title: RNA-Seq Analysis of Wild Type and Scn5aΔ/+ left ventricle at dark:light and light:dark phase transitions

first: Elizabeth

middle: Anne

last: Schroder

state: KY

address: 800 Rose Street, MS508

institute: University of Kentucky

summary: We investigated differences in gene expression in left ventricular tissue from WT and ΔKPQ (Scn5aΔ/+) mice.  Tissue was collected diurnally at the phase transitions from dark to light (D:L) and light to dark (L:D).  We employed RNAseq (Novogene) to examine potential variances between the two strains of mice, as well as, any differences in expression at the two time points.  RNAseq provided a snapshot of gene expression which revealed an intact molecular clock for both strains. Previous studies have demonstrated circadian peak or trough at the light phase changes in cardiac tissue in mice for many core molecular clock components. Similar to these studies both strains demonstrated a significant difference in expression between core molecular clock genes Bmal1, Clock, Per1, Per2, Per3 assessed at the phase transitions.  This assessment revealed 39 diurnally expressed genes.  To our surprise, only 6 genes were differently expressed between the two strains of mice.

overall_design: Ventricular mRNA profiles of wild type (WT) and ΔKPQ (Scn5aΔ/+) mice 12 months of age were generated by deep sequencing, 3 pooled samples for each strain/timepoint, using Novogene RNA-seq, Illumina Platform PE150 (NovoSeq 6000)

first: Brian

middle: P

last: Delisle


title: Differentially expressed miRNAs in GSF cells infected by Orf virus at 18h.p.i (OV18h.p.i) and 30h.p.i (OV30h.p.i) compared with the mock-infected GSF cells [miRNA-seq]

status: Public on Mar 06 2020

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

country: China

institute: Hainan University

type: Non-coding RNA profiling by high throughput sequencing

summary: To find out differentially expressed miRNAs in OV18h.p.i and OV30h.p.i compared with GSF cells.

overall_design: Three OV18h.p.i samples, three OV30h.p.i samples and three negative controls

first: Fengyang

last: Wang


title: Differentially expressed mRNAs in GSF cells infected by Orf virus at 18h.p.i (OV18h.p.i) and 30h.p.i (OV30h.p.i) compared with the mock-infected GSF cells [mRNA-seq]

type: Expression profiling by high throughput sequencing

summary: To find out differentially expressed mRNAs in OV18h.p.i and OV30h.p.i compared with GSF cells.


title: Analysis of circRNA,mRNA and miRNA in depolarized neuroblastoma cells

city: Newcastle

first: Ebrahim

last: Mahmoudi

state: NSW

address: Callaghan

country: Australia

institute: University of Newcastle

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

overall_design: Refer to individual Series


title: Next Generation Sequencing analysis of the effects of seed HSF (HaHSFA9 or HSFA4a) overexpression in transgenic tobacco

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

summary:
Background: Heat Stress Factor A9 (A9), a seed-specific transcription factor contributing to seed longevity, also enhances phytochrome-dependent seedling greening
Results: The RNA-seq analyses of imbibed-seed transcripts here reported indicated, potential, additional effects of A9 on cryptochrome-mediated blue-light responses. These analyses also suggested that in contrast to the A9 effects on longevity, which require coactivation by additional factors as A4a, A9 alone might suffice for the enhancement of photomorphogenesis at the seedling stage. We find that upon its seed-specific over-expression, A9 indeed enhanced the expected blue-light responses. Comparative loss-of-function analyses of longevity and greening, performed by similar expression of dominant-negative and inactive forms of A9, not only confirmed the additional greening effects of A9, but also were consistent with A9 not requiring A4a (or additional factors) for the greening effects
Conclusion: Our results strongly indicate that A9 would differentially regulate seed longevity and photomorphogenesis at the seedling stage, A9 alone sufficing for both the phytochrome- and cryptochrome-dependent greening enhancement effects

overall_design: Transcriptome profiling and differential expression analyses between samples of transgenic and non-transgenic Nicotiana tabacum lines

first: Concepción

last: Almoguera

first: Pilar

last: Prieto-Dapena

first: Raul

last: Carranco

middle: L

last: Ruiz

first: Juan

last: Jordano


title: mRNA analysis in depolarized neuroblastoma cells

summary: We profiled mRNA using RNA-seq in the depolarized neuroblastoma cells

overall_design: There were two conditions including depolarized cells (4 samples) treated with KCl and sham-depolarized controls (4 samples) without KCl treatment.

first: Murray

last: Cairns

first: Dylan

last: Kiltschewskij


title: CircRNA analysis in depolarized neuroblastoma cells

summary: We profiled circRNA using RNA-seq in the depolarized neuroblastoma cells to detect depolarization associated circRNAs

overall_design: There were two conditions including depolarized cells (2 samples) treated with KCl and sham-depolarized controls (3 samples) without KCl treatment.


title: miRNA analysis in depolarized neuroblastoma cells

summary: We profiled miRNA using RNA-seq in the depolarized neuroblastoma cells


title: Genome-wide analysis of mRNA polyadenylation in Cortex/Striatum of CPEB4 modified mice [II]

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: To test the mRNA polyadenylation status in brain of CPEB4 modified mice we performed poly(U)-chromatography on RNA purified from a pool of cortex and striatum tissues of control and TgCPEB4∆4 mice

overall_design: Control and TgCPEB4∆4 mice (n=3) were sacrificed at the age of 6 weeks. The cortex and striatum together were quickly dissected, homogenized and total RNA (INPUT) was extracted. The poly(A) RNA fraction was purified by poly(U)-chromatography. Differential elution with 25% or 90% formamide yielded two fractions of mRNAs enriched for short (WASH) or long (ELUTED) poly(A)-tails, respectively. mRNA fractions were extracted, purified and amplified. cDNA was hybridized in GeneChip Mouse PrimeView arrays and CEL files were generated from DAT files using Affymetrix Command Console software.

first: Alberto

last: Parras

first: Hector

last: Anta

last: Stephan-Otto Attolini

last: Mendez

middle: J

last: Lucas


title: Genome-wide analysis of mRNA polyadenylation in Cortex/Striatum of CPEB4 modified mice [I]

summary: To test the mRNA polyadenylation status in brain of CPEB4 modified mice, we performed poly(U)-chromatography on RNA purified from a pool of cortex and striatum tissues of WT and CPEB4 KOGT/+ and CPEB4 KO

overall_design: WT, CPEB4 KOGT/+ and CPEB4 KO (n=2) were sacrificed at the age of 6 weeks. The cortex and striatum together were quickly dissected, homogenized and total RNA (INPUT) was extracted. The poly(A) RNA fraction was purified by poly(U)-chromatography. Differential elution with 25% or 90% formamide yielded two fractions of mRNAs enriched for short (WASH) or long (ELUTED) poly(A)-tails, respectively. mRNA fractions were extracted, purified and amplified. cDNA were hybridized in GeneChip Mouse PrimeView arrays and CEL files were generated from DAT files using Affymetrix Command Console software.


title: Genome-wide analysis of mRNA polyadenylation in prefrontal cortex of idiopathic ASD patients

summary: The aim of this work was to test the mRNA polyadenylation status in the brain of autistic patients. We performed poly(U)-chromatography on RNA purified from post-mortem prefrontal cortex tissue of control and idiopathic ASD cases.

overall_design: Brain specimens from postmortem prefrontal cortex - BA8/9 of male ASD patients and CTRL of an age ranging between 5-23 years  were homogenized and total RNA (INPUT) was extracted. The poly(A) RNA fraction was purified by poly(U)-chromatography. Differential elution with 25% or 90% formamide yielded two fractions of mRNAs enriched for short (WASH) or long (ELUTED) poly(A)-tails, respectively. mRNA fractions were extracted, purified and amplified. cDNA was hybridized in GeneChip Human PrimeView arrays and CEL files were generated from DAT files using Affymetrix Command Console software.


title: CPEB1 and CPEB4-associated mRNAs in mice striatum

summary: To identify CPEB1 and CPEB4 regulated RNA we performed CPEB1 and CPEB4 RNA immunoprecipitation (RIP) followed by microarray hybridization analysis with striatal (St) RNA from wild-type (WT) and R6/1 mice (HD mice).

overall_design: Four male WT and HD mice were sacrified at the age of 7-8 months. Striatum tissue was pooled by genotype. mRNA-protein complexes were crosslinked with formaldehyde in PBS and samples were homogenized in lysis buffer. Lysates were precleared with unconjugated dynabeads and aliquot was stored (INPUT). The rest of the extract was immunoprecipitated with the antibody-conjugated dynabeads (anti-CPEB1, anti-CPEB4 and rabbit igG). Input and immunoprecipitated RNAs were extracted, purified and amplified. cDNA was hybridized in GeneChip mouse arrays and CEL files were generated from DAT files using Affymetrix Command Console software.


title: Genome wide RNA-sequencing of human pluripotent stem-cell derived endothelial cells 48h after transduction with adenoviruses expressing either empty vector, single or multiple transcription factors

status: Public on Mar 05 2020

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG


title: Histone variant H2A.Z.2 primes MITF promoter to direct specification of melanocyte precursors

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

summary: Stem cell establishment and fate assignment are critical for both early development, as well as regeneration. A committed cell state is characterized by its unique transcriptional landscape. In contrast, the upstream fate-biased state is often metastable and transitory, thereby mechanisms of specification are difficult to identify. In this study, we elucidate the role of a histone variant H2a.z.2 in  specification of melanocyte lineage from multipotent neural crest cells. Silencing of H2a.z.2 reduces the number of melanocyte precursors in developing zebrafish embryos, and from mouse embryonic stem cells in vitro. We demonstrate that this histone variant occupies nucleosomes in the promoter of key melanocyte determinant Mitf, and enhances its induction. CRISPR-Cas9 based targeted mutagenesis of this gene in zebrafish drastically reduces adult melanocytes, as well as their regeneration. Thereby our study establishes a histone based specification code upstream to the core gene regulatory network in the neural crest lineage leading to melanocytes. This epigenetic code renders the promoter of key determinant in a poised state conducive for activation by external instructive signals and facilitates establishment of downstream cell fate.

overall_design: Total RNA was extracted from Control morpholino and h2a.z.2 morpholino injected sox10:GFP positive neural crest cells at 16-18hpf. The RNA was quality controlled and quantified using agilent bioanalyzer. The samples were analyzed by Agilent_zebrafish_GXP_8X60K array. Two biological replicates each of control and h2a.z.2 morpholino injected sox10:GFP positive cells were analyzed. We acknowledge Genotypic Technology Private Limited Bangalore for the microarray processing and data analysis reported in this publication.

first: Desingu

middle: A

last: Raja


title: Binding of the Capicua repressor in response to pulses of ERK signaling in the early Drosophila embryo

city: Princeton

first: Stanislav

middle: Y

last: Shvartsman

state: NJ

address: Carl Icahn Lab, Washington Road

department: Chemical and Biological Engineering

country: USA

institute: Princeton University/ Lewis-Sigler Institute for Integrative Genomics

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We have measured by ChIP-seq the binding of Capicua transcriptional repressor (Cic) in Drosophila melanogaster embryos at early nuclear cycle 14. We compared binding in response to ERK activation, utilizing optogenetics.

