title: SZ 95 sebocytes - OLR1 knockdown - treated with UV-oxidized PAPC

status: Public on Apr 15 2020

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

institute: Medical University Vienna

summary: Human SZ95 sebocytes were transfected by lipofection with either scramble siRNA or OLR1 siRNA and after 24h were treated with 25µg/ml of UV-oxidized 1-palmitoyl-2-arachidonoyl-sn-phosphocholine (UVPAPC) for 7 hours. Phospholipid oxidation products (OxPL) are versatile stress signaling mediators in the skin. These lipid signaling molecules can be generated non-enzymatically or enzymatically by ultraviolet light, the major extrinsic skin aging factor. OxPL regulate cytoprotective, immunological and metabolic adaptation of the skin to oxidant stress. We here investigated whether the scavenger receptor Oxidized Low Density Lipoprotein Receptor 1 (OLR1, LOX-1) would have a function in cutaneous oxPL signaling. We found that OLR1 is expressed in several cutaneous cell types, most prominently in cells of the sebaceous gland and in keratinocytes. We repressed OLR1 expression with siRNA in SZ95 sebocytes, exposed cells to oxidized 1-palmitoyl-2-arachidonoyl-sn-phosphatiylcholine (PAPC) and performed transcriptomic profiling. Bioinformatic analysis revealed that OxPL exposure induced the Nrf2 antioxidant stress response and aldosterone signaling. The analysis also revealed that OLR1 is not required for the transcriptional regulation induced by oxidized PAPC, but interestingly, OLR1 knockdown affected expression of CNN2, HMRR, ITGB6 and KIF20A, all genes governing cell proliferation and motility. We identify sebocytes as cutaneous cells responsive to lipid mediated redox stress which is not dependent on the scavenger receptor OLR1.

overall_design: 4 conditions, 3 replicates each.

first: Ionela

last: Nagelreiter

first: Masomeh

last: Parvadeh

first: Marie

last: Narzt

first: Lucian

last: Beer

first: Christopher

last: Kremslehner

first: Ximena

last: Muresan

first: Johannes

last: Grillari

first: Christos

last: Zouboulis

first: Erwin

last: Tschachler

first: Florian

last: Gruber


title: CD5 levels define functionally heterogeneous populations of naïve human CD4+ T cells

city: Montreal

first: Heather

last: Melichar

state: Quebec

address: 5415 Boulevard de l'Assomption

department: Immunology-Oncology Unit

country: Canada

institute: Maisonneuve-Rosemont Hospital Research Center

type: Expression profiling by high throughput sequencing

summary: Studies from mouse models show that differences in self-reactivity, as read-out by CD5 levels, identifies naïve T cell subsets with distinct functional properties during an immune response. Whether CD5 levels can also be used to parse functional biases in naive human CD4+ T cells is incompletely understood. Our study establishes CD5 as a reliable marker of T cell self-reactivity and functional heterogeneity in human CD4+ T cells.

overall_design: Naïve CD4+ T cells from peripheral blood mononuclear cells of 2 human donors were sorted on top and bottom 15% of CD5 expression. (2 biological replicates; 4 conditions: CD5lo and CD5hi for each donor).

first: Aditi

last: Sood


title: CD34+ cells from mast cell leukemia and healthy bone marrow

status: Public on Apr 14 2020

country: Austria

summary: In patients with mast cell leukemia, the CD34+ bone marrow fraction contains a subset of disease-initiating and propagating cells. The aim of this study was to compare the gene expression profile of these cells with that of CD34+ cells obtained from the bone marrow of healthy donors, in order to find aberrantly expressed genes and pathways.

overall_design: CD34+ cell samples were obtained from 6 patients with mast cell leukemia and 3 healthy controls.

first: Gregor

last: Eisenwort

first: Peter

last: Valent


title: mTORC1 Loss Impairs Epidermal Adhesion via Rho Kinase Activation

city: BALTIMORE

first: KAUSHAL

middle: VIJAY

last: ASRANI

state: MD

address: 1550 ORLEANS

country: USA

institute: JOHNS HOPKINS MEDICINE

summary: In this study, we use the epidermis as a model system to elucidate the cellular effects and signaling feedback sequelae of mTORC1 loss-of-function in epithelial tissue. In mice with conditional epidermal loss of mTORC1 components Rheb or Rptor, we find that mTORC1 loss-of-function unexpectedly results in a profound skin barrier defect with epidermal abrasions, blistering and early postnatal lethality, due to a thinned epidermis with decreased desmosome expression and incomplete biochemical differentiation.   Impaired cell-cell adhesion in the context of mTORC1 loss-of-function is caused by constitutive activation of Rho kinase (ROCK) signaling with increased cytoskeletal tension, and inhibition or silencing of ROCK1 is sufficient to rescue keratinocyte adhesion and biochemical differentiation.  mTORC1 loss-of-function results in marked feedback up-regulation of upstream TGF-β signaling, triggering ROCK activity and its downstream effects on desmosomal gene expression.  These findings elucidate a novel role for mTORC1 in the regulation of epithelial barrier formation, cytoskeletal tension and cell adhesion and underscore the complexity of signaling feedback after mTORC1 inhibition

overall_design:
We analysed gene expression changes between wild-type (3 biological replicates) and  Rheb cKO (3 biological replicates) epidermal RNA samples, using  the Partek Genomics Suite and QIAGEN Ingenuity Pathway Analysis platforms.

The 'Rptor KRT14cre' and 'Rheb KRT14cre' mice have the C57BL/6J and C57BL/6J-*Aw-J*/J background, respectively.

first: Tamara

middle: L

last: Lotan

first: Kaushal

last: Asrani

first: Akshay

first: Alba

last: Torres

first: Dan

last: Georgess

first: Pornima

last: Phatak

first: Harsimar

last: Kaur

first: Amber

last: Dubin

first: C

middle: C

last: Talbot Jr

first: Loubna

last: Elhelu

first: Andrew

middle: J

last: Ewald

first: Bo

last: Xiao

first: Paul

last: Worley


title: A critical role of histone deacetylases, Mbd3/NuRD and Tet2 in epithelial-mesenchymal cell plasticity and in tumor invasion and metastasis

status: Public on Apr 10 2020

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

summary: We have generated and employed reversible and irreversible EMT models of murine breast cancer cells to identify the key players establishing cell state transitions during a reversible and an irreversible EMT. We demonstrate that the Mbd3/NuRD complex, involving histone deacetylases (HDACs) and Tet2 hydroxylase, acts as an epigenetic block in epithelial-mesenchymal plasticity. These epigenetic modifiers keep breast cancer cells in a stable mesenchymal state, and their pharmacological inhibition or genetic ablation leads to a mesenchymal-epithelial transition (MET) and represses primary tumor growth and metastasis formation of highly aggressive, mesenchymal breast cancer cells.

overall_design: We performed RNA-sequencing of 2 replicates of each treatment and cell line

first: Ayse-Nihan

last: Kilinc

first: Ravi

middle: R

last: Kalathur

first: Gerhard

last: Christofori


title: Epigenetic regulator function through mouse gastrulation

status: Public on Apr 07 2020

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

type: Methylation profiling by high throughput sequencing

summary: Development of a multicellular organism uses the same genetic code to generate a broad diversity of cell types, which is instructed by extracellular cues and orchestrated by transcriptional activators and repressors. While transcription factors establish cell identities according to the central dogma, a number of enzymes, which index and regulate chromatin, appear to perform essential functions as well. We optimized a versatile experimental and analytical approach that allows for rapid perturbation of genes and the recovery of high replicate powered phenotypic information. We applied this set-up to investigate a panel of epigenetic regulators that are essential for early gestation. Our comparative analysis approach enabled us to pinpoint affected genetic pathways and cell lineage-specific effects that distinguish even closely related regulators, such as polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Moreover, by incorporating additional epigenetic data, we were able to identify early aberrations that partially explain how certain developmental abnormalities emerge at the onset of gastrulation.

