequencing (dsRIP-Seq) approach, we identify 1523 expressed A-to-I edited regions and characterize their expression during Caenorhabditis elegans development. We observe that edited regions are highly expressed in early development and are closely associated with protein-coding genes. Edited dsRNA structures give rise to abundant small interfering RNAs (siRNAs) that are negatively correlated with ADAR expression and regulate the developmental expression of associated genes.

overall_design: RNA-Seq of total RNA and RNA immunoprecipitated with a dsRNA-specific antibody (dsRIP) from whole C. elegans at four stages of development: embryos, early stage larvae (L1-L2), late stage larvae (L3-L4), and young adults.

first: Daniel

last: Reich

first: Katarzyna

middle: M

last: Tyc


title: Quantitating transcription factor redundancy: The relative roles of the ELT-2 and ELT-7 GATA factors in the C. elegans endoderm

status: Public on Feb 22 2018

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

summary: Two GATA transcription factors, ELT-2 and ELT-7, function in the differentiation of the Caenorhabditis elegans intestine. Though loss of elt-7 causes no discernable phenotype on its own, it significantly enhances intestinal morphology defects in elt-2 loss-of-function mutants. We sought to identify the cohorts of gene targets unique to or shared by ELT-2 and ELT-7 in an effort to determine the logic underlying their differential impact on intestinal development.

overall_design: To quantitate the relative transcriptional influences of ELT-2 and ELT-7, we isolated pure populations of (1) wild-type, (2) elt-2(-), (3) elt-7(-), and (4) elt-7(-); elt-2(-) double mutant L1-stage larvae and compared their transcriptional profiles. Three to four replicates were performed for each condition for a total of 15 samples.

first: Aidan

last: Dineen

first: Barbara

last: Goszyczynski

first: Joel

middle: H

last: Rothman

first: James

last: McGhee


title: Characterization of transcriptomics landscape in HUVEC cells exposed to oxidative stress (Small RNA)

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

summary: The aim of the project was to characterize the transcriptional landscape of human HUVEC cells exposed to oxidative stress (oxstress). In order to do so cell cultures have been exposed to 200uM H2O2 for either 16 hours or 36 hours to induce oxstress. Total ribodepleted RNA obtained from both time points have been sequenced and small RNA for the 16 hours time point have been sequenced as well. Datasets have been characterized and overlapped. This entry contains the dataset of small RNA.

overall_design: Two conditions are available: control untreated HUVEC cells and HUVEC cells exposed to 200uM H2O2 for 16 hours. Each condition is available in triplicate. All samples underwent two unpooled rounds of sequencing, for a total of 24 samples.

first: Carrara

last: Matteo

first: Jose

last: Garcia-Manteiga

first: Paola

last: Fuschi


title: Migrating interneuron transcriptomes in Wt and CCP1 cKO mouse embryos

city: Liège

first: Elise

last: PEYRE

address: Quartier Hopital Avenue Hippocrate 15, Tour B36

department: Giga neuroscience

country: Belgium

institute: University of Liège

summary: CCP1 is a deglutamylase responsible for protranslational modification of proteins. CCP1 cKO interneurons show impaired acto-myosin contraction and increased invasion of the cortex. Transcriptome analysis of Wt and cKO interneurones aimes at uncovering secondary disregulation of gene expression.

overall_design: E13.5 interneurons RNA profiles in Wt and CCP1 cKO embryos generated by deep sequencing of ribosome depleted RNA extracts in triplicates using paired-end sequencing on an Illumina HiSeq2000.

first: Carla

last: Silva

last: Peyre

first: Sylvia

last: Tielens

first: Laurent

last: Nguyen


title: Characterization of transcriptomics landscape in HUVEC cells exposed to oxidative stress (Total RNA)

summary: The aim of the project was to characterize the transcriptional landscape of human HUVEC cells exposed to oxidative stress (oxstress). In order to do so cell cultures have been exposed to 200uM H2O2 for either 16 hours or 36 hours to induce oxstress. Total ribodepleted RNA obtained from both time points have been sequenced and small RNA for the 16 hours time point have been sequenced as well. Datasets have been characterized and overlapped. This entry contains the dataset of total ribodepleted RNA.

overall_design: Three conditions are available: control untreated HUVEC cells, HUVEC cells exposed to 200uM H2O2 for 16 hours, HUVEC cells exposed to 200uM H2O2 for 36h. Each condition is available in triplicate, for a total of 9 samples.


title: Characterization of transcriptomics landscape in HUVEC cells exposed to oxidative stress