overall_design: Capicua was endogenously tagged with super-folder GFP, and ChIP-seq was performed using a GFP antibody.  We evaluated binding of Cic in response to pulses of ERK activation, controlled using an optogenetic construct known as OptoSOS.  Cic binding was measured in WT embryos, and optogenetic embryos exposed to no light,1 minute of light, 5 minutes of light, or 30 minutes of light.  Cic binding was also measured in embryos with constitutively active Torso receptor (TorD4021) as a control. OreR embryos ChIPped with the GFP antibody were used as a negative control, to understand what the GFP antibody non-specifically pulls down.  All samples, except for the 1 minute light condition, were done with 3 biological replicates.  The 1 minute light condition had 2 biological replicates. Lastly, 1% inputs for all samples were also sequenced

first: Shannon

middle: E

last: Keenan

first: Shelby

last: Blythe

first: Eric

middle: F

last: Wieschaus


title: Genome wide RNA-sequencing of human pluripotent stem-cell derived endothelial cells 48h after transduction with adenoviruses expressing either empty vector or single transcription factor

summary: To induce barrier of stem-cell derived endothelial cells in vitro cells have been transduced with adenoviruses overexpressing transcription factors with potential role in endothelial cell barrier stabilization.  Adenoviruses overexpressing either ETS1 or FOXC1 or FOXF2 or KLF11 or SOX18 or SOX7 or TAL1 or LEF1 or LMO2 have been been used at 80 MOI. As control adenovirus overexpressing empty vectors has been used (80 MOI).

overall_design: Human pluripotent stem cell-derived endothelial cells have been transduced with adenoviruses expressing empty vector or transcription factors. MOI of used virus has been 80 MOI . Transduction lasted for 48h. Afterwards cells were lyzed using RLT buffer with 1%  β-mercaptoethanol.

first: Filip

last: Roudnicky


title: Genome wide RNA-sequencing of human pluripotent stem-cell derived endothelial cells 48h after transduction with adenoviruses expressing either empty vector of different combination of transcription factors

summary: To induce barrier of stem-cell derived endothelial cells in vitro cells have been transduced with a mixture of adenovirus overexpressing transcription factors with potential role in endothelial cell barrier stabilization.  Adenoviruses overexpressing ETS1, SOX18 and SOX7 have been part of both transcription factor mixtures. As fourth transcription factor in the mixture included TAL1 while the other mixture included LEF1. Each transcription factor was used at 20 MOI. As control adenovirus overexpressing empty vectors has been used (80 MOI).

overall_design: Human pluripotent stem cell-derived endothelial cells have been transduced with adenoviruses expressing empty vector or transcription factors. MOI of used virus has been 80 MOI (empty vector, N=4) or 20 MOI (combination of individual factors, N=3). Transduction lasted for 48h. Afterwards cells were lyzed using RLT buffer with 1%  β-mercaptoethanol.


title: RNA-seq of podocytes treated with glomerular endothelial cell vesicles

city: Nashville

first: Danielle

last: Michell

state: TN

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

summary: The effect of miRNA delivery from glomerular endothelial cells (GEnCs) to podocytes in vitro was examined by mRNA epression in podocytes untreated and treated with extracellular vesicles from GEnCs under varied activation conditions.

overall_design: RNA sequencing of human podocytes untreated (UT) or treated with extracellular vesicles (EVs) derived from human glomerular endothelial cells  (GEnCs) for 24 hours.  EVs were isolated by ultracentrifugation from supernatants of GEnCs in a steady state (SS) or activated with glucose (Glu) or puromycin aminonucleoside (PAN) for 24 hours.

first: Nicola

last: Hill

first: Charles

last: Pusey

first: Kasey

middle: C

last: Vickers

first: Kevin

last: Woollard


title: Glomerular endothelial derived vesicles mediate podocyte dysfunction via extracellular transfer of miRNA-200c-3p


title: Autism-like phenotype and risk gene-RNA deadenylation by CPEB4 mis-splicing

last: Stephan Otto Attolini

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2

city: Mainz

first: Stefanie

last: Ebersberger

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology


title: sRNA-seq of podocytes treated with glomerular endothelial cell vesicles

summary: The effect of miRNA delivery from glomerular endothelial cells (GEnCs) to podocytes in vitro was examined by miRNA epression in podocytes untreated and treated with extracellular vesicles from GEnCs under varied activation conditions.

overall_design: Small RNA sequencing of primary human podocytes untreated (UT) or treated with extracellular vesicles (EVs) derived from human glomerular endothelial cells  (GEnCs) for 24 hours.  EVs were isolated by ultracentrifugation from supernatants of GEnCs in a steady state (SS) or activated with glucose (Glu) or puromycin aminonucleoside (PAN) for 24 hours.


title: iCLIP-based modeling uncovers 3’ splice site definition: how U2AF65 specificity relies on regulation by co-factors

summary: Alternative splicing generates distinct mRNA isoforms and is crucial for proteome diversity in eukaryotes. The RNA-binding protein (RBP) U2AF65 is central to splicing decisions, as it recognizes 3' splice sites and recruits the spliceosome. We established 'in vitro iCLIP' experiments, in which recombinant RBPs are incubated with long transcripts, to study how U2AF65 recognizes RNA sequences and how this is modulated by trans-acting RBPs. We quantitatively measure U2AF65 affinities at hundreds of binding sites, and compare in vitro and in vivo binding landscapes by mathematical modelling. We find that trans-acting RBPs extensively regulate U2AF65 binding in vivo, including enhanced recruitment to 3' splice sites and clearance of intronic regions. Using machine learning, we identify novel trans-acting RBPs (including FUBP1, BRUNOL6 and PCBP1) that modulate U2AF65 binding and affect splicing outcomes. Our study offers a blueprint for the high-throughput characterization of in vitro mRNP assembly and in vivo splicing regulation.

overall_design: Comparison of in vitro and in vivo iCLIP data of U2AF65 and other regulatory RBPs


title: Trib1 regulates T cell differentiation during chronic infection by restraining the effector program

city: Philadelphia

first: Warren

last: Pear

address: 556 BRB II/III 421 Curie Blvd.

institute: University of Pennsylvania

summary: Using the 10X Genomics platform, we performed single cell RNA-sequencing on activated T cells from LCMV clone 13-infected control or CD4-cre+ Trib1-floxed mice to determine how Trib1 regulates T cell population dynamics during chronic infection.

overall_design: Activated (CD44+) T cells (TCRb+) sorted from spleens of control or Trib1 cKO (CD4-cre) mice at day 15 post-LCMV clone 13 infection.

first: Kelly

middle: S

last: Rome

first: Gregory

middle: W

last: Schwartz


title: Expression data from ABCB5-positive and ABCB5-negative GBM cells

city: Boston

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

summary: We analyzed, by HTA 2.0, the GBM cell lines LN-18, LN-229, and U-87 MG after fluoresence-activated cell sorting (FACS) into ABCB5+ and ABCB5- fractions. Poor prognosis associated with glioblastoma multiforme (GBM) results from tumor resistance to therapy and high rate of recurrence. Compelling evidence suggests this is driven by subpopulations of slow-proliferating cancer stem cells with tumor-initiating potential. ATP-binding cassette member B5 (ABCB5) has been identified as a molecular marker for distinct subsets of chemoresistant tumor-initiating cell populations in diverse human malignancies. In the current study, we examined the potential role of ABCB5 in growth and chemoresistance of GBM. We found ABCB5 to be preferentially expressed in clinical GBM tumors and co-expressed with the stem cell marker CD133 in subpopulations of human GBM cell lines U-87 MG, LN-18 and LN-229. Antibody-mediated functional ABCB5 blockade inhibited proliferation and survival of human GBM cells and sensitized them to temozolomide (TMZ)-induced apoptosis. Likewise, in an in vivo GBM xenograft study in immunodeficient mice, anti-ABCB5 monoclonal antibody treatment inhibited tumor growth and sensitized tumors to TMZ therapy. Mechanistically, we demonstrated that ABCB5 regulates cell cycle checkpoint molecules to revoke drug-induced G2-M arrest and augments drug-mediated cell death. Overall, our data establish ABCB5 as a marker of GBM chemoresistance and point to the potential of ABCB5 targeting in improvement of current GBM therapies.

overall_design: Three GBM cell lines were FACS sorted for ABCB5 using anti-ABCB5 mAb clone 3C2-1D12. The sorted populations were collected for RNA extraction and microarray analysis.

first: Catherine

last: Lee


title: Cell type composition and circuit organization of neocortical radial clones

city: Solna

first: Leonard

last: Hartmanis

address: Solnavägen 9

department: Cell & Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: Excitatory neurons arising from a common progenitor establish radially-oriented clonal units in the neocortex which have been proposed to serve as elementary information processing modules. To characterize the cell types and circuit diagram within these clonal units, we performed single-cell RNA-sequencing and multi-cell patch clamp recordings of neurons derived from Nestin-positive progenitors. We found that radial clones do not appear to be fate-restricted, but instead individual clones are composed of a random sampling of the transcriptomic cell types present in a particular cortical area. The effect of lineage on synaptic connectivity depends on the type of connection tested: pairs of clonally related neurons were more likely to be connected vertically, across cortical layers, but not laterally within the same layer, compared to unrelated pairs. We propose that integration of vertical input from related neurons with lateral input from unrelated neurons may represent a developmentally programmed motif for assembling neocortical circuits.

overall_design: Electrophysiological measurements were performed on clonal neurons from a common progenitor spanning multiple brain layers and sampled across a multitude of regions in the mouse brain. mRNA was extracted from the same cells and made into sequence ready libraries using the Patch-seq/ Smart-Seq2 library preparation method

first: Rickard

last: Sandberg


title: Chromatin accessibility analysis of Chx10-Cre Rb1/p107 and Chx10-Cre Rb1/p107/Hells P21 retinae

status: Public on Mar 09 2020

city: Irvine

first: Claudia

last: Benavente

state: CA

address: 839 Medical Sciences Ct, Sprague Hall 108

institute: University of California, Irvine

summary: We used novel genetically engineered mouse models to investigate the role of HELLS during tumorigenesis. Loss of HELLS drastically decreased the incidence of retinoblastoma, delayed tumor progression, and increased overall survival. Retinae from Rb1/p107 DKO and Rb1/p107/Hells TKO mice at postnatal day 21 were analyzed for gene expression using ATAC-seq.

overall_design: Retinal ATAC profiles of 21-day-old Chx10-Cre Rb1/p107 and Chx10-Cre Rb1/p107/Hells mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Jie

last: Wu


title: Contextual epigenetic regulation of lung adenocarcinoma by GATA6 [RNA-Seq]