overall_design: Single-cell RNAseq data was collected on whole early mouse embryos generated using B6/CAST F1 sperm and B6D2F1 oocytes. Each experiment consists of 4-12 embryo replicates from developmental stages E6.5, 7.0, 7.5, 8.0, 8.5 for wild-type, of E8.5 for all epigenetic regulator knockouts (KOs) and for Eed KO additionally from E6.5 and 7.5.  All scRNA-seq data was generated using the 10X Genomics single cell RNA sequencing platform.  Sample titles with "a" or "b" represent distinct sets of cells sequenced from the same experiment.  Additional epigenetic data was generated for E6.5 embryos generated by natural mating B6D2F1 females with B6D2F1 males for each KO and WT.  Macroscopically dissected embryonic (epiblast) and extraembryonic (extraembryonic ectoderm) fractions were collected in pools of ~10 embryos per KO and whole-genome bisulfite sequencing data was generated using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences).

first: Stefanie

last: Grosswendt

first: Zachary

middle: D

last: Smith

first: Abhishek

last: Sampath Kumar

first: Sven

last: Klages

first: Shankar

last: Mukherji

first: Alexander

last: Meissner


title: RNA-sequence data of liver sinusoidal endothelial cells in quiescent versus fibrotic and wild-type versus endothelial RBPj-deficent mice

status: Public on Apr 01 2020

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

country: China

institute: Fourth Military Medical University

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

overall_design: Refer to individual Series


title: RNA-sequence data of liver sinusoidal endothelial cells from control and endothelial RBPj-deficent mice with liver fibrosis

summary: Endothelial notch signaling dominantly regulates liver physiology and pathology. To further explore the role and mechanisms of endothelial notch in modulating development and progression of liver fibrogenesis, we established endothelial RBPj conditinal knock-out mice to specifically block notch activity in endothelium. After development of CCl4-induced liver fibrosis, SECs from control and RBPj knock-out mice were isolated and processed for RNA-seq.

overall_design: mRNA profiles of SECs in control and endothelial RBPj knock-out mice with liver fibrosis were generated by RNA sequencing, in triplicate, using Illumina HiSeq 3000

first: Lin

last: Wang

first: Juanli

last: Duan


title: RNA-sequence data of hepatic stellate cells and liver sinusoidal endothelial cells from control and CCl4-treated mice

summary: We utilized RNA-sequencing strategy to explore the characterstics of gene expression profile of LSECs during CCl4-fibrosis, and to compare the activation feature between fibrotic-LSECs and fibrotic-HSCs which are the most acknowledged gatekeepers holding the key to liver fibrogenesis.

overall_design: mRNA profiles of quiescent(Q) or fibrotic(F) hepatic stellate cells(HSC) and liver sinusoidal endothelial cells(SEC) in control or CCl4-treated mice were generated by RNA sequencing, in triplicate, using Illumina HiSeq 3000.


title: Overcoming Wnt-β-catenin dependent anticancer therapy resistance in leukaemia stem cells.

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Leukaemia stem cells (LSCs) underlie cancer therapy resistance but targeting these cells remains difficult. The Wnt–β-catenin and PI3K–Akt pathways cooperate to promote tumorigenesis and resistance to therapy. In a mouse model in which both pathways are activated in stem and progenitor cells, LSCs expanded under chemotherapy-induced stress. Since Akt can activate β-catenin, inhibiting this interaction might target therapy-resistant LSCs. High-throughput screening identified doxorubicin (DXR) as an inhibitor of the Akt–β-catenin interaction at low doses. Here we repurposed DXR as a targeted inhibitor rather than a broadly cytotoxic chemotherapy. Targeted DXR reduced Akt-activated β-catenin levels in chemoresistant LSCs and reduced LSC tumorigenic activity. Mechanistically, β-catenin binds multiple immune-checkpoint gene loci, and targeted DXR treatment inhibited expression of multiple immune checkpoints specifically in LSCs, including PD-L1, TIM3 and CD24. Overall, LSCs exhibit distinct properties of immune resistance that are reduced by inhibiting Akt-activated β-catenin. These findings suggest a strategy for overcoming cancer therapy resistance and immune escape.

overall_design: Cohorts of leukemic mice were treated with vehicle, chemotherapy, [Low]DXR, clinical-dose DXR or chemotherapy + [Low]DXR as in Figure S4. At 10 days post-treatment (day 1 = start of treatment), blast cells, LSCs, and HSPCs were sorted using stringent gates (see Figure 5A) for these populations. For each population, two biological replicates were made with 1-3 technical replicates each.  Each biological replicate was a pool of sorted cells from 4-5 male and 4-5 female mice.  Technical replicates were samples of sorted cells from each biological replicate. 1,000 cells per sample were sorted into 96-well plates with 7 ul lysis buffer containing RNase inhibitor (2 U/μl) from BM. First-strand cDNA synthesis and cDNA libraries were constructed using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech) following the manufacturer’s instructions. cDNA quality was determined by Agilent high sensitivity DNA kit on Agilent 2100 BioAnalyzer (Agilent Technologies). Libraries were sequenced at 50bp on the Illumina HiSeq 2500.  Reads were aligned to UCSC mm10 with Tophat 2.1.1 [Kim et al 2013], using gene models from Ensembl 80.  Read counts per gene were obtained with HTSeq-count 0.6.0 [Simon et al 2014].  Analysis was done in R with the EdgeR package [Robinson et al 2010] using default methods. Significantly changed genes were determined at FDR<1e-3 and fold change exceeding ±1.5. GO analysis was generated using significantly changed genes by Metascape (www.metascape.org). Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. . Genome Biology 2013, 14:R36 Simon Anders, Paul Theodor Pyl, Wolfgang Huber. HTSeq — A Python framework to work with high-throughput sequencing data. Bioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638 Robinson MD, McCarthy DJ and Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26, pp. -1.

first: John

last: Perry

first: Linheng

last: Li


title: cFLIP prevents TNFR1-dependent lethal dermatitis and TNFR1-independent blockade of epidermal differentiation

city: Tokyo

first: Ryodai

last: Shindo

state: Ota-ku

address: 5-21-16 Omori-Nishi

country: Japan

institute: Toho univercity

summary: Cellular FLICE-inhibitory protein (cFLIP) prevents the development of dermatitis by blocking TNFα-dependent apoptosis of keratinocytes. However, it is unclear whether TNFα-independent signal might also contribute to the development of dermatitis in epidermis-specific Cflar-deficient (Cflar) mice. Here we show that Cflar;Tnfrsf1a-/- mice were born at the expected Mendelian ratio, but developed severe dermatitis and succumbed soon after birth. While keratinocytes still died by apoptosis, expression of epidermal differentiation markers, such as Loricrin, Filaggrin, and Keratin (Krt)10, but not Krt5 were severely downregulated in the skin of Cflar;Tnfrsf1a-/- mice at both mRNA and protein levels. Conversely, inflammatory cytokines, such as interleukin (IL)-6 and Il17a were elevated in the skin of Cflar ;Tnfrsf1a-/- mice. Treatment of primary keratinocytes with IL-6, to a lesser extent IL-17A suppressed expression of Loricrin, Filaggrin, and Krt10. Together, cFLIP suppresses TNFR1-independent apoptosis of keratinocytes and prevents IL-6-dependent blockade of epidermal differentiation.

overall_design: To identify the genes that might block epidermal differentiation and proliferation of keratinocytes, we compared gene expression of the skin between CflarF/F;Tnfrsf1a+/- and CflarF/F;K5-Cre;Tnfrsf1a+/- mice by microarray.