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

overall_design: Refer to individual Series


title: TFEB target in epithelial cells during DSS colitis

city: Worcester

first: Javier

middle: Elbio

last: Irazoqui

address: 368 Plantation street

department: Microbiology

institute: University of Massachusetts Chan Medical School

summary: TFEB in IEC has a protective role in DSS colitis. The goal is to examine what genes/pathways are TFEB target during DSS colitis

overall_design: Epithelial cells are isolated from TFEB flox(WT) and TFEB IEC KO(KO) mice on day0(basal), day4 and day11 during DSS treatment

first: Tatsuro

last: Murano

first: Kara

last: Lassen

first: Ramnik

last: Xavier


title: Genome-wide transcriptome analysis of NIPBL iPSC and commited cardiomyoctes

city: Philadelphia

first: Jason

middle: Adam

last: Mills

state: PA

address: 422 Curie Blvd

department: Ophthalmology

institute: The University of Pennsylvania

summary:
The purpose of this study was to compare the transcriptome of NIPBL patient derived iPSCs and patient-derived cardiomyocytes to healthy unaffected individuals
Methods: iPSC transcriptome profiles of three CdLS patient iPSCs harboring mutations in the NIPBL gene  and cardiomyocytes derived from patient-iPSCS were generated by deep sequencing, in triplicate, using Illumina XXXXXX. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the  human genome and identified XXXX transcripts in CdLS-iPSCs and XXXXXX transcripts in control-iPSCs with XXXX workflow.
Conclusion: Our data is the represents the first human developmental model for studying CdLS through pluripotent stem cells and lineage commited subtypes (cardiomyocytes). This data highlights NIPBLs role in regulating transcriptional regulation and has significant consequences on DNA nucleosome involvement as it relates to global gene expression.  This work provides preliminary evidence that NIPBL  is required for normal epigenetic and DNA landscape establishment during embryonic cardiomyocyte generation.

overall_design: Examine transcriptome of Control and NIPBL iPSC and Cardiomyoyctes

middle: A

first: Ian

last: Krantz


title: RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with coronary heart disease

first: Shengli

last: Li

address: 270 Dong An Road

institute: Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences

summary: Exosomes are small membrane vesicles of endocytic origin secreted by most cells, and contain a wealthy cargo of protein and RNA species that can modulate recipient cells’ behaviors and may be used as biomarkers for diagnosis of human diseases. They have been found in blood and are valuable sources for biomarkers due to selective cargo loading and resemblance to their parental cells. The goal of this study is to identify circRNA, lncRNA and mRNA profiles in human blood by high-throughput RNA sequencing (RNA-seq). 1-4 ml plasma or serum were used to extract exosomal RNAs by exoRNeasy Serum/Plasma Maxi kit (Qiagen). The exosomal RNAs were further treated with DNAse I and subjected to ribosome minus low-input RNAseq library preparation. The libraries were sequenced by Illumina Hiseq platform.

overall_design: Human blood exosomal RNAs were generated by deep sequencing using Illumina Hiseq.

first: Yuan

last: Tang


title: RNA sequencing of prostate cancers reveal insights on the prognostic significance of visibility on multi-parametric MRI

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

summary: Not all prostate cancers are visible on multiparametric MRI. The biologic basis and clinical implication of MRI visibility are unknown. We sought to identify genes associated with prognosis and MRI visibility.

overall_design: Patients with MRI-visible and MRI-invisible lesions who underwent radical prostatectomy were identified. The location, size and Gleason score for each tumor were mapped. Representative lesions were macrodissected for RNA sequencing (RNA-seq).

first: Hyung

last: Kim


title: RNA-Seq of treatment response of platinum sensitive and platinum resistant ovarian cancer cells

city: Dresden

first: Konrad

last: Grützmann

address: Schubertstraße 15

department: Core Unit for Molecular Tumor Diagnostics

institute: National Center for Tumor Diseases partner site Dresden

summary: Resistance to platinum-based chemotherapy is a clinical challenge in the treatment of ovarian cancer (OC) and limits survival. Therefore, innovative drugs against platinum-resistance are urgently needed. Our therapeutic concept is based on the conjugation of two chemotherapeutic compounds to a monotherapeutic pro-drug, which is taken up by cancer cells and cleaved into active cytostatic metabolites. Here, we explore the activity of the duplex-prodrug 5-FdU-ECyd, covalently linking 2'-deoxy-5-fluorouridine (5-FdU) and 3'-C-ethynylcytidine (ECyd), on platinum-resistant OC cells. RNA-Sequencing was used for characterization of 5-FdU-ECyd treated platinum-sensitive A2780 and isogenic platinum-resistant A2780cis.

overall_design: Platinum-sensitive A2780 and platinum resistant-cells A2780cis were treated with 5−FdU−Ecyd for 6h and 12h, there are also 6h and 12h untreated controls, all groups are in triplicates

first: Sarah

last: Schott

first: Pauline

last: Wimberger

first: Barbara

last: Klink

first: Julian

last: Puppe

first: Ulrike

middle: S

last: Wauer

first: Daniel

last: Klotz

first: Evelin

last: Schröck

first: Jan

last: Kuhlmann


title: Transcriptomes of iPSC-derived and post-mortum Hypothalamus Neurons from obese and control donors

city: Los Angeles

first: Dhruv

last: Sareen

state: CA California

address: 8700 Beverly Blvd

department: Board of Governors Regenerative Medicine Institute

summary: We sequenced the transcriptomes of seven samples of hypothalamic neurons dervied from pluripotent stem cells taken from healthy patients; five samples of hypothalamic neurons derived from pluripotent stem cells of constitutionally obese donors; five samples of sectioned hypothalami from post-mortem dissection of brains, and two samples for motor neurons derived from pluripotent stem cells of healthy donors in order to assess the similarity of our iPSC-derived cells against those of sectioned brains and to identify possible transcriptional disfunction which might underlie extreme, inherited obesity.