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary:
Lineage selective transcription factors (TFs) are important regulators of tumorigenesis, but their biological functions are often context dependent and their epigenetic mechanisms of action undefined.
In this study, we uncover a conditional role for the endodermal and pulmonary specifying TF GATA6 during the initiation and progression of Kras mutant lung adenocarcinoma (LUAD). Inhibition of Gata6 in genetically engineered mouse models dampens the proliferation and increases the differentiation of LUAD tumors.
These effects are influenced in part by the epithelial cell type that is targeted for transformation. In lung cancer cells derived from surfactant protein C expressing progenitors, we identify multiple genomic loci that are bound by GATA6. Moreover, suppression of Gata6 in these cells significantly alters chromatin accessibility, particularly at distal enhancer elements. Analogous to its paradoxical activity in the developing lungs, GATA6 expression fluctuates during different stages of LUAD progression and can control diverse lineage gene expression networks associated with cell proliferation, alveolar specification, BMP signaling, and epithelial plasticity.
These findings demonstrate how GATA6 can broadly modulate the epigenome of lung tumor cells, which in turn may potentiate its divergent functions during cancer progression

overall_design: RNAseq, ChIPseq (Gata6, H3K4me3, H3K27ac) and ATACseq of SPC-Cre KP and KPG murine cell lines

first: Anna

last: Arnal-Estape

last: Lopez-Giraldez

first: Wesley

last: Cai

first: Don

middle: X

last: Nguyen


title: Contextual epigenetic regulation of lung adenocarcinoma by GATA6

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

overall_design: Refer to individual Series


title: Contextual epigenetic regulation of lung adenocarcinoma by GATA6 [ChIP-Seq]


title: Transcriptome profiling of Hu sheep testicular development associated with dietary energy restriction and during compensatory compensation

city: nanjign

first: yi

middle: xuan

last: fan

address: No 1 weigang

institute: nanjing agricultural university

summary: To investigate the effect of energy levels on sheep testicular development, we systematically investigated mRNAs using high-throughput sequencing at two dietary energy levels of Hu sheep (maintenance energy and 55% energy levels) chrysophanol alone treatment and combination treatment as well as revealed that the combination treatment the most defence-related genes induced expression changes. We identified numerous differentially expressed genes that exhibited distinct expression patterns, and defence-related genes that were highly differentiated between the physcion and chrysophanol alone treatment and combination treatment. These genes have known or potential roles in defense response and were enriched in functional gene categories potentially responsible for cucumber resistance. Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to defense response.

overall_design: mRNA profiles of Hu sheep were generated by deep sequencing, three testis samples for each dietary energy levels, including maintenance energy and 55% energy levels, using Illumina.

first: Yixuan

last: Fan

first: Yanli

last: Zhang


title: Transcriptional profiling of macaques treated with ALVAC- and NYVAC-SIV+gp120 alum vaccines

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University

summary: We compare the immunogenicity of ALVAC- or NYVAC- based SIVmac251 vaccine regimens combined with gp120/alum boosts and their relative efficacy in a cohort of 65 female rhesus macaques. Both NYVAC- and ALVAC-based regimens induced equivalent titers of serum binding antibodies to gp120, whereas NYVAC elicited significantly higher envelope specific T cell responses. Surprisingly, however, only the ALVAC-based regimen was able to significantly decrease the risk of SIVmac251 acquisition following repeated low-dose intravaginal challenges. The risk of virus acquisition was associated negatively with the frequency of classical monocytes and positively with non-classical. The systems biology approach used to investigate the molecular basis of the different vaccine efficacies demonstrated specific expression profiles elicited by the ALVAC-based regimen that correlate with efficacy.

overall_design:
A total of 65 female rhesus macaques were randomized into five groups: ALVAC-SIV/gp120 (20 animals), NYVAC-SIV/gp120 (20 animals), ALVAC-control (10 animals), NYVAC-control (10 animals), and naïve (5 animals). The animals in the ALVAC-SIV/gp120 and NYVAC-SIV/gp120 groups were immunized at weeks 0, 4, 12, and 24 with ALVAC-SIV (vCP180) or NYVAC-SIV (VP1071) carrying the identical Env-Gag-Pol genes, respectively. At weeks 12 and 24, the animals from these groups received an alum-formulated gp120 protein boost. The animals in the ALVAC-control and NYVAC-control groups were immunized at weeks 0, 4, 12, and 24 with empty ALVAC-SIV (vCP180) or NYVAC-SIV (VP1071) vectors, respectively. At weeks 12 and 24, the animals from these groups received alum.
technical replicate: P168_A06015_w0.6h, P168_A06015_w0.6h_rep1
technical replicate: P168_A06028_w0.6h_rep1, P168_A06028_w0.6h_rep2
technical replicate: P168_A06082_w0.0h, P168_A06082_w0.0h_rep1
technical replicate: P168_A06083_w0.24h, P168_A06083_w0.24h_rep1

first: Rafick-Pierre

last: Sékaly

first: Michael

last: Gale

first: Genoveffa

last: Franchini

first: Giacomo

last: Gorini


title: Long noncoding RNA expression profiles in granulosa cells from PCOS patients and women with normal ovarian reserve

city: Guangzhou

first: Yudong

last: Liu

state: Guangdong

address: NO.1838 GuangZhou Northern Road

department: Center for Reproductive Medicine, Department of Gynecology and Obstetrics

institute: Nanfang Hospital, Southern Medical University

summary: LncRNAs and mRNAs profiling of gonadotropin-stimulated granulosa cells from PCOS patients and controls (women with normal ovarian reserve)

overall_design: Two-condition experiment, PCOS vs. non-PCOS Biological replicates: 7 PCOS replicates, 7 non-PCOS replicates

first: Yu-dong

first: Shi-ling

last: Chen


title: Contextual epigenetic regulation of lung adenocarcinoma by GATA6 [ATAC-Seq]


title: Gene expression in human endometrium cells (ATCC 4003) [control]

status: Public on Mar 04 2020

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

summary: To detect the gene profiles in non-decidualized stromal cells, cultured stromal cells were collected and subjected to RNA-Seq. After aligned to mouse mm10 by HISAT2, RPKM value was calculated by Edger. Our results show that SOX4 is one of the most abundant gene in the whole SOX family. The expression of SOX4 was further confirmed by qPCR, ISH and immunofluorescence. The expression of SOX4 in human endometrium indicated the essential role of SOX4 for reproduction. This RNA-Seq data provides fundamental information for our further physiological study of SOX4.

overall_design: Total RNAs in whole uterus from cultured 4003 stromal cells were extracted by TRIzol and purified by ploy-A before subjected to RNA-Seq by HiSeq2500. The expression of level of each gene is normalized to RPKM.


title: Microbial communities of vineyard BRO11-BRO12 soils (GeoChip)

city: FIRENZE

first: Stefano

last: MOCALI

state: FI

address: VIA di Lanciola 12/a

department: AA

country: Italy

institute: CREA

summary: In this work, we used a functional gene microarray approach (GeoChip) to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a “within-vineyard” scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar

platform_organism: Bacteria Archaea Fungi Viruses

overall_design: Three replicates of each top-soil hosting vine plants yielding grapes and wine of different quality were collected and compared among the two areas (BRO11 and BRO12) within the same vineyard in Brolio (Tuscany, Italy)

last: Mocali


title: Nanoengineered Osteoinductive Bioink for Three-Dimensional Bioprinting Bone Tissue

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

summary: Bioprinting is an emerging additive manufacturing approach to the fabrication of patient-specific, implantable three-dimensional (3D) constructs for regenerative medicine. However, developing cell-compatible bioinks with high printability, structural stability, biodegradability, and bioactive characteristics is still a primary challenge for translating 3D bioprinting technology to preclinical and clinal models. To overcome this challenge, we develop a nanoengineered ionic covalent entanglement (NICE) bioink formulation for 3D bone bioprinting. The NICE bioinks allow precise control over printability, mechanical properties, and degradation characteristics, enabling custom 3D fabrication of mechanically resilient, cellularized structures. We demonstrate cell- induced remodeling of 3D bioprinted scaffolds over 60 days, demonstrating deposition of nascent extracellular matrix proteins. Interestingly, the bioprinted constructs induce endochondral differentiation of encapsulated human mesenchymal stem cells (hMSCs) in absence of osteoinducing agents such as dexamethasone or bone morphogenic protein-2 (BMP-2). Using next-generation transcriptome sequencing (RNA-seq) technology, we establish the role of nanosilicates, a bioactive component of NICE bioink, to stimulate endochondral differentiation at the transcriptome level. Overall, the osteoinductive bioink has the ability to induce formation of osteo-related mineralized extracellular matrix by encapsulatedhMSCsingrowthfactor-freeconditions.Furthermore,wedemonstratedtheabilityofNICEbioinktofabricatepatient-specific, implantable 3D scaffolds for repair of craniomaxillofacial bone defects. We envision transformation of this NICE bioink technology toward a realistic clinical process for 3D bioprinting patient-specific bone tissue for regenerative medicine.

overall_design: Establish the role of nanosilicates, a bioactive component of NICE bioink, to stimulate endochondral differentiation

first: David

last: Chimene

first: L

last: Miller

last: Cross

first: Gaharwar

middle: K

last: Akhilesh


title: Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq)

city: Illkirch

first: Kenny

last: Schumacher

address: 1, rue Laurent Fries

department: Department of Developmental Bioliogy and Stem Cells

country: France

institute: IGBMC

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae


title: The function and mechanism about how ORAOV1-B potentiates the OSCC metastasis.

city: Chengdu

first: Qianming

state: Sichuan

address: Renmin Nan Street Section 3 NO.14

department: oral medicine

institute: Sichuan University

summary:
Lymph node metastasis, a powerful prognostic indicator of oral squamous cell carcinoma (OSCC), is chiefly responsible for cancer death. Long non-coding RNA (lncRNA) is recently addressed to significantly account for modulating OSCC metastasis. Here, we identified a novel alternative splice of Oral Cancer Overexpressed 1 (ORAOV1), ORAOV1-B, which was subsequently validated as an lncRNA and correlated with OSCC lymph node metastasis; significantly increased invasion and migration were observed in ORAOV1-B-overexpressed OSCC cells; In the metastatic model, ORAOV1-B also significantly contributed to OSCC-related lung metastasis. cDNA microarrays was performed to compare up- or down-regulated genes in EV and ORAOV1-B sets of OSCC, which suggested TNFα as a potential downstream of ORAOV1-B and the upregulation of pro-inflammatory genes, indicating the activation of NF-κB pathway.
In summary, the novel splice variant ORAOV1-B is an lncRNA, which significantly potentiates OSCC invasion and metastasis by binding to Hsp90 and activating the NF-κB-TNFα loop. Our study implies that ORAOV1-B might serve as an attractive OSCC metastasis intervention target.

overall_design: OSCC tissue study showed that ORAOV1-B was significantly higher in OSCC patients with lymph node metastasis. Overexpression of ORAOV1-B by lentivirus in OSCC cells could verify the function and mechanism of ORAOV1-B in OSCC progression. HSC-3 and HSC-4 cells were transduced with EV or ORAOV1-B lentivirus to generate the stably cells with overexpressed ORAOV1-B or not. cDNA microarray was performed on   EV or ORAOV1-B sets of HSC-3 and HSC-4 cells to detect some ORAOV1-B-regulating pathways or genes involved in the process of tumor invasion and metastasis.