first: Xuehua

last: Piao

first: Ryosuke

last: Miura

first: Hiroyasu

last: Nakano


title: Differential expression of microRNAs in human postmortem brain tissues of MDMA addiction

status: Public on Mar 24 2020

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: In this study, we performed miRNA profiling of nucleus accumbens (NAc) and ventral tegmental area (VTA) in MDMA users and control postmortem human brains, which were obtained from Council of Forensic Medicine (Istanbul). According to the microarray analysis of significantly differentially expressed miR-1202 and miR-7975 were selected for further validation using quantitative reverse-transcription PCR (qRT-PCR). qRT-PCR analysis demonstrated that the expression level of miR-7975 was significantly lower in 30 VTA region of MDMA samples compared to 30 control samples. Another significantly deregulated miR-1202 was down-regulated in 30 NAc region of MDMA samples in comparison to 30 control samples. To the best of our knowledge, this is the first study demonstrating that changes in miRNA expression levels are associated with postmortem MDMA users’ brains. Alteration of these miRNAs can serve as novel biomarkers for prediction of MDMA addiction. Our findings suggest that certain differentially expressed miRNAs in MDMA seeking behavior can be used as diagnostics and therapeutic markers.

overall_design:
In this study, we performed miRNA profiling of nucleus accumbens (NAc) and ventral tegmental area (VTA) in MDMA users and control postmortem human brains, which were obtained from Council of Forensic Medicine (Istanbul).
Multiple group comparison

first: Esra

last: Guzel

first: Yiqun

last: Zhang


title: Genome-wide Identification of genes that transcriptionally respond to altered states of Hedgehog signaling in embryos of the spider Parasteatoda tepidariorum

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

institute: JT Biohistory Research Hall

summary: Hedgehog signaling plays pivotal roles in formation of the embryonic anterior-posterior axis in the spider Parasteatoda tepidariorum. In this work, using the combination of RNA-sequencing and parental RNA interference (pRNAi), we genome-widely identified genes that transcriptionally responded to altered states of Hedgehog signaling in spider embryos, which were caused by Pt-hedgehog (Pt-hh) pRNAi and Pt-patched (Pt-ptc) pRNAi. The identified genes were classified into four classes (Classes I to IV) based on the positive/negative responses to the Pt-hh pRNAi and Pt-ptc pRNAi states. The Class II genes were negatively regulated by Hh signaling (positive response to Pt-hh pRNAi and negative response to Pt-ptc pRNAi). Among the Class II genes, we identified Pt-msx1 as a key segmentation gene in the spider embryo. Moreover, we conducted a transcriptomic analysis of Pt-msx1 pRNAi embryos and identified additional genes whose expression showed patterns associated with segmentation.

overall_design: We used RNA-sequencing to obtain transcriptomic data for comparison between untreated (normal) and Pt-hh pRNAi-treated embryos, between untreated (normal) and Pt-ptc pRNAi-treated embryos, and between untreated (normal) and gfp pRNAi-treated embryos. We obtained at least two replicates from independent parents for each comparison. Poly(A) RNA was extracted from early stage 3 and late stage 5 embryos derived from mated females before (normal) and after (pRNAi-treated) injection of dsRNA targeted for each of Pt-hh and Pt-ptc. The RNAs were sequenced using the Illumina Miseq, and differentially expressed genes (DEGs) were evaluated in each comparison using EdgeR. The comparisons between the untreated and the gfp pRNAi-treated embryos served as negative controls. Based on the analyses of the expression and function of the identified DEGs, our study was focused on the Pt-msx1 gene. An additional transcriptomic analysis of Pt-msx1 pRNAi embryos was carried out.

first: Yasuko

last: Akiyama-Oda


title: FTO demethyltion of N6-methyladenosine depends on the RRACH motif [CLIP-seq]

status: Public on Mar 22 2020

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: The fat mass and obesity-associated (FTO) protein is a well-characterized demethylase that removes N6-methyladenosine (m6A) from animal mRNAs. However, it is unclear yet how the demethylation operates in living cells. In this study, we applied genome-wide approaches to study how FTO finds its demethylation targets in human cells. We overexpressed FTO in human HeLa cells, demonstrating that FTO effectively removes m6A from the RRACH motif enriched in the 3’UTR regions and leaves m6A at other motifs unaffected. RRACH elements are clearly enriched at FTO binding sites; however, m6A has a lower tendency to be removed from the FTO-bound RRACH. Taken together with the experimental validaton results, we propose a model in which FTO effectivly recognizes m6A-containing RRACH motifs in RNAs, leading to a faster demethylation and dissociation kinetic than the association, and consequently undectable FTO-mRNA association. However, when FTO binds to the non-m6A RRACH motif, the binding has a lower dissociation kinetics, yielding the detectable FTO binding signals which would enable FTO to have roles in regulating other mRNA processing events.

overall_design: CLIP-seq analysis were performed with anti-FTO antibody in wide-type Hela cells for two biological replicates, as well as in FTO-overexpression Hela cells with anti-Flag antibody. Human FTO gene (GenBank: NM_001080432.2) encoding full length FTO was amplified by PCR and subcloned into pCMV-Tag.2B-flag vector (Stratagene), so  FTO–RNA complex is puriﬁed by immunoprecipitation by incubating with DynaBeads protein G conjugated with anti-Flag antibody.

first: Yi

first: Lei

last: Zhou

first: Kejing

last: Wu


title: Transcriptome signature of miRNA-26b KO mouse model suggests novel transcriptional interactions

status: Public on Mar 26 2020

city: Aachen

first: Emiel

last: van der Vorst

address: Pauwelstraße 30

institute: IMCAR/IZKF

summary: miR26b KO mice were generated by Laser assisted (XY-Clone Hamilton Thorne) injection of R1/E(129/Sv) cells into 8-cell stage C57Bl/6NCrl embryos.Chimaeras were crossed to C57Bl/6NCrl mice and their offspring was screened for germline transmission. Embryo donor and recipient mice: C57BL/6NCrl, Crl:CD1(ICR). We induced homologous recombination in embryonic stem (ES) cells using a construct containing 2.0 kb of gDNA, including exon 2,3 and 4, as also part of intron 4-5, a Neo Cassette was inserted in between Frt sites. 160 bp of gDNA, including miR26b was flanked by loxP sites (floxed). The construct was finished by introducing a 5.6 kb fragment of gDNA serving as 3’ recombination arm.A correctly targeted ES cell clones were injected into blastocysts to produce a chimeric mice which transmitted the modified allele through the germ line. A male heterozygous for the targeted allele was bred with a female expressing ubiquitous Flippase (Flp) transgene to ultimately produce animals that had deleted the Neo cassette, preserving the loxP sites flanking exon miR26b.

overall_design: Compare differential gene expression between naïve mouse and miRNA26B K.O

first: M

middle: A

last: Pepe

first: K

last: Bidzhekov

first: E

middle: P


title: FTO demethyltion of N6-methyladenosine depends on the RRACH motif [m6A-seq]

overall_design: We performed m6A-seq analyses in control (Flag) and FTO-overexpression (FTO) Hela cells to investigate the features and distribution dynamics of RNA m6A modification


title: Identification and characterization analysis of gene expression in mouse brain response to tMCAO

city: Nanjing

first: Bing

last: Han

address: Dingjiaqiao #87

institute: Southeast University

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

summary: Astrocyte activation is involved in the context of stroke. Our study provides a potential new therapeutic strategy to astrocyte activation in the context of stroke.

overall_design: Stroke induced gene expression in mouse brain was measured at 12 hours after tMCAO and sham group. Three independent experiments were performed at each group..