overall_design: We sequenced mRNA collected from post-mortem brains and from samples generated by differentiating pluripotent stem cells into hypothalamic neurons and motor neurons.

first: Uthra

last: Rajamani


title: DNA methylation signature defines genes modulated by stromal cell contents of human breast tumors

city: Lyon

first: Robert

last: Dante

address: 28, rue Laennec

department: Department of Tumoral Escape

institute: Cancer Research Center – Lyon

type: Methylation profiling by genome tiling array


title: AG221 and Ruxolitinib Treatment Effects on LSKs in IDH2-R140Q JAK2-V617F Transplant Recipients

city: New York

last: Spitzer

address: 411 E 67th St

institute: Memorial Sloan Kettering Cancer Center

summary: Transplant recipients of IDH2-R140Q JAK2-V617F expressing bone marrow were treated with AG221 and ruxolitinib monotherapy, combined therapy, or vehicle. LSKs were sorted from terminal samples and sequenced with three WT controls.

overall_design: 15 samples

first: Anna

last: McKenney

first: Ross

last: Levine


title: Genome-wide Screen for Differentially Methylated Long Noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as Regulated by Enhancer DNA Methylation with Prognostic Relevance for Human Breast Cancer

city: Heidelberg

first: Reka

last: Toth

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: The majority of long noncoding RNAs (lncRNAs) is still poorly characterized with respect to function, interactions with protein-coding genes, and mechanisms that regulate their expression. As for protein-coding RNAs, epigenetic deregulation of lncRNA expression by alterations in DNA methylation might contribute to carcinogenesis. To provide genome-wide information on lncRNAs aberrantly methylated in breast cancer we profiled tumors of the C3(1) SV40TAg mouse model by MCIp-seq (Methylated CpG Immunoprecipitation followed by sequencing). This approach detected 69 lncRNAs differentially methylated between tumor tissue and normal mammary glands, with 26 located in antisense orientation of a protein-coding gene. One of the hypomethylated lncRNAs, 1810019D21Rik (now called Esrp2-antisense (as)) was identified in proximity to the epithelial splicing regulatory protein 2 (Esrp2) that is significantly elevated in C3(1) tumors. ESRPs seem to have a dual role in carcinogenesis. Both gain and loss has been associated with poor prognosis in human cancers, but the mechanism regulating expression is not known. In-depth analyses indicate that coordinate overexpression of Esrp2 and Esrp2-as inversely correlates with DNA methylation. Luciferase reporter gene assays support co-expression of Esrp2 and the major short Esrp2-as variant from a bidirectional promoter, and transcriptional regulation by methylation of a proximal enhancer. Ultimately, this enhancer-based regulatory mechanism provides a novel explanation for tissue-specific expression differences and upregulation of Esrp2 during carcinogenesis. Knockdown of Esrp2-as reduced Esrp2 protein levels without affecting mRNA expression and resulted in an altered transcriptional profile associated with extracellular matrix (ECM), cell motility and reduced proliferation, whereas overexpression enhanced proliferation. Our findings not only hold true for the murine tumor model, but led to the identification of an unannotated human homolog of Esrp2-as which is significantly upregulated in human breast cancer and associated with poor prognosis.

overall_design: RNA Sequencing data of Esrp2-as knockdown and control in M6 cell lines and  Esrp2-as overexpression and control in 3T3-L1 and M27H4 cell lines

first: Katharina

last: Heilmann

first: Caroline

last: Bossmann

first: Karin

last: Klimo

first: Christoph

last: Plass

first: Clarissa

last: Gerhäuser


title: Identification of the RB loss-induced E2F1 cistrome in prostate cancer [ChIP-seq]

first: Christopher

last: McNair

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

summary: The retinoblastoma protein (RB) is preferentially lost in the progression to castrate resistant prostate cancer (CRPC). However, the alterations associated with such loss have been scantly described. The current study aims to provide molecular mechanisms underlying Rb loss-driven CRPC phenotypes.

overall_design: Alterations in E2F1 binding upon RB loss were assessed in hormone deficient conditions through ChIP-Seq of shCON and shRB LNCaP prostate cancer cells.

first: Karen

last: Knudsen


title: Somatic PRDM2 c.4459delA mutations in colorectal cancers control histone methylation and tumor growth

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary:
Purpose: To identify the contribution of PRDM2 c.4459delA mutation to colorectal tumorigenesis
Methods: We employed rAAV-mediated genome editing to correct somatic PRDM2 c.4459delA mutation in homozygously mutated cell line. Using next-generation sequencing we have compared transcriptional profile of parental and PRDM2-corrected cells.
Results: RNA-seq profiling revealed that several hallmark cancer gene sets are affected by PRDM2 c.4459delA

overall_design: To address if the PRDM2 wt cells were transcriptionally different at a global level compared to their parental cells that carry PRDM2 c.4459delA mutation, we performed RNA-sequencing of parental cells and three independently generated clones with corrected PRDM2.  RNA-seq profile was generated for cells grown under normal culture conditions (10% FBS) as well as reduced serum conditions (0.5% FBS).

first: Tatjana

last: Pandzic

first: Tobias

last: Sjöblom


title: Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) during hippocampal Long-Term Potentiation (LTP) [3'READS]