first: Xiaobo

last: Luo

first: Fangman

first: Yuchen

last: Jiang

first: Yan

last: Qiu

first: Hao

last: Xu

first: Zihao

last: Wei

first: Guoli

last: Tian

first: Wang

last: Gong

first: Yao

last: Yuan

first: Hui

last: Feng

first: Liang

last: Zhong

first: Ning

last: Ji

first: Xiaoping

first: Chongkui

last: Sun

first: Taiwen

last: Li

first: Jing

first: Xiaodong

first: Peng

first: Xin

last: Zeng

first: Min

last: Zhou

first: Yu

first: Hongxia

last: Dan

first: Lu


title: Gene expression in human endometrium cells (ATCC 4003)

first: Wenbo

last: Deng


title: Gene expression-based, identification of differential expression genes in MDA-MB-231 cells with or without knockout of CCDC25 gene and transfected with NET-DNA

first: linbin

last: Yang

address: yanjiangxilu 107

institute: Sun Yet-sen University

summary: To explore the intracellular function of CCDC25, we transfected NET-DNA into MDA-MB-231 cells with or without CCDC25-knockout, and performed comparative microarray analyses.

overall_design: MDA-MB-231 cells  transdecued with a control or sgRNA targeting CCDC25 were selected with puromycin for 2 weeks to get the stably transduced cells. 5 x 105 MDA-MB-231 with or without CCDC25 knockout were trasfected with 0.5 ug NET-DNA and cultured for 24 hours. The cells were isolated for further analyses and microarray

first: Linbin


title: Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Med14-Med17-doubleAID)

first: Kenny

last: Schumacher

summary: This project aims to understand the function of Mediator and the interplay  in transcription in S. cerevisiae. Thus we analyzed total and newly synthesized RNA levels in  a conditional Med14 and Med17 depletion strain. For this purpose we used an auxin inducible degron system system to specifically induce the degradation Med14 and Med17 by addition of auxin into the culture medium. We measured transcript levels after 30 min auxin or DMSO (control) treatment  induction of degradation of Med14 and Med17 by the addition of auxin (30 min) or with the carrier DMSO (control) followed by a 6 min labelling of newly synthesized RNA with 4-thiouracil (4tU). In parallel wiltype S.pombe cells were labelled with 4tU for 6min during midlog growth phase. Prior to RNA extraction (Ribopure Yeast Kit, Ambion) our labelled S.cerevisiae cells of interest were mixed with labelled S.pombe cells as a spike to allow normalization against an exogenous reference (ratio 3 S .cerevisiae for 1 S.pombe cell. From the total RNA we purified the 4tU labelled fraction of RNAs containing 4tU. Both the total RNA and the purified newly synthesized RNAs will then be subject to RNA-sequencing after ribosomal RNA depletion.  In summary, we will provide 8 samples for this project containing RNA from both S.cerevisiae and S.pombe. The sample read counts were normalized with size factors computed by the median-of-ratios method proposed by Anders and Huber (Anders et al. 2010) on S. pombe genes to make these counts comparable between samples.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Experiments were performed using biological replicates (labeled 1 or 2) for each condition. The analyzed cell line contains a knock-in of Tir1 from Oryza sativa and an AID tag on Med14 and Med17 that allows the specific degradation of both proteins in the presence of auxin. Cells were either treated with 3-IAA ("+ auxin") or DMSO ("-auxin") for 30 min followed by a 6 min labelling with 5 mM 4-thiouracil (4tU). total RNA was extracted and analyzed by RNA-seq. Furthermore 4tU labelled RNA (nsRNA) was purified from total RNA extracts and also analyzed by RNA-seq.


title: Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Sua7-AID)

summary: This project aims to understand the function of general transcription factor TFIIB in transcription in S. cerevisiae. Thus, we analyzed total and newly synthesized RNA levels in a conditional Sua7 (TFIIB) depletion strain. For this purpose we used an auxin inducible degron system system to specifically induce the degradation Sua7 by addition of auxin into the culture medium. We measured transcript levels after 30 min auxin or DMSO (control) treatment  induction of degradation of Sua7 by the addition of auxin (30 min) or with the carrier DMSO (control) followed by a 6 min labelling of newly synthesized RNA with 4-thiouracil (4tU). In parallel wiltype S.pombe cells were labelled with 4tU for 6min during midlog growth phase. Prior to RNA extraction (Ribopure Yeast Kit, Ambion) our labelled S.cerevisiae cells of interest were mixed with labelled S.pombe cells as a spike to allow normalization against an exogenous reference (ratio 3 S .cerevisiae for 1 S.pombe cell. From the total RNA we purified the 4tU labelled fraction of RNAs containing 4tU. Both the total RNA and the purified newly synthesized RNAs will then be subject to RNA-sequencing after ribosomal RNA depletion.  In summary, we will provide 8 samples for this project containing RNA from both S.cerevisiae and S.pombe. The sample read counts were normalized with size factors computed by the median-of-ratios method proposed by Anders and Huber (Anders et al. 2010) on S. pombe genes to make these counts comparable between samples.

overall_design: Experiments were performed using biological replicates (labeled 1 or 2) for each condition. The analyzed cell line contains a knock-in of Tir1 from Oryza sativa and an AID tag on Sua7 that allows the specific degradation of Sua7 in the presence of auxin. Cells were either treated with 3-IAA ("+ auxin") or DMSO ("-auxin") for 30 min followed by a 6 min labelling with 5 mM 4-thiouracil (4tU). total RNA was extracted and analyzed by RNA-seq. Furthermore 4tU labelled RNA (nsRNA) was purified from total RNA extracts and also analyzed by RNA-seq.


title: Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Med14-AID, Med17-AID)

summary: This project aims to understand the function of different mediator subunits (Med14 and Med17) in transcription in S. cerevisiae. Thus we analyzed total and newly synthesized RNA levels in conditional Med14 and Med17 depletion strains. For this purpose we used an auxin inducible degron system system to specifically induce the degradation Mediator subunits by addition of auxin into the culture medium. We measured transcript levels after 30 min auxin or DMSO (control) treatment  induction of degradation of Med14 or Med17 by the addition of auxin (30 min) or with the carrier DMSO (control) followed by a 6 min labelling of newly synthesized RNA with 4-thiouracil (4tU). In parallel wiltype S.pombe cells were labelled with 4tU for 6min during midlog growth phase. Prior to RNA extraction (Ribopure Yeast Kit, Ambion) our labelled S.cerevisiae cells of interest were mixed with labelled S.pombe cells as a spike to allow normalization against an exogenous reference (ratio 3 S .cerevisiae for 1 S.pombe cell. From the total RNA we purified the 4tU labelled fraction of RNAs containing 4tU. Both the total RNA and the purified newly synthesized RNAs will then be subject to RNA-sequencing after ribosomal RNA depletion.  In summary, we will provide 16 samples for this project containing RNA from both S.cerevisiae and S.pombe. The sample read counts were normalized with size factors computed by the median-of-ratios method proposed by Anders and Huber (Anders et al. 2010) on S. pombe genes to make these counts comparable between samples.

overall_design: Experiments were performed using biological replicates (labeled 1 or 2) for each condition. The analyzed cell line contains a knock-in of Tir1 from Oryza sativa and an AID(IAA7) tag on Med14 or Med17 that allows the specific degradation of Med14 or Med17 in the presence of auxin. Cells were either treated with 3-IAA ("+ auxin") or DMSO ("-auxin") for 30 min followed by a 6 min labelling with 5 mM 4-thiouracil (4tU). total RNA was extracted and analyzed by RNA-seq. Furthermore 4tU labelled RNA (nsRNA) was purified from total RNA extracts and also analyzed by RNA-seq.


title: Construction and Application of an Epigenetic Atlas of the Human Heart

city: Calgary

first: Steven

last: Greenway

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

type: Methylation profiling by high throughput sequencing

summary: Epigenetic modifications including DNA methylation regulate gene expression and contribute to specialization of cells. Currently, there is limited knowledge of the epigenetic patterns of human heart. We have used healthy cardiac tissues from different anatomical regions of the human heart to study unique methylation signatures specific to human heart.

overall_design: We have generated genome-wide methylomes using reduced representation bisulfite sequencing from healthy human cardiac tissues in triplicate such as left atrium, right atrium, left ventricle, right ventricle, aorta, pulmonary artery, mitral valve , tricuspid valve, aortic valve and pulmonary valve.  Using massively parallel sequencing technology, we have created a DNA methylation atlas of the human heart. This data provides a resource for future studies and may help identify new disease biomarkers and increase our understanding of cardiac development.

first: Dimple

last: Prasher

first: Patrick

middle: M

last: McCarthy

first: Gavin

last: Oudit

first: Paul

last: Fedak

first: Igor

last: Kovalchuk


title: ChIP-Seq analysis of IbBBX24 transgenic sweet potato plants

city: Beijing

first: Zhang

last: Huan

address: 2 yuanmingyuan west road

institute: China Agricultural University

summary: To better understand the regulatory mechanisms of IbBBX24-mediated Fusarium oxysporum Schlecht. f. sp. batatas (Fob) resistance, we performed ChIP-Seq analysis using overexpression line infected with Fob at 1 dpi.

first: Shaozhen

last: He

first: Huan

last: Zhang


title: RNA-Seq analysis of IbBBX24 transgenic sweet potato plants

summary: To better understand the regulatory mechanisms of IbBBX24-mediated Fusarium oxysporum Schlecht. f. sp. batatas (Fob) resistance, we performed RNA-Seq analysis using overexpression line, RNA interference and WT plants infected with Fob at 1 dpi.

overall_design: Sweet potato mRNA profiles of the leaves of WT (variety Lizixiang), IbBBX24-OE , and IbBBX24-RNAi plants treated by the spore infection method at 1 dpi were generated using the Illumina HiSeq X Ten PE150 system. Two independent biological replicates were taken.


title: Aberrant Development Corrected in Adult-Onset Huntington's Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation

first: Ryan

middle: Gar-Lok

last: Lim

state: California

address: 845 Health Sciences Rd.

department: MIND

institute: UC Irvine


title: Wapl-mediated release of Scc1-cohesin regulates chromosome structure and segregation in mouse oocytes

city: Vienna

first: Kikuë

last: Tachibana

state: --- Select a state ---

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

summary: Cohesin is essential for genome folding and chromosome inheritance through cell divisions. In somatic cells, both of these functions are mediated by Scc1-cohesin, which in mitosis is released from chromosomes by Wapl and separase. In mammalian oocytes, cohesion is mediated by Rec8-cohesin. Scc1 is also expressed but neither required nor sufficient for cohesion, and its function in oocytes is unknown. Likewise, it is unknown whether Wapl regulates one or both cohesin complexes and chromosome segregation in mature oocytes. Using conditional mouse mutagenesis, we show that in meiosis I Wapl is required for proper chromosome segregation, predominantly releases Scc1-cohesin from chromosomes and promotes production of euploid eggs. Using single-nucleus Hi-C, we found that Scc1 is essential for chromatin loops and topologically associating domains (TADs) in oocytes. Increasing Scc1 residence time on chromosomes by Wapl depletion leads to vermicelli formation and intra-loop structures but, unlike in mitotic cells, does not increase loop size. This implies that loop size has reached a maximum in oocytes, possibly because it is limited by barriers such as cohesive cohesin. We conclude that distinct cohesin complexes generate loops and cohesion in mammalian oocytes and propose that the same principle applies to all cell types and species.