first: Honghong

last: Yao


title: FTO demethyltion of N6-methyladenosine depends on the RRACH motif


title: Subcellular profiling of macrophage long non-coding RNAs

status: Public on Mar 16 2020

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

summary: Recent advances in next generation sequencing have improved human genome annotations and revealed thousands of previosly unknown long non-coding RNA loci. Here, we characterized immune-responsive long non-coding RNAs (lncRNAs) and determined their subcellular localization and co-sedimentation with protein complexes in primary human macrophages. To this end, we profiled LPS-responsive lncRNAs, isolated cytoplasmic and nuclear RNA fractions from mock- and LPS-treated cells and seperated cell lysates on 10-60 % glycerol gradients, followed by gradient fractionation. All samples were subjected to RNA-Seq analysis. LPS-responsive lncRNAs were found to be mostly cytoplasmic. Glycerol gradient datasets revealed that a substantial fraction of LPS-responsive lncRNAs, similar to mRNAs, co-sediments with ribosomal RNAs and also ribosomal proteins, as confirmed by mass-spectrometry analysis. LncRNAs not co-sedimenting with ribosomes displayed a highly heterogenous gradient distriubtion. Among these truly non-coding RNAs we identified lncRNA MaIL1 as a novel element of the macrophage TLR-TRIF signaling pathway contributing to antibacterial defense.

overall_design: Expression profiles of poly(A)-RNA from primary human macrophages (+/- LPS treatment) or subcellular macrophage fractions (+/- LPS treatment) were recorded in experimental replicates. RNA profiles of gradient fractionated lysates from LPS-stimulated macrophages were recorded without prior RNA enrichment or depletion steps. For MaIL1 and control RNAi experiments each RNA-Seq dataset (poly(A)-RNA) represents an equimolar pool of RNA from two independent experiments.

middle: N


title: Assessment of DNA methylation patterns related to femur bone morphology in marmoset bone using the 850K array

status: Public on Mar 15 2020

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

summary: The aim of this study was to characterize the genome-wide DNA methylation profiles of marmoset femur trabecular bone samples (n=6) and identify how they relate to aspects of femur bone morphology. The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

overall_design: Bisulphite converted DNA from the 6 marmoset bone samples were hybridized to the Illumina Infinium MethylationEPIC array.


title: Assessment of DNA methylation patterns related to femur bone morphology in nonhuman primate bone using the 850K array

summary: The aim of this study was to characterize the genome-wide DNA methylation profiles of nonhuman primate trabecular bone samples (n=58), identify how they relate to aspects of femur bone morphology, and assess how these epigenetic patterns vary between taxa. The Illumina Infinium MethylationEPIC array was used to assess genome-wide methylation patterns.

sample_organism:
Callithrix jacchus
Chlorocebus aethiops
Macaca mulatta
Pan troglodytes
Papio sp.

overall_design: Bisulphite converted DNA from the 58 nonhuman primate bone samples were hybridized to the Illumina Infinium MethylationEPIC array.


title: Assessment of DNA methylation patterns related to femur bone morphology in vervet bone using the 850K array

status: Public on Mar 14 2020

summary: The aim of this study was to characterize the genome-wide DNA methylation profiles of vervet femur trabecular bone samples (n=10) and identify how they relate to aspects of femur bone morphology. The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

overall_design: Bisulphite converted DNA from the 10 vervet bone samples were hybridized to the Illumina Infinium MethylationEPIC array.


title: Assessment of DNA methylation patterns related to femur bone morphology in macaque bone using the 850K array

summary: The aim of this study was to characterize the genome-wide DNA methylation profiles of macaque femur trabecular bone samples (n=10) and identify how they relate to aspects of femur bone morphology. The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

overall_design: Bisulphite converted DNA from the 10 macaque bone samples were hybridized to the Illumina Infinium MethylationEPIC array.


title: Whole Transcriptome Sequencing of Peromyscus maniculatus in Response to High Fat Diet

status: Public on Mar 12 2020

city: Columbia

first: Youwen

state: South Carolina

address: 715 Sumter Street CLS109

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina (Columbia)

summary: Whole genome sequencing was generated to perform single nucleotide polymorphism (SNP) variant calling.

overall_design: Analysis of RNA-seq gene expression between Peromyscus maniculatus that received a normal diet (n=6), P. maniculatus that received a high fat diet and developed steatosis (n=5), and P. maniculatus that received a high fat diet and did not develop steatosis (n=5). All RNA-seq samples are biological replicates.

first: Ioulia

last: Chatzistamou

first: Matthew

last: Lucius

first: Diego

last: Altomare

first: Ji

last: Hao

first: Vimala

last: Kaza

first: Michael

last: Shtutman

first: Hippokratis

last: Kiaris


title: Assessment of DNA methylation patterns related to femur bone morphology in baboon bone using the 850K array

summary: The aim of this study was to characterize the genome-wide DNA methylation profiles of adult baboon femur trabecular bone samples (n=28) and identify how they relate to aspects of femur bone morphology. The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

overall_design: Bisulphite converted DNA from the 28 baboon bone samples were hybridized to the Illumina Infinium MethylationEPIC array.


title: Gene expression profiling of Drosophila melangoaster Myb mutant wing discs of 3rd instar larvae. [NimbleGenGeneExpression-12plex]

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry and Molecular Biology

institute: University of Iowa

summary: Study of genome-wide differential gene expression of Drosophila Melanogaster Myb mutant wing discs of 3rd instar larvae compared to control animals.

overall_design: Wing discs were dissected from Myb mutant and control 3rd instar larvae. Total RNA was isolated and converted to cDNA for array hybridization. Each genotype was represented with three biological replicates, each with four technical replicates (one biological replicate of wild type animals had three technical replicates instead of four).

first: Juan

middle: F

last: Santana

first: Mrutyunjaya

last: Parida

first: Abby

last: Long

first: Joshua

last: Wankum

first: John

last: Manak


title: Genome-wide analysis of trimethylation of lysine 27 of histone 3 (H3K27me3) in Drosophila melangoaster Myb mutant wing discs of 3rd instar larvae.

type: Genome binding/occupancy profiling by genome tiling array

summary: Study of genomic distribution of H3K27me3 in Drosophila melanogaster Myb mutant wing discs of 3rd instar larvae compared to control animals.

overall_design: H3K27me3 was immunoprecipitated from wing imaginal discs from Myb mutant and control 3rd instar larvae. Each genotype was represented with two biological replicates.


title: Genome-wide analysis of trimethylation of lysine 4 of histone 3 (H3K4me3) in Drosophila melangoaster Myb mutant wing discs of 3rd instar larvae.

summary: Study of genomic distribution of H3K4me3 in Drosophila melanogaster Myb mutant wing discs of 3rd instar larvae compared to control animals.

overall_design: H3K4me3 was immunoprecipitated from wing imaginal discs from Myb mutant and control 3rd instar larvae. Each genotype was represented with two biological replicates.


title: Genome-wide analysis of RNA polymerase in Drosophila melangoaster Myb mutant wing discs of 3rd instar larvae.

summary: Study of genomic distribution of RNA polymerase in Drosophila melanogaster Myb mutant wing discs of 3rd instar larvae compared to control animals.

overall_design: RNA polymerase was immunoprecipitated from wing imaginal discs from Myb mutant and control 3rd instar larvae. Each genotype was represented with two biological replicates.


title: Genome-wide analysis of Myb binding sites in Drosophila melangoaster wing discs of 3rd instar larvae.

summary: Study of genomic distribution of Myb binding in Drosophila melanogaster Myb wing discs of 3rd instar larvae.

overall_design: Myb protein was immunoprecipitated from wing imaginal discs from 3rd instar larvae. Two biological replicates were performed.


title: Local states of chromatin compaction in HepG2 cells

status: Public on Mar 10 2020

city: Wako

first: Itoshi

last: Nikaido

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: We reported chromatin compaction states within several nucleosomes in HepG2 cells. To assess the local compaction, fromaldehyde-treated chromatin was appled to fractionation via a sedimentation velocity cetrifugation. While less-crosslinked nucleosomes remained in upper fractions as open chromatin, well-crosslinked nucleosomes were sedimented to lower fractions as compact chromatin.