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: This study was aimed at elucidating the mechanisms underlying activity-dependent gene regulation during LTP of mouse hippocampal CA3-CA1 synapses. Deep sequencing of the 3’ end of transcripts allowed to identify changes in APA induced 1 hour and 3 hours after LTP induction. We detected APA changes that only affected the 3'UTR (3'UTR-APA events) and APA changes that also affected the coding sequence (CDS-APA events).

overall_design: We performed 3’ region extraction and deep sequencing (3'READS) of acute hippocampal slices 1 hour and 3 hours after LTP induction, and of time-matched control slices. Hippocampal slices were prepared from 2-3 month old C57BL/6 wild-type mice, the dentate gyrus was trimmed, and the slices were placed in interface chambers to recover for 2 hours with continuous ACSF perfusion. From the same animal, half of the mini-slices were used for LTP induction (using a pharmacological protocol, cLTP) and the remaining slices were treated with a DMSO vehicle solution as controls. We sequenced triplicates (samples 1-3) of controls and cLTP treated slices for the 1 hour and 3 hours time-point.

first: Mariana

last: Fontes

first: Aysegul

last: Guvenek

first: Dinghai

last: Zheng

first: Alden

last: Huang

first: Victoria

last: Ho

first: Patrick

last: Chen

first: Xiaochuan

last: Liu

first: Thomas

last: O’Dell

first: Giovanni

last: Coppola

first: Bin

last: Tian

first: Kelsey

middle: C

last: Martin


title: Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP)


title: O antigen acts as a shield to delay early plant immune recognition of the pathogenic bacterium, Xylella fastidiosa

city: Berkeley

first: Abraham

last: Morales-Cruz

address: 1 Cyclotron Road

institute: Joint Genome Institute

summary: PAMP-triggered immunity (PTI) is the first line of plant defense against invading organisms. Initiated through the perception of conserved pathogen-associated molecular patterns (PAMPs), such as lipopolysaccharide or flagellin, PTI can provide early protection against a broad range of pathogens. Active suppression of PTI by microbial effector proteins, particularly those secreted by the Type III secretion system (T3SS), is a well-known strategy employed by bacterial plant pathogens that enables them to subvert PTI and successfully colonize their hosts. In this study, we demonstrate that the xylem-limited bacterium, Xylella fastidiosa, which lacks a T3SS, utilizes an alternative strategy to delay elicitation of innate immune responses. By decorating its LPS PAMP molecule with a high molecular weight O antigen, this bacterium physically masks itself from early recognition by the grapevine innate immune system. We have elucidated the chemical structure of the O antigen and found that it is primarily an α1,2-linked rhamnan polymer. X. fastidiosa cells lacking O antigen elicited hallmarks of PTI such as ROS production, specifically in the plant xylem tissue compartment, which is comprised primarily of non-living cells. By coupling histological and genome-wide transcriptional profiling, we demonstrate that X. fastidiosa lacking its O antigen shield activates defense-related genes in grapevine. This includes a stronger and more prolonged oxidative burst at concentrations high enough to inhibit pathogen proliferation. To begin exploring translational applications of our findings, we also demonstrate that purified X. fastidiosa LPS elicitor can prime grapevine defenses, thereby conferring host tolerance to subsequent challenge with X. fastidiosa.

overall_design: Grapevine petioles were inoculated with wild type X. fastidiosa, wzy mutant and buffer. For RNAseq analysis petioles (three biological replicates) were collected locally (i.e., at point of inoculation) and distally at six timepoints (0 hours, 8 hours, 24 hours, 48 hours, 1 week, and 2 weeks after inoculation).

first: Jeannette

middle: N

last: Rapicavoli

first: Barbara

last: Blanco-Ulate

first: Rosa

last: Figueroa-Balderas

first: Parastoo

last: Azadi

first: Artur

last: Muszynski

first: Dario

last: Cantu

first: M

last: Roper


title: Astrocyte-specific deletion of SOX2 promotes recovery after traumatic brain injury

city: Dallas

first: Derek

middle: K

last: Smith

state: Texas

address: 5323 Harry Hines Blvd, NA5.202

department: Molecular Biology

institute: The University of Texas Southwestern Medical Center

summary: Injury to the adult brain induces activation of resident astrocytes, which serves as a compensatory response modulating tissue damage and recovery. However, the mechanism governing astrocyte activation and the role of reactive astrocytes remain largely unknown. Here we show that SOX2, a transcription factor critical for stem cells and brain development, is also required for injury-induced activation of adult cortical astrocytes. Genome-wide ChIP-seq analysis reveals that SOX2 binds to regulatory regions of genes associated with signaling pathways controlling reactive gliosis, such as Socs3, Nr2e1, Notch1, and Akt2. Inducible deletion of Sox2 in adult astrocytes greatly diminishes their response to traumatic injury and, most unexpectedly, restricts injury-induced cortical loss. Together, these results uncover an essential role of SOX2 in terminally differentiated cells and implicate that SOX2-dependent reactive astrocytes may be targeted for regeneration after traumatic brain injury.

overall_design: SOX2 (1 input dataset, 3 immunoprecipitation datasets)

first: Smith

last: Derek K.