overall_design: We generated Scc1-control (Scc1fl/fl), Scc1-KO (Scc1∆/∆), Wapl-control (Waplfl/fl) and Wapl-KO (Wapl∆/∆) Hi-C libraries from single NSN and SN oocytes of 2-2.5 months old mice: Scc1fl/fl, Scc1fl/fl (Tg)Zp3-Cre, Waplfl/fl and Waplfl/fl (Tg)Zp3-Cre, respectively.  Number of oocytes analyzed and Hi-C libraries prepared: 21 NSN Scc1fl/fl oocytes, 17 SN Scc1fl/fl oocytes, 20 NSN Scc1∆/∆ oocytes, 15 SN Scc1∆/∆ oocytes, 12 NSN Waplfl/fl oocytes, 11 SN Waplfl/fl oocytes, 20 NSN Wapl∆/∆ oocytes, 16 SN Wapl∆/∆ oocytes.

first: Mariana

last: Silva

first: Sean

last: Powell

first: Sabrina

last: Ladstätter

first: Johanna

last: Gassler

first: Roman

last: Stocsits

first: Antonio

last: Tedeschi

first: Jan-Michael

last: Peters


title: RNA-sequencing of ex vivo nasal and tracheal epithelial cells from a paediatric cohort including non-atopic non-wheezers, atopic non-wheezers, atopic wheezers, and non-atopic wheezers

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

institute: University of Western Australia

summary: Rationale: Emerging evidence suggests that disease vulnerability is expressed throughout the airways; the so-called “unified airway hypothesis” but the evidence to support this is predominantly indirect. Objectives: To establish the transcriptomic profiles of the upper and lower airway and determine their level of similarity irrespective of airway symptoms (wheeze) and allergy. Methods: We performed RNA-sequencing on upper and lower airway epithelial cells from 63 children with or without wheeze and accompanying atopy, utilizing differential gene expression and gene co-expression analyses to determine transcriptional similarity. Results: We observed ~91% homology in the expressed between the two sites. When co-expressed genes were grouped into modules relating to biological functions, all were found to be conserved between the two regions, resulting in a consensus network containing 16 modules associated with ribosomal function, metabolism, gene expression, mitochondrial activity and anti-viral responses through interferon activity. Although symptom associated gene expression changes were more prominent in the lower airway, they were reflected in nasal epithelium and included; IL1RL1, PTGS1, CCL26 and POSTN. Through network analysis we identified a cluster of co-expressed genes associated with atopic-wheeze in the lower airway, which could equally distinguish atopic and non-atopic phenotypes in upper airway samples. Conclusions: We show that the upper and lower airway are significantly conserved in their transcriptional composition, and that variations associated with disease are present in both nasal and tracheal epithelium. Clinical Implication: Findings from this study supporting a unified airway imply that clinical insight regarding the lower airway in health and disease can be gained from studying the nasal epithelium.

overall_design: Four participant groups; non-atopic non-wheezers, atopic wheezers, atopic non-wheezersand non-atopic wheezers - paired nasal and bronchial brushing samples for most participants. Matching replicate numbers indicate paired samples unless otherwise specified.

first: Anthony

last: Kicic

first: Kak-Ming

last: Ling

first: Kirsty

last: Nichol

first: Denise

last: Anderson

first: Peter

last: Wark

first: Darryl

last: Knight

last: Bosco

first: Stephen

last: Stick


title: Brain endothelial cells are exquisite sensors of age-related circulatory cues

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

institute: Stanford

summary: single cell RNAseq of  brain endothelial cells in normal aging, aged and young plasma treatment, and LPS treatment

overall_design: single cell RNAeq of murine brain endothelial cells

middle: B


title: Dynlrb1 is Essential for Dynein Mediated Transport and Neuronal Survival

city: Los Angeles

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: We identified Dynlrb1 as an essential gene for sensory neuron survival and performed RNA sequencing to identify the molecular mechanism mediating the role of  Dynlrb1 in sensory neuron survival.

overall_design: We analyzed of mRNA expression between wild type and Dynlrbtm1a/+ heterozygous mice at 12, 24 and 48h in culture. 3 time points, 2 genotypes, 3 biological repat per time point per genotype.

first: Marco

last: Terenzio

first: Agostina

last: Di Pizio

first: Ida

last: Rishal

first: Letizia

last: Marvaldi

first: Pierluigi

last: Di Matteo

first: Giovanni

last: Coppola

first: Giampietro

last: Schiavo

first: Elizabeth

last: Fisher

first: Mike

last: fainzilber


title: small RNAs, degradome and transcriptome sequencing in Populus × euramericana “Neva” leaves in response to para-hydroxybenzoic acid [leaf, miRNA-Seq]

city: Nanjing

first: Chen

last: Jishuang

state: Jiangsu

address: NO.30 Puzhu Road(S)

department: College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

summary: In this study, we combined the analyses of the transcriptome, small RNAs (sRNAs), and the degradome in Populus × euramericana “Neva” leaves to identify key regulatory miRNA-targeted circuits under different para-hydroxybenzoic acid concentration treatments.

overall_design: Leaf-miRNA

first: Guoting

last: Liang


title: Small RNAs, degradome and transcriptome sequencing in Populus × euramericana “Neva” roots in response to para-hydroxybenzoic acid [root, miRNA-Seq]

summary: In this study, we combined the analyses of the transcriptome, small RNAs (sRNAs), and the degradome in Populus × euramericana “Neva”roots to identify key regulatory miRNA-targeted circuits under different para-hydroxybenzoic acid concentration treatments.

overall_design: Root-miRNA


title: small RNAs, degradome and transcriptome sequencing in Populus × euramericana “Neva” leaves and roots in response to para-hydroxybenzoic acid

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

overall_design: Refer to individual Series


title: small RNAs, degradome and transcriptome sequencing in Populus × euramericana “Neva” leaves in response to para-hydroxybenzoic acid [leaf, RNA-Seq]

overall_design: Leaf-RNA


title: A circular RNA from the MDM2 locus regulates proliferation by suppressing basal p53 levels

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: Circular RNAs (circRNAs) are a class of noncoding RNAs produced by a non-canonical form of alternative splicing called back-splicing. To investigate a potential role of circRNAs in the p53 pathway, we analyzed RNA-seq data from colorectal cancer cell lines (HCT116, RKO and SW48) in the presence or absence of DNA damage. Surprisingly, unlike the strong p53-dependent induction of hundreds of p53-induced mRNAs, only a few circRNAs were induced from the p53-induced genes. Circ-MDM2, an annotated circRNA from the MDM2 locus, was one of the handful of circRNAs that originated from a p53-induced gene. Given the central role of MDM2 in suppressing p53 protein levels and p53 activity, we investigated the function of circ-MDM2. Knocking down circ-MDM2 with siRNAs that targeted the circ-MDM2 junction and had no effect on linear MDM2 mRNA, resulted in increased basal p53 levels and growth defects in vitro and in vivo. Consistent with these results, transcriptome profiling showed increased expression of several direct p53 targets, reduced Rb phosphorylation and defects in G1-S progression upon silencing circ-MDM2. Our results reveal the role of a novel circRNA by which the MDM2 locus suppresses p53 levels and cell cycle progression.

overall_design: RNA samples were collected in biological duplicates from HCT116 control and circ-MDM2 knockdown HCT116 cells.

first: Xiao

middle: L

last: Li

first: Ritu

last: Chaudhary


title: Mechanisms of heat-induced transcriptional memory profiled in mouse embryonic fibroblasts (MEFs).

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

institute: KTH Royal Institute of Technology

summary: Precision run-on sequencing (PRO-seq) of nascent RNA synthesis across the mouse genome. The PRO-seq data was generated from MEFs that were either unconditioned (unC) or preconditioned with a single 1h heat shock exposure, followed by a 48-h recovery (preC).The unconditioned and preconditioned cells were subjected to a single heat shock, during which the the kinetics of nascent transcription response was monitored.

overall_design:
Genome-wide nascent transcription profiles mapped in MEFs in non-strss conditions, upon 1h heat shock and 4h recovery from heat shock. Additionally, MEFs were either unconditioned or preconditioned with a single heat shock exposure, and the kinetics of transriptional response to heat shock monitored with PRO-seq upon 0', 12.5', 25' and 40' additional heat shock exposure.

Please note that [1] the Normalized_*.bigWig processed data was generated from all replicates combined and is linked to the corresponding replicate 1 sample records (i.e.*BR1, *BR1a samples) [2] the Normalized_PROseq_MEF_uC_12HS_BRs_*Strand.bigWig processed data was generated from GSM1843440 (GSE71708) raw data (5' adapter sequence: TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) and is linked as Series supplementary files.

first: Dig

last: Mahat

first: John

middle: T

last: Lis


title: Small RNAs, degradome and transcriptome sequencing in Populus × euramericana “Neva” roots in response to para-hydroxybenzoic acid [root, RNA-Seq]

overall_design: Root-RNA


title: RNA-Seq and ChIP-seq analysis of IbBBX24 transgenic sweet potato plants

first: Zhang

last: Huan


title: Differentially expressed miRNAs and mRNAs in GSF cells infected by Orf virus at 18h.p.i (OV18h.p.i) and 30h.p.i (OV30h.p.i) compared with the mock-infected GSF cells

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

institute: Hainan University


title: Expression data from mouse heart after aortic binding surgery for 2 weeks

city: Wuhan

first: yanfang

last: su

state: Hubei

address: No. 169, EastLakeRoad, Wuchang, Wuhan

department: Zhongnan hospital

institute: Wuhan University

summary:
We found that tmbim1 is decreased in heart samples from patients with heart failure and in heart tissues from mice with aortic banding (AB)-induced cardiac hypertrophy. Furthermore, deleting Tmbim1 aggravates the AB-induced cardiac hypertrophy. To investigate the potential mechanism by which tmbim1 regulates cardiac hypertrophy, we treated wild type and tmbim1 knockout mice with aortic binding surgery for 2 weeks, and performed microarray to identify the expression pattern and the potential important targets.
We used microarrays to detect the global gene expression in the hearts of wild type and Tmbim1 knockout mice after treatment with aortic binding surgery for 2 weeks and identified distinct classes of altered genes

overall_design: Eight weeks old wild type (n=3) and Tmbim1 knockout (n=3) mice were treated with aortic binding surgery for 2 weeks, and the hearts were dissected after.  Total RNA was extracted and a total of 400ng RNA was used following Affymetrix instruction. 3 biological samples for each genotype

first: Yanfang

last: Su

first: Peng

last: Zhang


title: Neutrophil-mediated immune response as a possible mechanism of acute unilateral vestibulopathy

status: Public on Mar 03 2020

city: Yangsan

first: Jae-Hwan

last: Choi

address: Kumo-ro 20, Beomo-ri, Mulgum-eup

department: Neurology

country: South Korea

institute: Pusan National University Yangsan Hospital

summary:
Acute unilateral vestibulopathy (AUV) is the third most common peripheral vestibular disorder after BPPV and Meniere’s disease. Several hypotheses have been proposed for the etiology of AUV including viral infection, vascular occlusion, and autoimmune disease, but the exact pathogenesis still remains unknown.
The aim of this study was to investigate the underlying pathogenesis of AUV using the gene expression profiling combined with bioinformatic analysis.