overall_design: NGS analyses of DNA flagments prepared from the uppermost and the lowermost fractions of the chromatin fractionation.

first: Satoru

last: Ishihara

first: Yohei

last: Sasagawa

first: Takeru

last: Kameda


title: Gene expression profiling of Drosophila melangoaster Myb mutant wing discs of 3rd instar larvae. [NimbleGen tiling array]

type: Expression profiling by genome tiling array

summary: Study of genome-wide expression of Drosophila Melanogaster Myb mutant wing discs of 3rd instar larvae compared to control animals.

overall_design: Wing discs were dissected from Myb mutant and control 3rd instar larvae. Total RNA was isolated and converted to cDNA for array hybridization. Each genotype was represented with two biological replicates. A two chip array set (Chip1 and Chip2) representing the Drosophila melanogaster genome was used.


title: Intra- and Inter-Specific Investigations of Skeletal DNA Methylation Patterns and Femur Morphology in Nonhuman Primates

status: Public on Mar 11 2020

first: Genevieve

last: Housman

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

overall_design: Refer to individual Series


title: A spatio-temporal translatome of mouse tissue development

city: Guangzhou

first: Hongwei

last: Wang

state: Guangdong

address: No 7 Jinsui Rd, Research Building, Rm 301

department: Zhongshan Ophthalmic Center

institute: Sun Yat-Sen University

summary: Functional specification of mammalian tissues is a result of precise regulation of gene expression during development. Although previous transcriptomic and proteomic analyses have provided great biological insight into tissue specific gene expression and their physiological relevance in development, our understanding of translational regulation in developing tissues is lacking. Here, we report a spatio-temporally resolved translatome analysis of six mouse tissues at embryonic and adult stages to quantify the effects of translational regulation and identify new translational components. We quantified the spatial and temporal divergence of gene expression and showed specific changes in gene expression and pathways underlying the divergence. We further showed dynamic translational control by modulating translational efficiency, enhancing tissue specificity during development. We discovered thousands of actively translated upstream open read frames (ORFs) that exhibited spatio-temporal patterns and demonstrated their regulatory roles in translational regulation. Finally, we identified known and novel micropeptides encoded by small ORFs from long non-coding RNAs with functional relevance to tissue development. Our data and analyses facilitate a better understanding of complex translational regulation across tissue and developmental spectra and serve as a useful resource of mouse translatome.

overall_design: Ribosome profiling (Ribo-seq) and RNA sequencing (RNA-seq) were performed for six embryo tissues and six adult tissues separately from wild-type C57BL/6 mice at embryonic day (E) 15.5 and postnatal day (P) 42, including ectoderm-derived brain and retina, mesoderm-derived heart and kidney, as well as endoderm-derived liver and lung. For each tissue, two biological replicates were performed.

first: Yan

first: Jiaqi

last: Yang

last: Tang

first: Zhi

last: Xie


title: Drosophila melangoaster Myb mutant wing discs of 3rd instar larvae.


title: Temporal RNA-sequencing of cytologically-normal mouse airway epithelia during tobacco carcinogen-associated lung tumorigenesis

status: Public on Feb 28 2020

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Smoking perpetuates in cytologically-normal airways a molecular “field of injury” that is pertinent to lung cancer and early detection. The evolution of airway field changes prior to lung cancer onset is poorly understood largely due to the long latency of lung malignancy in smokers. Here we studied airway expression changes prior to lung cancer onset in mice with knockout of the Gprc5a gene and tobacco carcinogen (nicotine-specific nitrosamine ketone; NNK) exposure and that develop the most common type of lung cancer, lung adenocarcinoma (LUAD). Cytologically-normal airway epithelial brushings were collected before exposure and at multiple times following NNK exposure until time of LUAD development and then analyzed by RNA-sequencing (RNA-Seq).

overall_design: Groups of five to six eight week old mice (Gprc5a-/-) were intraperitoneally administered 50 mg/kg body weight NNK three times per week for 8 weeks. Normal airway (tracheal) epithelia were collected by brushing and studied at baseline (prior to NNK exposure) from six mice and immediately following the eight-week exposure (t=0) to understand early effects of tobacco carcinogen exposure on the airway transcriptome (Figure 1).  Airway epithelia were also collected every two months following completion of NNK treatment (t=2, t=4, and t=6) and studied to understand progressive or lasting field effects following exposure and until time of LUAD development (t=6). In total, airway brushings (n=28) from 28 mice were sequenced.

first: Jake

last: Kantrowitz

first: Smruthy

last: Sivakumar


title: Binding of Runx1 and Runx3 in CD4+ T cells.

status: Public on Mar 02 2020

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Runx1 and Runx3 are expressed during T cell development, and define different differentiation stages. Here we address their gene target specicifity in the naïve CD4+ T cell stage genomewide using ChIP-sequencing analysis

overall_design: Examination of Runx1 and Runx3 binding in mouse CD4+ T cells

first: Ludovica

last: Bruno

first: Matthias

last: Merkenschlager


title: Multi Lineage Heterogeneity and Plasticity in Urothelial Carcinoma of the Bladder

status: Public on Mar 01 2020

city: New York

first: Yang

last: Hu

state: New York

address: 1305 York Avenue Y-1322

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Single cell transcriptome analyses of mouse and human model systems of bladder cancer

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: OHBBN-induced mouse bladder tumors were dissociated to the single cell level and separated into total viable CD45-negative and CD45-positive cells followed by 10x Chromium single cell isolation and RNA sequencing

last: Sfakianos

first: Jorge

last: Daza

first: David

last: Mulholland


title: small RNA NGS based diagnostic survey of Hungarian grapevine rootstock plantations

status: Public on Feb 24 2020

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

summary:
Several pathogens infect grapevine, including viruses and viroids. Considering that there are no effective plant protection treatments against these pathogens and vineyards are cultivated through decades usage of high quality and pathogen-free propagation material (rootstocks and scions) is essential.
Although presence of regulated pests is routinely checked using ELISA or rarely RT-PCR, these diagnostics methods can detect only particular pathogens moreover can fail to detect variant strains. High-throughput  sequencing of small RNAs can be an effective, alternative method to avoid these disadvantages. Since for production of grafts, pathogen free cultivars and rootstocks must be used, 17 grapevine rootstock plantations and 2 rootstock variety collections were selected for characterisation of their virom by high throughput sequencing of virus derived small RNAs.

overall_design: Virus diagnotics of 17 Hungrarian grapevine rootstock plantation and 2 grapevine rootstock variety collection by Illumina sequencing of the small RNAs

first: Emese

last: Demián

first: Nikoletta

last: Jaksa-Czotter

first: János

last: Molnár

first: Gábor

middle: E

last: Tusnády

first: László

last: Kocsis


title: Overexpression of nuclear receptor 5A1 induces  and maintains an intermediate state of conversion  between primed and naive pluripotency

status: Public on Feb 22 2020

city: Kyoto

first: Hirofumi

last: Suemori

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Institute for Frontier Life and Medical Sciences

institute: Kyoto University

summary: Naive and primed human pluripotent stem cells (hPSCs) have provided useful insights into the regulation of pluripotency. However, the molecular mechanisms regulating naive conversion remain elusive. Here, we report intermediate naive conversion induced by overexpressing nuclear receptor 5A1 (NR5A1) in hPSCs. The cells displayed some naive features, such as clonogenicity, glycogen synthase kinase 3β and mitogen activated protein kinase (MAPK) independence, expression of naive-associated genes, and two activated X chromosomes, but lacked others such as KLF17 expression, transforming growth factor β independence, and imprinted gene demethylation. Notably, NR5A1 negated MAPK activation by fibroblast growth factor 2, leading to cell-autonomous self-renewal independent of MAPK inhibition. These phenotypes may be associated with naive conversion, and were regulated by a DPPA2/4-dependent pathway that activates the selective expression of naive-associated genes. This study increases our understanding of the mechanisms regulating the conversion from primed to naive pluripotency.