first: Chen

last: Chunhai

first: Yang

last: Jianjing

first: Zhang

last: Chun-Li


title: DNA methylation signature defines genes modulated by stromal cell contents of human breast tumors [RNA-seq]

first: Robert

last: Dante

summary: Using genome-wide approaches, we have identified groups of genes modulated by CAF-secreted factors from human breast cancer cell lines grown in different CAF-conditioned medium. The genes modulated by CAF secreted factors were characterized by a specific DNA methylation pattern: hypermethylation at transcription start site (TSS) and shore regions. Approximately 60% of them exhibited a methylation-dependent expression level and 20% of them were also dependent on the methyl-CpG-binding protein domain 2. Thus, these specific DNA methylation patterns were linked to an epigenetic control of their expression, upon CAF-secreted factors. We have therefore identified some molecular events defining the responsiveness of groups of genes to stromal cell contents in human breast tumors.

overall_design: RNAseq of untreated SKBR3 cells and AU565 cells, CAF-conditionned medium treated cells, DAC treated cells, siMBD2 treated cells, siCtrl, in duplicates or in quadriplicates for untreated SKBR3 cells

first: Pauline

last: Mathot

first: Mélodie

last: Grandin

first: Guillaume

last: Devailly

first: Frédérique

last: Souaze

first: Vincent

last: Cahais

first: Sebastian

last: Moran

first: Mario

last: Campone

first: Zdenko

last: Herceg

first: Manel

last: Esteller

first: Philippe

last: Juin

first: Patrick

last: Mehlen


title: Human NPY/AgRP hypothalamic cell lines for study of obesity susceptibility (miRNA-Seq)

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Recent data suggests that common genetic risk for metabolic disorders such as obesity may be human-specific and exert effects through the central nervous system.  To overcome the limitation of human tissue access for study, we have generated induced human pluripotent stem cell (hiPSC)- derived neuronal cultures which recapture many features of hypothalamic neurons within the arcuate nucleus.  Here we have comprehensively characterized this model across development and benchmarked these neurons to in vivo events.  We also demonstrate their utility in study of obesity risk variants. The dynamic transcriptome across neuronal maturation was examined using microarray and RNAseq methods at 9 time points.  K-means clustering of the longitudinal data was conducted to identify co-regulation and miRNA control of biological processes.  The transcriptomes were compared to those of 103 samples from 13 brain regions reported in the Genotype-Tissue Expression database (GTEx) using principal components analysis.  Genes with proximity to body mass index (BMI)-associated genetic variants were mapped to the developmentally expressed genesets, and enrichment significance was assessed with Fisher’s exact test. The human neuronal cultures have a transcriptional and physiological profile of NPY/AgRP hypothalamic neurons.  The neuronal transcriptomes were highly correlated with adult hypothalamus as compared to any other brain region from the GTEx. Also, roughly 25% of the transcripts showed changes in expression across maturation stages and potential co-regulation of biological processes that mirror neuronal development in vivo. These developmentally expressed genes were significantly enriched for genes in proximity to BMI-associated variants.

overall_design: We collected small RNA at each of the 9 time points, day 0, 10, 25, 35, 45, 55, 75, 95, 115 , from day 0 to 115 during the differentiation and maturation process.  Small RNA was isolated with the TruSeq™ Small RNA sample prep kit v2 (Illumina) according to the instructions of the manufacturer

first: Li

last: Yao

first: Yuanhang

last: Liu

first: Iriscilla

last: Ayala

first: Zhifang

last: Qiu

first: Sateesh

last: Kumar

first: Joanne

last: Curran

first: Donna

last: Lehman


title: Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP) [RNA-Seq]

first: Riki

last: Kawaguchi

summary: This study was aimed at elucidating the mechanisms underlying activity-dependent gene regulation during long-term potentiation (LTP) of mouse hippocampal CA3-CA1 synapses. Transcriptome analysis allowed to identify changes in gene expression and alternative splicing induced 1 hour and 3 hours after LTP induction.

overall_design: We performed RNA-sequencing of acute hippocampal slices 1 hour and 3 hours after LTP induction, and of time-matched control slices. Hippocampal slices were prepared from 2-3 month old C57BL/6 wild-type mice, the dentate gyrus was trimmed, and the slices were placed in interface chambers to recover for 2 hours with continuous ACSF perfusion. From the same animal, half of the mini-slices were used for LTP induction (using a pharmacological protocol, cLTP) and the remaining slices were treated with a DMSO vehicle solution as controls. We sequenced triplicates (samples 1-3) of controls and cLTP treated slices for the 1 hour and 3 hours time-point.

first: Mariana

last: Fontes

first: Aysegul

last: Guvenek

first: Dinghai

last: Zheng

first: Alden

last: Huang

first: Victoria

last: Ho

first: Xiaochuan

first: Thomas

last: O’Dell

first: Giovanni

last: Coppola

first: Bin

last: Tian

first: Kelsey

last: Martin


title: Genome-wide DNA methylation maps during rehydration in gametophores of Physcomitrella patens.