overall_design: Total RNAs were extracted from peripheral blood mononuclear cells of 10 AUV patients and 10 normal controls. Using the Affymetrix Human Clariom S Assay, the differentially expressed genes (DEGs) between AUV and normal control samples were screened by the cut-off criteria (|fold changes| > 1.5 and p-value < 0.05). Functional enrichment analysis for DEGs was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and the protein-protein interaction (PPI) network was constructed using the STRING database.

first: Eun

middle: H

last: Oh

first: Je-Keun

last: Rhee


title: Dnmt3a and Dnmt3b-mediated decommissioning of fetal enhancers linked to kidney disease

city: Philadelphia

first: Hongbo

last: Liu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary:
Cytosine methylation is an epigenetic mark that dictates cell fate and response to stimuli. The timing and establishment of methylation logic during kidney development remains unknown. DNA methyltransferase 3a and 3b are the enzymes capable of establishing de novo methylation.
We generated mice with genetic deletion of Dnmt3a and Dnmt3b in nephron progenitor cells (Six2Cre Dnmt3a/3b) and kidney tubule cells (KspCre Dnmt3a/3b). We characterized KspCre Dnmt3a/3b mice at baseline and after injury. Unbiased omics profiling, such as whole genome bisulfite sequencing, reduced representation bisulfite sequencing and RNA sequencing were performed on whole-kidney samples and isolated renal tubule cells.
KspCre Dnmt3a/3b mice showed no obvious morphologic and functional alterations at baseline. Knockout animals exhibited increased resistance to cisplatin-induced kidney injury, but not to folic acid–induced fibrosis. Whole-genome bisulfite sequencing indicated that Dnmt3a and Dnmt3b play an important role in methylation of gene regulatory regions that act as fetal-specific enhancers in the developing kidney but are decommissioned in the mature kidney. Loss of Dnmt3a and Dnmt3b resulted in failure to silence developmental genes. We also found that fetal-enhancer regions methylated by Dnmt3a and Dnmt3b were enriched for kidney disease genetic risk loci. Methylation patterns of kidneys from patients with CKD showed defects similar to those in mice with Dnmt3a and Dnmt3b deletion.
Our results indicate a potential locus-specific convergence of genetic, epigenetic, and developmental elements in kidney disease development.

overall_design: WGBS of Cdh16 positive cell from kidneys of 3 weeks old control mice and KspCreDnmt3a/3b double knock-out mice (week 3); RRBS of kidneys from 3 weeks old control mice, Six2CreDnmt3a/3b double knock-out mice, and KspCreDnmt3a/3b double knock-out mice (week 3); RNA-seq of kidneys from 3 weeks old control mice and KspCreDnmt3a/3b double knock-out mice.

first: Yuting

last: Guan

first: Katalin

last: Susztak


title: Bacteria boost mammalian host NAD metabolism by engaging the deamidated biosynthesis pathway

city: Durham

first: Jian-Liang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Nicotinamide adenine dinucleotide (NAD), a cofactor for hundreds of metabolic reactions in all cell types, plays an essential role in diverse cellular processes including metabolism, DNA repair, and aging. NAD metabolism is critical to maintain cellular homeostasis in response to environmental signals, however, how it is impacted by the environment remains unclear. Here, we report an unexpected trans-kingdom cooperation between bacteria and mammalian cells wherein bacteria contribute to host NAD biosynthesis. Bacteria confer mammalian cells with the resistance to inhibitors of NAMPT, the rate limiting enzyme in the main vertebrate NAD salvage pathway. Mechanistically, a microbial nicotinamidase (PncA) that converts nicotinamide to nicotinic acid, a key precursor in the alternative deamidated NAD salvage pathway, is necessary and sufficient for this protective effect. This bacteria-enabled bypass of the pharmacologically induced metabolic block in mammalian cells represents a novel paradigm in drug resistance. This host-microbe metabolic interaction also dramatically enhances the hepatic NAD-boosting efficiency of nicotinamide and nicotinamide riboside supplementation, demonstrating a crucial role of microbes, gut microbiota in particular, in systemic NAD metabolism.

overall_design: Comparison of the effects of an NAMPT inhibitor, STF118804, on the transcriptomes of clean and mycoplasma-infected tumors.

first: Igor

last: Shats

first: Xiaojiang

last: Xu

first: Jian

first: Xiaoling


title: Transcriptomic response of in vitro potato (Solanum tuberosum L.) to piezoelectric ultrasound

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

summary: As part of a wider project to assess the impact of ultrasound on in vitro plant growth, this paper aimed to determine whether the application of piezoelectric ultrasound (PE-US) would induce changes to the transcriptome of in vitro potato (Solanum tuberosum L.). After exposing explants (single-node segments with a single leaf) to PE-US (35 kHz; 70 W) for 20 min, the effect of this stressor was determined at 0 h, 24 h, 48 h, 1 w and 4 w to assess the possible immediate and residual effects of PE-US on the potato transcriptome.

overall_design: Total RNA was purified from the samples as three biological replicates. rRNA was removed from the 30 total RNA samples and the three biological replicates were pooled. Ten mRNA libraries were derived from the three biological replicates of five treatments and five controls. Deep sequencing (150 bp paired-end reads, expected data volume was 100 M reads/sample) was conducted.

first: Jaime

middle: A

last: Teixeira da Silva

first: Andrea

last: Gulyás

first: Bianka

last: Tóth

first: Judit

last: Dobránszki


title: Keep a distance to be different: axillary bud initiating at a distance to the shoot apical meristem are crucial for the perennial life style of Arabis alpina

city: cologne

first: Udhaya

last: Ponraj

state: NRW

department: Department of chromosome biology

institute: Max Planck Institute for Plant Breeding research

summary:
Purpose: In higher plants, perennialism is achieved through axillary buds and side-shoots that stay vegetative. This work aims to analyze the pattern of axillary bud (AB) formation in the perennial model plant Arabis alpina and to study the role of LATERAL SUPPRESSOR (AaLAS) gene in this process.
Methods: This study combines stereomicroscopic analysis with RNA sequencing to monitor how patterns of AB formation and gene expression correlate. The role of AaLAS was studied using an RNAi approach.
Results: During vegetative development, ABs initiate at a distance to the SAM, whereas after induction of flowering ABs initiate adjacent to the SAM. Dormant buds are established before onset of vernalization. Transcript profiles of ABs initiated at a distance were different from that of the SAM, whereas transcript patterns of buds initiated in close proximity were similar to the corresponding SAM. Knock-down of AaLAS leads to loss of both dormant buds and vegetative side-shoots, strongly compromising perennial life style.
Conclusions: AB formation is regulated differently during vegetative and reproductive development. New meristems that show gene expression profiles different from the SAM are established at a distance to the SAM. AaLAS plays an essential role in perennial life cycle modulating the establishment of dormant buds and vegetative side-shoots.

overall_design: Comparison of very young axillary bud soon after initiation with its corresponding shoot apical meristem harvested at different developmental stages using Illumina HiSeq3000

first: Klaus

last: Theres


title: Efficient differentiation and purification of human induced pluripotent stem cell-derived endothelial progenitor cells and expansion with the use of inhibitors of ROCK, TGF-β and GSK3β

city: Nagoya

first: Hiromasa

last: Aoki

address: 3-1 Tanabe-dori, Mizuho-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Nagoya City University

summary: Endothelial cells (ECs) and endothelial progenitor cells (EPCs) play crucial roles in maintaining vascular health and hemostasis. Both cell types have been used in regenerative therapy as well as in various in vitro models; however, the properties of primary human ECs and EPCs are dissimilar owing to differences in genetic backgrounds and sampling techniques. Although human induced pluripotent stem cells (hiPSCs) are an alternative cell source of ECs and EPCs, the differentiation and purification processes have not been optimized. Besides, owing to limited expandability, it is difficult to produce these cells in large numbers. Here we report the development of relatively simple differentiation and purification methods for hiPSC-derived EPCs (iEPCs). Furthermore, we discovered that a combination of three small molecules, that is, Y-27632 (a selective inhibitor of Rho-associated, coiled-coil containing protein kinase [ROCK]), A 83-01 (a receptor-like kinase inhibitor of transforming growth factor beta [TGF-β]), and CHIR-99021 (a selective inhibitor of glycogen synthase kinase-3β [GSK3β] that also activates Wnt), dramatically stimulated protein synthesis-related pathways and enhanced the proliferative capacity of iEPCs. These findings will help to establish a supply system of EPCs at an industrial scale.

overall_design: Analysis of gene expressions of iEPCs treated with DMSO or Y-27632, A 83-01, and CHIR-99021 (YAC)

first: MIsaki

last: Yamashita

first: Tadahiro

last: Hashita

first: Koichi

last: Ogami

first: Shinichi

last: Hoshino

first: Takahiro

last: Iwao

first: Tamihide

last: Matsunaga


title: Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell (24h after surgery)

city: Tokyo

first: Sayaka

last: Katagiri

institute: Tokyo Medical and Dental University

summary: The purpose of this study was to evaluate comprehensive and sequential gene expressions in Er;YAG laser ablated bone, bur-drilled bone, and non-treated control bone to clarify the biological responses for bone healing.

overall_design: Er;YAG laser ablated bone, bur-drilled bone, and non-treated control bone at calvaria were measured at 24 hours after surgery.

first: Akira


title: Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell (72h after surgery)

overall_design: Er;YAG laser ablated bone, bur-drilled bone, and non-treated control bone at calvaria were measured at 72 hours after surgery.


title: Characterization of Triptolide-Induced Hepatotoxicity by Imaging and Transcriptomics in a Novel Zebrafish Model

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution


title: Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell


title: Genome-wide identification and analysis of circular RNAs in the pineal in rats between day and night

city: Changchun

first: bao

last: yuan

address: 5333 Xi'an Road

institute: Jilin University

summary: Circular RNAs (circRNAs) are a new class of RNAs with covalently closed circular structures that are involved in many biological processes. However, information about circRNAs in the pineal gland is limited, especially in rats. In this study, 331 circRNAs were identified by the Illumina platform as being expressed in the pineal glands of rats during the night and day. Forty circRNAs with differential expression were found. A total of 737 GO terms were significantly enriched, and 121 KEGG pathways were found to contain differentially expressed genes. We predicted 6837 interactions between 65 cicRNAs and 549 miRNAs by using miRanda. We also found that high expression of miR-328a-3p in the daytime inhibits AANAT translation through targeting of the AANAT 3’UTR region. CircRNA-WNK2, which is highly expressed in the rat pineal gland during the night and functions as a miRNA sponge, removes this inhibitory effect and promotes the AANAT expression and melatonin secretion. The circadian expression profile of circRNAs in the rat pineal gland may provide more information on the roles of circRNAs in the regulation of melatonin circadian rhythm changes.