overall_design: Gene expression profiles of parental cells and NR5A1 transfectant cultured under TF or CHIR conditions

first: Kaori

last: Yamauchi

first: Tatsuhiko

last: Ikeda

first: Mihoko

last: Hosokawa

first: Norio

last: Nakatsuji

first: Eihachiro

last: Kawase

first: Shinichiro

last: Chuma

first: Kouichi

last: Hasegawa


title: lncRNA expression in C2C12 myoblasts and myotubes

status: Public on Feb 18 2020

first: Rui

last: Chen

address: 466 Xin Gang Zhong Road

department: Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute

institute: Guangdong Second Provincial General Hospital

summary: To determine the lncRNA expression profile in C2C12 myoblasts and myotubes, we used mouse lncRNA microarray from Arraystar to examine the expression of lncRNAs in C2C12 myoblasts and myotubes.

overall_design: Cells from cell line C2C12 were distributed into two experimental groups: myoblast group and myotube group, then perform lncRNAs chips by Arraystar mouse lncRNAs chip. Three independent experiments were performed at each group.

first: Yanling

last: She

first: Ting

last: Jiang


title: Flow cytometric micronucleus assay and TGx-DDI transcriptomic biomarker analysis of ten genotoxic and non-genotoxic chemicals in human HepaRG™ cells

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary:
Background: Modern testing paradigms seek to apply human-relevant cell culture models and integrate data from multiple test systems to accurately inform potential hazards and modes of action for chemical toxicology. In genetic toxicology, the use of metabolically competent human hepatocyte cell culture models provides clear advantages over other more commonly used cell lines that require the use of external metabolic activation systems, such as rat liver S9. HepaRG™ cells are metabolically competent cells that express Phase I and II metabolic enzymes and differentiate into mature hepatocyte-like cells, making them ideal for toxicity testing. We assessed the performance of the flow cytometry in vitro micronucleus (MN) test and the TGx-DDI transcriptomic biomarker to detect DNA damage-inducing (DDI) chemicals in human HepaRG™ cells after a 3-day repeat exposure. The biomarker, developed for use in human TK6 cells, is a panel of 64 genes that accurately classifies chemicals as DDI or non-DDI. Herein, the TGx-DDI biomarker was analyzed by Ion AmpliSeq whole transcriptome sequencing to assess its classification accuracy using this more modern gene expression technology as a secondary objective.
Methods: HepaRG™ cells were exposed to increasing concentrations of 10 test chemicals (six genotoxic chemicals, including one aneugen, and four non-genotoxic chemicals). Cytotoxicity and genotoxicity were measured using the In Vitro MicroFlow® kit, which was run in parallel with the TGx-DDI biomarker.
Results: A concentration-related decrease in relative survival and a concomitant increase in MN frequency were observed for genotoxic chemicals in HepaRG™ cells. All five DDI and five non-DDI agents were correctly classified (as genotoxic/non-genotoxic and DDI/non-DDI) by pairing the test methods. The aneugenic agent (colchicine) yielded the expected positive result in the MN test and negative (non-DDI) result by TGx-DDI.
Conclusions: This next generation genotoxicity testing strategy is aligned with the paradigm shift occurring in the field of genetic toxicology. It provides mechanistic insight in a human-relevant cell-model, paired with measurement of a conventional endpoint, to inform the potential for adverse health effects. This work provides support for combining these assays in an integrated test strategy for accurate, higher throughput genetic toxicology testing in this metabolically competent human progenitor cell line.

overall_design: HepaRG™ cells were exposed to increasing concentrations of 10 prototype test chemicals (six genotoxic chemicals, including one aneugen, and four non-genotoxic chemicals). Cytotoxicity and genotoxicity were measured using the In Vitro MicroFlow kit, which was run in parallel with the TGx-DDI transcriptomic biomarker. The biomarker is a panel of genes that is altered in a predictable way following exposure to genotoxic agents and it accurately classifies chemicals as DNA damage-inducing (DDI) or non-DDI in human TK6 cells. The TGx-DDI biomarker was analyzed in HepaRG™ cells using Ion AmpliSeq™ whole transcriptome sequencing in this study to test the ability of the biomarker to accurately classify chemicals using a different human cell line and gene expression technology. All ten chemicals were accurately classified by pairing these test methods.

first: Julie

middle: K

last: Buick

first: Andrew

last: Williams

first: Rémi

last: Gagné

first: Carol

last: Swartz

first: Leslie

last: Recio

first: Stephen

middle: S

last: Ferguson

first: Carole

last: Yauk


first: Hirofumi

last: Suemori

overall_design: Examination of two distinct pluripotent states, primed and naive, with ChIP-seq of H3K4me3, H3K27me3, and NR5A1 (FLAG)

first: Kaori

last: Yamauchi

first: Tatsuhiko

last: Ikeda


title: Cripto shapes macrophage plasticity and restricts EndMT in injured and diseased skeletal muscle

status: Public on Feb 06 2020

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

summary: The membrane protein Cripto plays a key role in shaping macrophage plasticity in skeletal muscle during regeneration and disease. Cripto acts as an extrinsic modulator of macrophage  plasticity and is required for the proper expansion/maintenance of the CD206+ anti-inflammatory macrophage population. Nevertheless, Cripto deletion does not change the gene expression profile of F4/80+/Ly6CLow macrophages suggesting that Cripto was dispensable to induce/maintain the Ly6CLow phenotype.

overall_design: RNAseq analysis: total RNA from FACS isolated macrophages (F4/80+/Ly6CLow) from WT and Tg:LysMCre::Cripto-/- mice was extracted using a protocol combining QIAzol Lysis Reagent and RNAeasy minikit columns (Qiagen) following the manufacturer’s instructions. RNAseq services were provided by the CNIC Genomics Unit, including quality control tests of total RNA using Agilent Bioanalyzer and Nanodrop. spectrophotometry. cDNA library preparation and amplification were performed from 200 ng total RNA using NEBNext Ultra RNA Library Prep Kit for Illumina. RNAseq analysis was performed with 3 samples per condition, using Illumina Hiseq 2500.

first: Gabriella

last: Minchiotti

first: Francescopaolo

last: Iavarone


title: YY1 Control of Mitochondrial-Related Genes does not Account for Regulation of Immunoglobulin Class Switch Recombination

status: Public on Feb 13 2020

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

institute: University of Alberta

summary: Immunoglobulin class switch recombination (CSR) occurs in activated B cells with increased mitochondrial mass and membrane potential.  Transcription factor YY1 is critical for CSR and for formation of the DNA loops involved in this process.  We therefore sought to determine if YY1 knockout impacts mitochondrial gene expression and mitochondrial function in murine splenic B cells, providing a potential mechanism for regulating CSR.  We identified numerous genes in splenic B cells differentially regulated when cells are induced to undergo CSR.  YY1 conditional knockout caused differential expression of 1129 genes, with 59 being mitochondrial-related genes.  ChIP-seq analyses showed YY1 directly bound to nearly half of these mitochondrial-related genes.  Surprisingly, at the time when YY1 knockout dramatically reduces DNA loop formation and CSR, mitochondrial mass and membrane potential were not significantly impacted, nor was there a significant change in mitochondrial oxygen consumption, extracellular acidification rate, or mitochondrial complex I or IV activities. Our results indicate that YY1 regulates numerous mitochondrial-related genes in splenic B cells, but this does not account for the impact of YY1 on CSR, or long-distance DNA loop formation.