city: Beijing

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

institute: Capital Normal University

summary: To examine the P. patens genome-wide methylation landscape and assess its functional significance during dehydration, we generated the first single-base resolution genome methylation maps for  P. patens gametophores of hydrated (HD), moderate dehydrated (MDH), severe dehydrated (SDH), partially recovered (PRE) and fully recovered (FRE). The overall density of methyl-cytosine was not broadly altered by dehydration and recovery. There is, however, a small increase in intensity both for the whole genome and regionally during MDH and FRE. Only 225 differentially expressed genes were located in differentially methylated regions (DMRs) during the dehydration-recovery cycle. The finding may provide an important clue for exploring molecular mechanisms and the regulation of desiccation tolerance at the whole-genome level.

overall_design: Examination of DNA methylation by BS-Seq in hydrated (HD), moderate dehydrated (MDH), severe dehydrated (SDH), partially recovered (PRE) and fully recovered (FRE) gametophores of P. patens.


title: Genome-wide transcriptome analysis during dehydration and recovery in gametophores of  Physcomitrella patens

summary: Gene transcript abundances were analyzed with samples taken from hydrated (HD), moderate dehydration (MDH), desiccated (SDH), partially recovered (PRE) and fully recovered (FRE) gametophores of P. patens by using RNA-Seq. Totally, 14686 transcripts were identified as differentially expressed transcripts.The results provided insight for exploring the mechanisms of desiccation tolerance and their evolution.

overall_design: Examination of mRNA transcript abundances in hydrated (HD), moderate dehydration (MDH), desiccated (SDH), partially recovered (PRE) and fully recovered (FRE) gametophores, for each treatment, three biological replicates were included.


title: Genome-wide transcriptome analysis during dehydration in leaf tissues of Boea hygrometrica (10%, 50% and 100%)

summary: Gene transcript abundances were analyzed with samples taken from desiccated (10% RWC), rehydrated to 50% RWC (RE50% RWC) and rehydrated to 100% RWC (RE100% RWC) leaf tissues of resurrection plant species B. hygrometrica by using RNA-Seq. Totally, 10207 genes were identified as differentially expressed genes.The results provided insight for exploring the mechanisms of desiccation tolerance.

overall_design: Examination of mRNA transcript abundances in desiccated (10% RWC), rehydrated to 50% RWC  (RE50% RWC) and rehydrated to 100% RWC (RE100% RWC) leaf tissues, for each treatment, three biological replicates were included.


title: Transcriptomics and Real-Time PCR analysis reveals a cross-modulatory effect between riboflavin and iron and outlines common and specific responses to riboflavin biosynthesis and uptake in Vibrio cholerae

status: Public on Feb 21 2018

city: Cuernavaca

first: Luis

middle: Fernando

last: Lozano

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México

summary: Riboflavin-derived molecules such as flavin mononucleotide and flavin adenine dinucleotide comprise the most important redox coenzymes all across life kingdoms. Vibrio cholerae, a pandemic diarrheagenic bacterium, is able to synthesize riboflavin through the riboflavin biosynthetic pathway (RBP) and to internalize exogenous riboflavin using the RibN importer. This bacterium thrives in different environments such as estuarine waters and the human intestinal tract. The presence of two independent riboflavin supply pathways in this species may be related to the variable riboflavin availability and requirements across different niches. In order to gain insights into the role of the riboflavin provision pathways in the physiology of V. cholerae, we analyzed the bacterial transcriptomics response to extracellular riboflavin and to the deletions of ribD (RBP-deficient strain) or ribN. Notably, many genes responding to riboflavin have been previously reported to belong to the iron regulon. Real time PCR analysis confirmed this effect and further documented that reciprocally, iron regulates RBP and ribN genes in a riboflavin-dependent way. A subset of genes were responding to both ribD and ribN deletions. Nonetheless, a group of genes was specifically affected in the ∆ribD strain, on which the functional terms protein folding and oxidation reduction process were enriched. Also, a subset of genes was affected specifically in the ∆ribN strain, on which the cytochrome complex assembly functional term was enriched.  Results indicate that iron and riboflavin interrelate to regulate its respective provision genes and suggest that both common and specific effects of biosynthesized and internalized riboflavin exist.

overall_design:
Strains and growth conditions. V. cholerae N16961 strain and its ∆ribD and ∆ribN derivatives were grown overnight in LB plates at 37 °C. 5 ml of LB broth were inoculated with a colony of the plate cultures and incubated at 37 °C in an orbital shaker at 150 rpm until they reached an OD600 nm of 1.0. Next, cultures were centrifuged and pellet washed twice with T minimal medium (Wyckoff and Payne, 2011) and resuspended in 1 ml of fresh T medium. 10 ml of plain T medium or T + 2 µM riboflavin were inoculated with 10 µl of the resuspensions and incubated at 37 °C and 180 rpm until an OD600 nm of 0.8. 1 ml of each culture was centrifuged and subjected to RNA extraction. When indicated, iron was omitted in T media, in which case 3 ml of cultures at OD600 nm = 0.3 were harvested for RNA extraction. This growth protocol was similar for RNA subjected to transcriptomics and RT-PCR.