overall_design: Three rats were anesthetized and sacrificed under dark conditions (under red light) from 04:00 to 05:00 and were considered the dark group; these rats were named C04, C05 and C06 . Another three rats were anesthetized and sacrificed in bright sunlight from 16:00 to 17:00 and were considered the light group; these rats were named C01, C02 and C03 .The BioProject number is PRJNA600669 and SRA Project is: SRP241812.

first: Bao

last: Yuan

first: Yi

last: Zheng


title: Good quality day 7 embryos display disturbed cellular functions during post-hatching development when oocytes were matured under lipotoxic conditions: novel insights from a bovine embryo-transfer model

city: Wilrijk

first: Karolien

middle: LJ

last: Desmet

state: Antwerpen

address: Universiteitsplein 1

department: Veterinary Sciences

country: Belgium

institute: University of Antwerp

summary:
Objective: To study post-hatching development after transfer of morphologically good quality embryos that survived in vitro maturation under lipolytic conditions using a well-established and recognized bovine model.
Design: prospective study with a crossover design.
Setting: research laboratory.
Animals: 8 healthy multiparous non-lactating Holstein cows used in repeated embryo transfers.
Intervention(s): Bovine cumulus oocyte complexes (COCs) were in vitro matured in the presence of either 1) a combination of elevated pathophysiological concentration of palmitic acid (PA) and physiological concentrations of stearic acid (SA) and oleic acid (OA) (HIGH PA), or 2) physiological concentrations of PA, SA and OA (BASAL). Matured oocytes were fertilized and cultured in FA-free conditions until day 7.7 p.i. Equal proportions of normal and expanded blastocysts were subsequently transferred to synchronized cows. Conceptuses were transcervically recovered 7 days after the transfer.
Main Outcome Measure(s): Recovered embryos were morphologically assessed and dissected into embryonic disc (ED) and extraembryonic tissue (EXT). Samples of EXT were used for analysis of interferon-τ (IFN-τ) secretion and measurement of cellular metabolic activity. ED and EXT samples were subjected to RNA sequencing in order to evaluate the genome wide transcriptome patterns of recovered day 14 embryos.
Results: Recovered embryos resulting from metabolically compromised oocytes were retarded in growth or less elongated than their control counterparts. Furthermore, they exhibited a decrease in glucose consumption and lactate production. Importantly, lipolytic conditions resulted in reduced capacity of the embryo to signal its presence to the mother through IFN-τ secretion. The transcriptome profile was altered in the recovered embryos with main effects in pathways related to redox-regulating mechanisms, apoptosis, cellular growth, interaction and differentiation, energy metabolism, and epigenetic mechanisms.

overall_design: A total of 53 samples (extraembryonic tissue (EX) and embryonic discs (ED)) were used for RNA/DNA extraction, representative for the pool of recovered day 14 embryos, the embryo morphology, the recipient cows (embryos from one of the eight cows were excluded for RNA sequencing) and replicates.

first: Waleed

middle: F

last: Marei

first: Christophe

last: Richard

first: Katrien

last: Sprangers

first: Gerrit

last: Beemster

first: Pieter

last: Meysman

first: Kris

last: Laukens

first: Ken

last: Declerck

first: Wim

last: Vanden Berghe

first: Peter

middle: E

last: Bols

first: Isabelle

last: Hue

first: Jo

last: Leroy


title: Expression data from cholangiocarcinoma cell lines with PTEN overexpression

city: Shanghai

first: Tian-Yi

last: Jiang

address: 366 Qianju Road

country: China

institute: National Center for Liver Cancer, the Second Military Medical University

summary:
To explore the mechanism of PTEN function, we determined the gene expression profiles of RBE and HCCC-9810 cells infected with PTEN adenovirus.
Pathway and GO-term enrichment analyses suggested that the proteasome and ubiquitin-mediated proteolysis pathways were specifically affected in HCCC-9810 cells

overall_design: we analyzed two representative cell lines HCCC-9810 and RBE infected with PTEN or GFP adenovirus to identify PTEN function.

first: Tianyi

first: Liwei

last: Dong


title: Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell (6h after surgery)

first: Sayaka

last: Katagiri

overall_design: Er;YAG laser ablated bone, bur-drilled bone, and non-treated control bone at calvaria were measured at 6 hours after surgery.

first: Akira

last: Aoki


title: Inactivation of Zeb1 in GRHL2-deficient mouse embryos rescues mid-gestation viability and secondary palate closure

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

summary:
Aim: Identify molecular pathways controlling palate closure
Methods: First pharygneal arch of wild-type and Grhl2-/- e10.5 moues embryos was subjected to RNAseq
Results: Grhl2-/- PA1 displayed a shift from epithelial to mesenchymal gene expression
Conclusions: Grhl2 maintains epithelial cellular identity during palate closure

overall_design: First pharygneal arch mRNA profiles of e10.5 mouse embryos wre generated by deep sequencing, with 5 wild-type and 5 knock-out samples, using Illumina HiSeq technology

first: Marina

last: Carpinelli

first: Nick


title: Preservation of stemness in high-grade serous ovarian cancer organoids requires low Wnt environment

city: Berlin

first: Thomas

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

summary: High-grade serous ovarian cancer (HGSOC) creates a unique clinical challenge due to late detection, limited therapeutic options and wide-spread resistance to chemotherapy, all of which lead to very low survival rates. It is now widely recognized that this cancer emerges as metastasis from the fallopian tube and the lack of suitable in vitro disease models poses a major obstacle for efforts to improve our understanding of this deadly disease. We used organoids of healthy human FT epithelium as a model for stepwise genetic modification towards malignancy, using shRNA-mediated knockdown (KD) of three major HGSOC driver genes: P53, PTEN and Retinoblastoma (RB). Moreover, we successfully established patient-derived HGSOC organoids from solid tumor deposits. After combinatorial screening approach of different media compositions we have established 15 organoid lines which depend on the absence of exogenous Wnt3a in the medium. We could show that those cultures closely resemble the parental tumor tissue and express hallmarks of HGSOC phenotype as revealed by histology and global gene expression profiles of the matching organoid and tissue samples. Expression and sequencing analysis revealed that all samples were characterized by p53 mutation and/or aberrant p53 expression. Interestingly, the addition of Wnt agonists to cancer organoids leads to rapid growth arrest and a sharp drop in stemness, as proven by cell viability assay and the number of CD133 positive cells, respectively. Complementary to this finding, we can show that the medium optimized for ovarian cancer organoids also improves the growth of the modified organoid lines, showing that changes within the niche environment are required  to promote stemness upon depletion of P53/PTEN/RB. Taken together, our data reveal that critical changes in the paracrine environment are likely to represent early events during HGSOC development and provide a starting point to further analyze how specific mutations and paracrine signals influence pathways of stemness regulation and thus drive malignant transformation in ovarian carcinogenesis.

overall_design: Microarray experiments were performed as single-color hybridizations on Agilent 4x44K Mouse Genome Microarrays.

first: Mirjana

last: Kessler

first: Karen

last: Hoffmann

first: Hans

last: Mollenkopf

first: Hilmar

last: Berger


title: The 11q13.5 immune disease risk locus contains a distal enhancer required for Treg-mediated suppression of gut inflammation  [ATAC-Seq]

status: Public on Mar 02 2020

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Much of the genetic variation underlying susceptibility to common autoimmune and allergic diseases is concentrated within protein non-coding regulatory elements termed enhancers{Enhancer; Hsniz}. It has been difficult to assign functions to a majority of enhancers that overlap immune disease-associated variants due to their distance from the genes they regulate, our lack of understanding of the cell types in which they operate and our inability to recapitulate the biology of immune-mediated diseases in vitro. Here, using syntenic analysis and CRISPR-based mutagenesis to model enhancer function in mice, we show that a prominent human autoimmune/allergic disease risk locus at 11q13.5 contains a distal enhancer commissioned in Foxp3+ regulatory T (Treg) cells and required for Treg-mediated resistance to gut inflammation. Highly conserved binding sites within the enhancer recruit the transcription factor STAT5 to mediate interleukin (IL)-2-driven expression of Lrrc32, encoding Glycoprotein A Repetitions Predominant (GARP). Whereas disruption of the Lrrc32 gene results in loss of embryonic viability, mice lacking the enhancer (hereinafter Lrrc32 +70k) are viable but lack GARP expression on Foxp3+ Treg cells which subsequently are unable to control gut inflammation. In human Treg cells disease-risk alleles at 11q13.5 reduce levels of histone acetylation and are associated with reduced levels of LRRC32 expression. These findings define a function for the 11q13.5 risk locus in Treg-mediated immunoregulation and provide evidence of a causal involvement of Treg cells in the pathophysiology of polymorphic immune-mediated diseases at the intersection of genetics and the environment.

overall_design: ATAC-Seq profiles of Foxp3EGFP+ Treg and Tconv cells derived from Lrrc32+ 70k enhancer KO and WT Foxp3-IRES-EGFP reporter animals

first: Rabab

last: Nasrallah

first: Charlotte

last: Imianowski

first: Lara

last: Bossini-Castillo

first: Firas

last: Sadiyah

first: Dafni

last: Glinos

first: Teresa

last: Lozano

first: Panagiota

last: Vardaka

first: Carina

last: Nava

first: Hodaka

last: Fujii

first: Enrico

last: Lugli

first: Suman

last: Mitra

first: Derya

last: Unutmaz

first: Gosia

last: Trynka

first: Rahul

last: Roychoudhuri


title: Comparative Transcriptome Analyses of Drug-sensitive and Drug-resistant Strains of Eimeria tenella by RNA-sequencing

first: Hongyu

last: Han

address: No.518, Ziyue Road

institute: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences

summary: To gain insights into the molecular mechnism governing the drug resistance of Eimeria tenella, two drug-resistant strains of E. tenella, maduramicin-resistant (MRR) strain and diclazuril-resistant (DZR) strain were induced.We carried out comparative transcriptome analyses of a drug-sensitive strain (DS) and two drug-resistant strains (MRR and DZR) of E. tenella by RNA-seqencing. A total of 1070 DEGs, 672 upregulated and 398 downregulated, were identified in MRR vs. DS; and 379 DEGs, 330 upregulated and 49 downregulated, were detected in DZR vs. DS. Functional annotation analysis identified several DEGs coding for proteins associated with catalytic activity in the DZR strain that were involved in glycolysis and the tricarboxylic acid (TCA) cycle. Other DEGs were associated with ion binding and ion transmembrane transporter activity in the MRR strain. Some DEGs coded for surface antigens that were downregulated in two drug-resistant strains involved invasion, pathogenesis, and host–parasite interactions.These results contribute to developing rapid molecular methods to detect drug resistance of Eimeria spp. in poultry.