overall_design: Follicular B cells were isolated from the spleens of 3 C57Bl/6 yy1 fl/fl mice. For each spleen, 1/3 of the cells were not treated with any reagent (naive cells), 1/3 the cells received mock treatment (mock cells) and 1/3 received TATCRE (tatcre cells). The mock and tatcre samples were then grown in RPMI medium along with LPS+IL4 and 10% FBS for 72 hours. All cells were lysed and RNA was isolated for library preparation. Expression differences between Mock and TATCRE treated cells were determined to understand the role of yy1 in B cell activation.

first: Satabdi

last: Nandi

first: Michael

last: Atchison


title: An ExtendedCulture System that Supports Human Primordial Germ Cell-Like Cells Survival and Initiation of DNA Methylation Erasure

status: Public on Jan 31 2020

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

summary: In this study, we evalauted the transcriptionl profiles of human primordial germ cell-like cell (hPGCLCs) cultured for an extended period on STO feeders in FR10 media for an additional 10 days  (D4C10). The hPGCLCs were obtained from two different human embryonic stem cell line (hESCs), UCLA 1 (XX) and UCLA2 (XY) for the RNA sequencing data. For whole genome bisulfite sequencing, we evaluate primed UCLA2 hESCs,  directly out of the aggragate hPGCLCs (Day 4= D4) and extended culture hPGCLCs D4C10. Our D4C10 hPGCLCs were compared to prior RNA-sequencing data generated in our laboraty, which revealed that D4C10 hPGCLCs retain germline identy and closely resemble D4 hPGCLCs at the transcriptional level. Our WGBS data revealed that extended culture hPGCLCs at D4C10 have a decrease in CG methlyation, as compared to the starting hESCs and D4 hPGCLCs.

overall_design: There are 6 RNAseq and 6 WGBS samples  in total.

first: Joanna

last: Gell

first: Yu

last: Tao

first: Wanlu

last: Liu


title: Identification of differentially expressed miRNAs and mRNAs in synovial tissues of osteoarthritis via RNA-sequencing

status: Public on Feb 15 2020

city: Deyang

first: hong

middle: Yue

state: Sichuan

address: No. 173, Taishan North Road, Jingyang District

department: People’s Hospital of Deyang City

institute: Department of Orthopedics

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Osteoarthritis (OA) is the most common form of arthritis and a leading cause of disability. This study attempted to investigate the key mRNAs and miRNAs related to OA.
Patients and methods: From April 17th, 2018 to May 17th, 2018, five patients with OA and three normal controls were enrolled in this present study. To identify the differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) between patients with OA and normal controls, RNA-sequencing was performed. Then, DEmiRNA-target DEmRNAs analysis and functional annotation of DEmiRNA-target DEmRNAs were performed. To validate the RNA-sequencing results, quantitative real time-PCR (RT-PCR) and western blot analysis were performed as well.
Results: A total of 1068 DEmRNAs, 21 DEmiRNAs and 395 DEmiRNA-DEmRNA pairs were identified in synovial tissues of patients with OA. The functional annotation of DEmiRNA-target DEmRNAs revealed that Pathways in cancer and PI3K-Akt signaling pathway were significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. QRT-PCR and western blot results revealed that except for TLR7, the expression level of the others was consistent with the RNA-sequencing results, generally.
Conclusion: The findings of this present study may provide new clues for the roles of DEmRNAs and DEmiRNAs in the pathogenesis of OA.

overall_design: mRNA and miRNA profiles of synovial tissues of five patients with OA and three normal controls were obtained based on HiSeq x-ten platform (Illumina) and SE50, BGIseq, respectively.

last: Zhou

first: Zhicong

last: Wang

first: Xi

last: Chen

first: Jianjun

last: Zhang

first: Ling

last: Yang

first: Shuping

first: Yuehong


title: High gene expression of IL8 in peripheral blood mononuclear cells from bladder cancer patients is associated with nonresponders to atezolizumab

status: Public on Feb 14 2020

city: SOUTH SAN FRANCISCO

first: Kobe

last: Yuen

address: 1 DNA WAY

department: Oncology Biomarker Development

institute: Genentech

summary: Elevated plasma interleukin-8 (IL8) has been associated with poor outcome to immune checkpoint blockade. Here we performed single cell RNAseq with peripheral blood mononuclear cells (PBMCs) of patients treated with atezolizumab (anti-PD-L1 mAb) from bladder cancer from a Phase II trial IMvigor210. We found that high IL8 gene expression is enriched in nonresponders to atezolizumab

overall_design:
Single-cell RNA-seq of baseline pretreatment PBMC samples from 10 cancer patients with 5 responders and 5 nonresponders.
------------------------------------
Authors state "The authors have submitted the Responder and NonResponder raw data files to EGA: EGAS00001004008".
Authors state "The authors have submitted the Blood and Tumor raw data files to EGA: EGAS00001004230".

first: Lifen

first: Vinita

last: Gupta

first: Shravan

last: Madireddi

first: Shilpa

last: Keerthivasan

first: Congfen

last: Li

first: Deepali

last: Rishipathak

first: Patrick

last: Williams

first: Edward

last: Kadel

first: Hartmut

last: Koeppen

first: Ying-Jiun

first: Zora

last: Modrusan

first: Jane

last: Grogan

first: Romain

last: Banchereau

first: Ning

last: Leng

first: AnnChristine

last: Thastrom

first: Xiadong

last: Shen

first: Kenji

last: Hashimoto

first: Darren

last: Tayama

first: Michiel

last: van der Heijden

first: Jonathan

last: Rosenberg

first: David

last: McDermott

first: Thomas

last: Powles

first: Priti

last: Hegde

first: Mahrukh

last: Huseni

first: Sanjeev

last: Mariathasan


title: RNAseq of C. elegans grown with different bacteria isolates

status: Public on Jan 17 2020

city: Montreal

first: Orcun

last: Hacariz

state: Quebec

address: 1001 Boul Décarie, Site Glen Pavilion E / Block E. E02.2143

institute: Research Institute of the McGill University Health Centre

summary: RNAseq was carried out to compare the gene expression profiles of the worms grown with individual bacteria to understand the bacterial effect

overall_design: C. elegans was grown with Chryseobacterium sp. CHNTR56, Comamonas sp. 12022 or E. coli OP50

first: Orçun

last: Haçariz

first: Charles

last: Viau

first: Jianguo

last: Xia


title: Transcriptional profiling of bladder carcinoma T24 cells following CD40 activation by membrane-bound CD40L (mCD40L) compared to soluble CD40L (sCD40L)

status: Public on Jan 24 2020

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary: We utilised the Affymetrix microarray analysis to compare the expression profiling of the CD40-positive bladder carcinoma T24 cells expressing mCD40L delivered by a replication-deficient adenovirus (RAdnCD40L) or treated with sCD40L (1µg/ml) for 24 hours

overall_design: Bladder carcinoma T24 cells were infected with 50 MOI RAdMock (RAd expressing GFP) or RAdnCD40L (RAd expressing noncleavable version of human CD40L) or left uninfected for 24 hours or treated with sCD40L (1 µg/ml) for  24 hours, total RNA was isolated and processed for microarray analysis

first: Taha

last: Elmetwali


title: High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis. [RNA-Seq]

status: Public on Jan 23 2020

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: Kaposi's sarcoma (KS), is an AIDS-associated neoplasm caused by the KS herpesvirus (KSHV). A mouse model of KSHV-dependent tumorigenicity, allowed us to induce KSHV viral-episome loss following tumor development to test the plausibility of “hit and run” mechanism by KSHV. RNA-seq-transcriptome analysis and CpG-methylation were performed on KSHV positive cells, KSHV positive tumors and tumors that developed following viral-episome loss. During KSHV tumorigenesis, hypo-methylation was detected of oncogenic and differentiation pathways. In contrast, during tumorigenesis following KSHV-episome loss, a tendency towards hyper-methylation was detected. We found the same set of innate-immunity related mutations undetected in KSHV-infected cells but present in all KSHV-positive tumors, indicating that pre-existing host mutations that provide an in vivo growth advantage are clonally-selected and contribute to KSHV-tumorigenesis. We found de novo mutations related to cell proliferation that, together with the PDGFRAD842V, were responsible for driving tumorigenesis in absence of the KSHV-episomes. Virally-induced irreversible genetic and epigenetic oncogenic alteration supports the possibility of “hit and run” KSHV-sarcomagenesis consistent with the existence of LANA-negative spindle-cells in KS lesions.