RNA extractions, retrotranscription, RNAseq and RT-PCR. RNA extraction was performed with the Thermo Scientific Genejet RNA purification kit according to manufacturer´s instructions. RNA extracts were digested with Turbo DNA-free DNAase at 37 °C for 1 hour. For RNAseq, rRNA was removed using the Ribo-Zero removal kit and cDNA libraries were constructed using the TruSeq mRNA stranded kit, according to manufacturer´s instructions. Next, RNA was sequenced using the Illumina HiSeq 2500 platform to produce 100bp paired-end reads, with ~40 million reads (per sample).  rRNA removal, cDNA libraries generation and RNAseq were performed at Genoma Mayor (Santiago, Chile). For RT-PCR analysis, the AffinityScript QPCR cDNA Synthesis kit (Agilent Technologies) was used for cDNA synthesis according to manufacturer´s instructions. As a control, a reaction with no reverse transcriptase was included for each sample in each run. RT-PCR was performed using the Brilliant II SYBR Green QPCR Master Mix kit in a One-Step Applen Biosystems (Life Technologies) thermocycler. Relative expression in the indicated conditions was determined through the ∆∆Ct method as developed before (Livak and Schmittgen, 2001). The 16s RNA subunit gene was used for normalization. For the assessment of the relative expression by RT-PCR of ribB, ribN, ribD and gyrB, the sets of primers used were ribB Fw/ribB Rv, ribN Fw/ribN Rv, ribD Fw/ribD Rv and gyrB Fw/gyrB Rv (Cisternas et al., 2017), respectively. Other RT-PCR primers are as follow: for tonB1, tonB1 Fw (5´- ggtgtttgccatgcctgctgg-3´) / tonB1 Rv (5´-GCGGCTTCACCTTCGGCTTAG-3´); for sodA, sodA Fw (5´-GCCAAGCGATATTCATCCAAGG-3´) / sodA Rv (5´-GCTCAGTGGCCTATCTTCATGC-3´).

RNAseq data analysis. Quality control visualization and analysis (adapter and quality trimming) was performed using FastQC version 0.11.2 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and Trim_galore version 0.4.1 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), respectively. Reads were mapped to the genome of Vibrio cholerae 01 biovar El Tor str. N16961 (RefSeq, NCBI) using Bowtie2 version 2.1.0 (Langmead and Salzberg, 2012). In all the samples the alignment percentage of reads were above 98%. Differential expression analysis between samples was performed with the Bioconductor package edgeR version 3.18.1 (Robinson et al., 2010) using negative binomial model and exact test based on quantile-adjusted conditional maximum likelihood method (qCML). Genes with a statistically significant change in expression (P<0.05) were selected for further analysis. Analyses of enrichment of Gene Ontology (GO) terms of biological processes in the indicated subsets of genes were performed on the online platform of the Gene Ontology Consortium (www.geneontology.org), and statistically significant (P<0.05) functional terms were retrieved.

This series contains only the RNA-seq data from wildtype, ∆ribD and ∆ribN strains grown in the presence or absence of riboflavin.

first: Ignacio

last: Sepúlveda-Cisternas

first: Andrés

last: Fuentes Flores

last: Vásquez Solis de Ovando

first: Víctor

last: García-Angulo


title: Genome wide DNA methylation analysis of C3(1) SV40TAg mouse model of breast cancer

first: Katharina

last: Heilmann

institute: German Cancer Research Centre

summary: Genome-wide screen for aberrant DNA methylation in mammary gland tumors of the C3(1) Sv40Tag mouse model of breast cancer in comparison with wildtype mammary glands.

overall_design: MCIp (methyl CpG immunoprecipitation)-seq on mammary gland tumors of C3(1) SV40TAg and wildtype mammary glands of 2 age groups. Three biological replicates for each group were analyzed.

first: Clarissa

last: Gerhäuser

first: Christoph

last: Plass


title: Coral larvae of A. gemmifera in responses to elevated CO2

city: Guangzhou, P. R. China

first: Xiangcheng

last: Yuan

address: 164 West Xingang Road, Guangzhou, 510301, P. R. China

institute: South China Sea Institute of Oceanology

summary: Acidified seawater not only resulted in the less settlement of A. gemmifera embryos, but also decreased juvenile sizes and slowed the development of skeleton. The solute carriers (SLC) (membrane transport proteins) responsible for the calcium and bicarbonate transports were downregulated due to elevated CO2.

overall_design: Triplicate control and elevated CO2 treatments (pH=7.6)

first: Tao


title: Autosomal dominant retinitis pigmentosa rhodopsin mutation Q344X drives specific alterations in gene transcription

city: Birmingham

first: Katie

middle: Leigh

last: Bales

state: AL

address: 1825 University Blvd

department: Optometry

institute: University of Alabama at Birmingham

summary: The goal of the study was to identify transcriptional modifications in retinal tissues from mouse model of rhodopsin mutation-associated retinitis pigmentosa (RP), Q344X compared to wild-type (WT). We implemented RNA-sequencing (RNA-seq) at poly(A) selected RNA for transcriptomic profiling. Differentially expressed genes were determined by DESeq2 using the Benjamini & Hochberg p-value adjustment and an absolute log2 fold change cutoff. The results indicate that there is specificity in transcriptional patterns in the retina from Q344x mice relative to WT, including differential expression in the potassium channel gene, Kcnv2, and differential expression in histone genes including the H1 family histone member, H1foo, the H3 histone family 3B, H3f3b, and the histone deacetylase 9, Hdac9.

overall_design: Retinal tissue was extracted from 3 week-old Q344X and WT mice and placed in stabilization reagent. The initial design included 3 replicates from each group but due to low quality RNA and outlier detection, the final animal count for statistical analysis is n=2 for Q344x and n=2 for WT. RNA-seq was performed at poly-A selected RNA.