overall_design: Eimeria tenella sporulated oocysts mRNA profiles of the drug-sensitive strain (DS) and two drug-resistant strains (maduramicin-resistant (MRR) strain and diclazuril-resistant (DZR) strain) were generated by deep RNA-sequencing, in triplicate, using Illumina HiSeq 2000

first: Yuxiang

last: Xie


title: TWEAK/Fn14 axis is a therapeutic target for post-angioplasty restenosis

city: Bronx

first: Julio

last: Madrigal-Matute

state: New York

address: 1300 Morris Park Ave, C504

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

summary:
Aim: Next generation sequencing-based methods were performed to identify genes and pathways regulated by TWEAK in VSMCs
Methods: Using a gene-set enrichment method, we found a functional module involved in cell proliferation defined as the minimal network connecting top TWEAK up-regulated genes.
Results: TWEAK increased the number of VSMCs in S phase and the total number of proliferative cells.
Conclusions: Our data define a major role of TWEAK/Fn14 in the control of VSMCs proliferation and migration during neointimal hyperplasia after wire injury in mice, and identify TWEAK/Fn14 as a potential target for treating restenosis after angioplasty. provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: VSMC mRNA profiles 3-7 pasage wild type (WT) cells treated with vehicle or recombinant TW (100 ng/mL)  were generated by deep sequencing, in triplicate, using Illumina TruSeq Stranded Total RNA library prep.

first: N

last: Mendez-Barbero

first: C

last: Gutierrez-Muñoz

first: J

first: P

last: Mínguez

last: Egido

last: Martín-Ventura

first: V

last: Esteban

first: L

last: Blanco-Colio


title: IL-6 derived from therapy-induced senescence facilitates the glycolytic phenotype in glioblastoma cells

city: guangzhou

first: liu

state: State...

address: guangdong

institute: sysu

summary: In this study, we aimed to determine the fate of GBM cells following cAMP-induced differentiation. We assessed the effect of dbcAMP treatment on the global gene expression pattern of the human GBM cell lines DBTRG and U87 using RNA sequencing (RNA-Seq) analysis

overall_design: DBTRG-05MG/U87 tumor cells were treated with 1 mol/L dbcAMP for 3 days, respectively. And we used RNA-seq to detail the drug resistance network based on time-course RNA-seq data.

middle: Y

last: Gu

first: X

last: Liu


title: Characterization of Triptolide-Induced Hepatotoxicity by Imaging and Transcriptomics in a Novel Zebrafish Model [RNA-seq]

first: Alasdair

last: Ivens

summary: Zebrafish larvae treated with triptolide (5 dpf larvae after exposure to triptolide (1.6μM) for 6 hours) or vehicle control.

overall_design: A total of 16 sequencing experiments were performed (control N=8 and treatment N=8). Each individual experiment consisted of 30 pooled larvae, therefore 480 larvae were included in total.

first: James

middle: W

last: Dear

first: A

middle: D

last: Vliegenthart


title: Functional subnetwork modules and discovery of hub genes with signal peptide using RNA-Seq (hybrid 33k44 vs. inbred B73)

city: College Station

first: Man

middle: S

last: Kim

address: 202N  LF Peterson, Texas A&M Univ., Plant Pathology & Microbiology

department: Plant Pathology & Microbiology

institute: Texas A&M University

summary: We performed a systematic computational network-based analysis of large-scale F. verticillioides RNA-seq datasets to identify gene subnetwork modules associated with virulence and fumonisin regulation.

overall_design: Investigation on two different strains (Maize inbred B73 kernels vs. maize hybrid 33k44 kernels)

first: Won-Bo

last: Shim


title: Characterization of Triptolide-Induced Hepatotoxicity by Imaging and Transcriptomics in a Novel Zebrafish Model [miRA-seq]


title: RNA-Seq and Ribo-Seq of P19 WT and SRSF7-GFP overexpressing cells

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

institute: Goethe University Frankfurt

summary: We used P19 cells that overexpress GFP-tagged SRSF7 by 3.4-fold.

overall_design: 1-2 biological replicates were subjected to RNA-Seq and Ribo-Seq.


title: Rocaglates Induce Gain-of-Function Alterations to eIF4A and eIF4F

city: Montreal

first: Jerry

last: Pelletier

state: Quebec

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

department: Biochemistry

institute: McGill university

summary: Rocaglates are a diverse family of biologically active molecules that have gained tremendous interest in recent years due to their promising activities in pre-clinical cancer studies. As a result, this family of compounds has been significantly expanded through the development of efficient synthetic schemes. However, it is unknown whether all members of the rocaglate family act through similar mechanisms of action. Here, we present a comprehensive study comparing the biological activities of >200 rocaglates to better understand how the presence of different chemical entities influence their biological activities. Through this, we find that most rocaglates preferentially repress translation of mRNAs containing purine rich 5’ leaders but intriguingly, certain rocaglates lack this bias in translation repression. We also uncover a novel aspect of rocaglate mechanism of action in which the pool of translationally active eIF4F is diminished due to sequestration of the complex onto RNA.

overall_design: Anti-FLAG eCLIP-seq with Input, vehicle (DMSO), Silvestrol, CR-1-31-B treatment in FLAG-tagged eIF4A strain

first: Jennifer

last: Chu

first: Wenhan

last: Zhang

first: Regina

last: Cencic

first: Patrick

last: O'Connor

first: Francis

last: Robert

first: William

middle: G

last: Devine

first: Asher

last: Selznick

first: Thomas

last: Henkel

last: Merrick

first: Lauren

last: Brown

first: Pavel

middle: V

last: Baranov

first: John

last: Porco Jr


title: Gene expression analysis of skin by active vitamin D3 analogue

city: Yokohama

first: Hidehiro

last: FUKUYAMA

state: Kanagawa

address: 1-7-22, Suehirocho, Tsurumi-ku

department: IMS

institute: RIKEN

summary: Total RNAs extracted from skin tissues of wild-type C57BL/6 or K5-Cre;VDR f/f mice stimulated by Oxarol and  their mRNA expression profiles were analyzed by RNA-sequencing

overall_design: mRNA profiles of skin tissues of wild-type C57BL/6 or K5-Cre;VDR f/f mice stimulated by Oxarol were generated by deep sequencing, using an NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

first: Chieko

last: Makino-Okamura

last: Fukuyama


title: RNA-seq analysis on pericytes derived from normal skin and burn eschar compared to human skin-derived fibroblasts

city: Cincinnati

first: Latha

last: Satish

state: OH

address: 3229 Burnet Avenue

department: Research

institute: Shriners Hospitals for Children

summary: The study was designed to determine the differential gene expression between burn eschar- and normal skin-derived pericytes. A comparison was also made to determine the gene expression between normal skin pericytes and normal skin fibroblasts and (2) comparison of differential gene expression between burn eschar pericytes and normal normal skin fibroblasts

overall_design: Total RNA was extracted from normal skin pericytes, burn eschar pericytes and normal skin fibroblasts


title: RNA-Seq, Ribo-Seq and iCLIP of P19 cells overexpressing SRSF7

last: Müller-McNicoll

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of DMSO treatment on mouse embryonic fibroblasts (MEFs) during cardiac transdifferentiation

city: Farmington

first: Efthymios

last: Motakis

state: CT

address: 10 Farmington Drive

department: Computational Sciences

institute: The Jackson Laboratory

summary: Cardiac transdifferentiation represents an attractive way of reversing heart damage caused by myocardial infarction. Yet, it is still in pre-clinical stage mainly due to the lack of efficacy with current transdifferentiation protocols. Here, we describe that dimethyl sulfoxide (DMSO) is capable of augmenting cardiomyocyte transdifferentiation in vitro. Treatment of Gata4, Hand2, Mef2c and Tbx5 (GHMT) - transduced mouse embryonic fibroblasts (MEFs) with 1% DMSO induced ~5 fold increase in the percentage of Myh6-mCherry+ cells, and significantly increased the global expression of cardiac genes. Transcriptomic studies were carried out to explore the underlying mechanism of how DMSO may enhance cardiac transdifferentiation.

overall_design: RNA-seq was carried out on both uninfected and GHMT-transduced cells that were treated with 1% DMSO from D2, 7 and 21, with their respective untreated controls

first: Choon

middle: K

last: Lim

first: Matias

last: Autio

first: Zenia

last: Tiang

first: Yiqing

middle: P

last: Li

first: Sik-Yin

middle: R

last: Foo


title: mRNAseq in SBMA and control iPSC-derived motor neurons

city: Nagakute

first: Yohei

last: Okada

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Neural iPSC Research, Institute for Medical Science of Aging

institute: Aichi Medical University

summary: RNA sequence was performed using mRNAs of motor neurons derived from iPSCs of four patients of spinal bulbar muscular atrophy (SBMA) and four age- and sex- matched controls. The analysis was performed using purified motor neurons by flowcytometry and cell sorting based on the expression of HB9e438::Venus reporter gene (P4) or unpurified motor neurons (NT).

overall_design: mRNA profiles obtained from motor neurons derived from four SBMA-iPSCs and four control-iPSCs, each of the group has NT and P4 fraction, were generated by deep sequencing using Illumina NextSeq500.

first: Kazunari

last: Onodea

first: Masato

last: Yano

first: Fuyuki

last: Miya


title: Pan-cancer molecular analysis of the RB-pathway

city: Buffalo

first: Ram

middle: Mohan

last: Nambiar

state: NY

address: 665 Elm Street

institute: Roswell Park

summary:
The retinoblastoma tumor suppressor (RB1) plays a critical role in coordinating multiple pathways that impact on tumor initiation, disease progression, and therapeutic responses.   Here we interrogated the TCGA pan-cancer data collection to probe fundamental molecular features associated with the RB-pathway across 31 tumor-types.
While the RB-pathway has been purported to exhibit multiple mutually exclusive events, only RB1 is mutually exclusive with multiple genetic events that deregulate CDK4/6 activity.  Using an isogenic ER+ breast cancer model with targeted RB1 deletion, we identified gene expression features that link CDK4/6 activity and RB-dependency (CDK4/6-RB integrated signature).   This gene expression signature is associated with prognosis across a spectrum of tumors that exhibit average lower signature value indicative of more indolent diseases.
Single copy loss on chromosome 13q encompassing the RB1 locus is prevalent in many cancers, and is associated with reduced expression of multiple genes on 13q including RB1, and inversely related to the CDK4/6-RB integrated signature supporting a genetic cause/effect relationship.
To probe the broader implications on tumor biology, we investigated genes that are positively and inversely correlated with the CDK4/6-RB integrated signature.   This approach defined tumor-specific pathways that could represent new therapeutic vulnerabilities associated with RB-pathway activity.

overall_design: MCF7 wild type and RB knockout cells were exposed to DMSO and Palbociclib (250 nM). Following 48 hours exposure, RNA was extracted from these cells using RNeasy plus kit (Quiagen) according to manufacturer's protocol and then subjected to RNA sequence analysis.

first: Erik

last: Knudsen

first: Spencer

last: Rosario

first: Dominic

middle: J

last: Smiraglia

first: David

last: Goodrich

first: Agnieszka

last: Witkiewicz