middle: L

first: Lara

last: Ianov

first: Andrew

last: Kennedy

first: J

last: Sweatt

first: Alecia

last: Gross


title: Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus

city: London

first: George

middle: E.

last: Gentsch

state: Greater London

address: 1 Midland Road

department: Developmental Biology Laboratory

country: United Kingdom

institute: The Francis Crick Institute

summary: We report on the implications of genetic KO versus MO-mediated KD of the mesoderm-specifying Brachyury paralogues in the Western clawed frog Xenopus tropicalis. While both KO and KD embryos fail to activate the same core gene regulatory network, resulting in virtually identical morphological defects, embryos injected with control or target MOs also show a systemic GC content dependent immune response and many off-target splicing defects.

overall_design: Comparison of poly(A) transcriptome between Brachyury null mutants and morphants over two tailbud stages.

middle: E

first: James

last: Smith


title: A Signaling and Transcription Architecture for the Specification of Human Germ Cell Lineage

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: The mechanism for human germ-cell specification, which sets out a complex program generating spermatozoa or oocytes, remains largely unknown.  We established a system for inducing human primordial germ cell-like cells (hPGCLCs) from induced pluripotent stem cells (hiPSCs) via incipient mesoderm-like cells (iMeLCs).  Here, we show that EOMESODERMIN (EOMES) elevates in iMeLCs through WNT signaling and is essential for activating SOX17, a key driver for hPGC(LC) specification, with the duration/dosage of the WNT signaling/EOMES expression dictating the germ-cell competence.  Upon hPGCLC induction, BMP signaling activates TFAP2C independently from SOX17, and SOX17 and TFAP2C instate the hPGCLC program, including BLIMP1 expression, in an interdependent fashion.  The hPGC(LC) specification program is highly consistent with the monkey program, but is divergent from the mouse one regarding key transcription factors and their hierarchy of actions.  These findings delineate evolutionary divergence of mammalian germ-cell specification, providing a foundation for further human germ-cell development in vitro.

overall_design: RNAseq analysis of hiPSCs, iMeLCs and hPGCLCs in multiple knockout/rescued lines

first: Yoji

last: Kojima

first: Kotaro

last: Sasaki

first: Shihori

last: Yokobayashi

first: Tomonori

last: Nakamura

first: Fumio

last: Nakaki

first: So

last: Nagaoka

first: Knut

last: Woltjen

first: Akitsu

last: Hotta

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Developmental Exposure to 2,2’,4, 4’ –Tetrabromodiphenyl Ether Induces Long-Lasting Changes in Liver Metabolism in Male Mice

city: Amherst

first: Alexander

last: Suvorov

address: 149A Goessman, 686 N.Pleasant Str

department: Environmental Health Sciences

institute: University of Massachusetts

summary: Polybrominated diphenyl ethers (PBDEs) were used as flame-retardant additives in a wide range of polymers starting in 1965 and were recently withdrawn from commerce in North America and Europe. Generations that were exposed perinatally to the highest environmental doses of PBDE have now reached 5-20 years of age and in the U.S. account for 1/5 of the total population. Emerging data indicates long-term impairment of metabolic health by PBDE exposure in humans and laboratory animals. We hypothesize that exposure to PBDE during sensitive developmental windows may result in long-lasting changes in liver metabolism. In this study pregnant CD-1 mice were exposed to 0.2 mg/kg 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47) from gestation day 8 till postnatal day 21 and liver RNA-seq was performed on  the last day of dam exposure and on postnatal week 20 in male offspring. Several groups of metabolic genes, including ribosomal and mitochondrial genes were significantly upregulated at both time-points. Genes regulated via mechanistic target of rapamycin (mTOR pathway), the gatekeeper of metabolic homeostasis, were whether up- or down- regulated at both time-points. Thus, perinatal exposure to environmentally relevant doses of BDE-47 in laboratory mice results in long-lasting changes in liver metabolism. Our evidence suggests involvement of the mTOR pathway in the observed metabolic programming of liver.

overall_design: RNA-seq analysis of liver genes in control and exposed male mice (n = 4-5/exposure) on postanatal day 21 and postnatal week 20 following perinatal exposure to BDE-47


title: Transcriptome analysis of secreted proteins responding to nutrient-selection pressure

first: Runmao

last: Lin

address: No. 12 Zhongguancun South Street, Haidian District

institute: The Institute of Vegetables and Flowers, CAAS

summary: To determine secreted proteins that involved in adaptation of nutrient sources and response to nutrient stresses, we analyzed transcriptomes of Pochonia chlamydosporia strain 170 under three different nutrient conditions, CD (nutrient rich medium) that was predicted to repress parasitism, MM (nutrient-poor liquid minimal medium) that was predicted de-repress genes associated with parasitism, and MM-eggs(minimal medium with root-knot nematode eggs) that was prepared to induce parasitism.

overall_design: Three biological replicates (a, b, c) for each of three different nutrient conditions (CD, MM, egg) were prepared and sequenced.

first: Baoming

last: Shen

first: Feifei

last: Qin

first: Xinyue

last: Cheng

first: Bingyan

last: Xie