overall_design: KSHV-infected KS lesions are composed of latently-infected cells, as well as cells expressing lytic genes that have been implicated in the development of the KS angioproliferative phenotype. The existence of KS lesions with varying levels of KSHV-infected cells suggests also the existence of virus-independent “hit and run” mechanisms of sarcomagenesis, whereby viral infection irreversibly induce genetic or epigenetic oncogenic alterations in host cells. We used the unique mECK36 animal model of multistep KSHV sarcomagenesis to dissect transcriptional, genetic and epigenetic mechanisms of KSHV direct and in-direct (“hit and run”) sarcomagenesis in an unbiased high-throughput fashion. These analyses revealed that KSHV in vivo tumorigenesis: A) Occurs predominantly with CpG hypo-methylation of oncogenic and differentiation pathways. B) Selects for pre-existing host mutations that allow the KSHV oncovirus to express the oncogenic lytic program by creating permissive environment for viral-induced innate immunity and inflammation, which provides a selective advantage in vivo conducive to tumorigenesis.

first: E

last: Mesri

first: J

last: Naipauer

first: M


title: Yap/Taz negatively regulate bone angiogenesis and osteogenesis

status: Public on Jan 15 2020

city: Muenster

first: Kishor Kumar

last: Sivaraj

address: Roentgenstrasse 20

department: Department of Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

summary: In long bone, the metaphyseal region is less hypoxic than the bone marrow (bone shaft). To study the regional differences of vasculatures, we isolated endothelial cells (ECs) expressing membrane-anchored mTomato protein and nuclear H2B-GFP from Cdh5-mT/nG transgenic reporter femoral metaphysis and diaphyseal bone marrow cavity by fluorescence-activated cell sorting (FACS) at high purity for RNA sequencing (RNA-seq). Next, to study the Hippo signaling in bone ECs, we performed RNA-seq analysis of freshly isolated bone ECs from  Cdh5Cre-ERT2-positive Yap1/Taz double floxed or Cdh5Cre-ERT2-positive Lats2 floxed allele and their Cre-negative corresponding littermate controls.

overall_design:
Control and  Cdh5(PAC)CreERT2-Yap1; Wwtr1 mutant bone endothelial cells were isolated by using FACS. RNA was isolated from control and EC-Yap1; Wwtr1 mutant endothelial cells.
Bone endothelial cells (Cdh5 mT/nG+) from metaphyseal and marrow transcripts were analyzed.  We studied gene expression changes in absence of Yap1/Taz and Lats2 in bone endothelial cells.

first: Kishor

first: Hyun-Woo

last: Jeong

first: Katsuhiro

last: Kato

first: Ralf

last: Adams


title: MEF2C Protein Isoform Transition to a Repressor Variant is Linked to Development of Heart Failure

status: Public on Jan 22 2020

city: Campinas

first: Marcelo

middle: Falsarella

last: Carazzolle

state: São Paulo

address: Rua Carl Von Linnaeus

country: Brazil

institute: Instituto de Biologia/Unicamp

summary:
The transcription factor MEF2C has been implicated in the pathogenesis of cardiac remodeling and heart failure. The underlying mechanisms of the MEF2C detrimental effects still remain elusive. MEF2C is unique among the MEF2 family in that alternative splice acceptors in the last exon give forms that include or exclude a short  domain, which has an inhibitory effect on the MEF2C activity.
Objective: To identify if MEF2Cγ+ repressor variant has a role in the cardiac detrimental effects of MEF2C. Conclusions: We conclude that upregulation of MEF2Cγ+ in adult hearts causes cardiac pathogenic features through dysregulation of cell cycle and dedifferentiation of cardiomyocytes.

overall_design: Culture of neonatal rat ventricular cardiomyocytes were treated with adenovirus particles of mef2Cγ+, mef2Cγ- or mef2Cγ+-23/24 or untreated Control. The samples were analyzed in triplicate.

first: Ana

last: Pereira

first: Alisson

last: Cardoso

first: Kleber

middle: G

last: Franchini


title: Epigenomic alterations are associated with mucosal microbiota and inflammation in inflammatory bowel disease

status: Public on Jan 29 2020

city: Cork

first: Rachel

middle: Siobhain

last: Fitzgerald

state: Cork

address: College Road

department: BIOSCIENCES INSTITUTE

country: Ireland

institute: University College Cork

type: Methylation profiling by genome tiling array

summary: Mucosal host DNA methylation was associated  with the presence of inflammation suggesting epigenetic changes in response to the microbiota. Hierarchical clustering of the microbiota indicated ten subgroups, whereas some were driven by certain Enterbacteriacae and Bacteroides keystone species, and which were associated with host  genotype and DNA methylation profiles, but with little influence from the habitual  diet.

overall_design: Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: F

middle: J

last: Ryan

last: Laserna-Mendieta

middle: M

last: Power

first: A

last: Clooney

first: P

last: McMurdie

first: S

last: Iwai

first: C

last: Christoph

last: Ahern

first: B

last: Flemer

middle: L

last: Zomer

last: Fanning

last: O’Callahgan

last: Walton

last: Temko

first: D

last: Sheehan

last: Moran

first: L

last: Jackson

first: W

last: Stack

middle: T

last: Bell

first: T

middle: Z

last: DeSantis

last: Shanahan

last: Clesson


title: ChIP-Seq for wild type strains arrested in metaphase with and without tension

status: Public on Jan 13 2020

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

institute: University of Edinburgh

summary: Purpose: The goal is to determine the requirement for Chl4 in association of cohesin with the centromere and pericentromere boundaries

first: Bonnie

last: Alver

first: Adele

last: Marston


title: Scc1 ChIP-Seq in a strain where the centromere on chromosome III has been moved to an ectopic site

summary: Genome binding/occupancy profiling of the cohesin subunit Scc1 by high throughput sequencing

overall_design: Purpose: Can the centromere set up new pericentromere borders on a chromosomal arm site?


title: Sgo1 ChIP-seq for wild type cells arrested in metaphase with and without tension

summary: Genome binding/occupancy profiling of Sgo1 by high throughput sequencing

overall_design: Purpose: to determine the association of shugoshin Sgo1 with the pericentromere in the presence and absence of tension


title: Convergent genes shape budding yeast pericentromeres

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

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Refer to individual Series


title: Mouse lung gene expression analysis after repetitive hyperbaric oxygen exposure based on RNA-seq

status: Public on Jan 10 2020

city: Southampton

first: Yihua

last: Wang

address: University Road

institute: University of Southampton

summary: Hyperbaric oxygen (HBO) is widely applied to treat a number of hypoxia-related diseases. Previous studies focused on the immediate effect of HBO-exposure induced oxidative stress on lungs, but knowledge regarding the chronic effects from repetitive HBO exposure is limited, especially at the gene expression level. We found that repetitive HBO exposure did not alter the morphology of murine lungs. However, by deconvolution of RNA-seq from those mice lungs using CIBERSORTx and the expression profile matrices of 8 mesenchymal cell subtypes obtained from bleomycin-treated mouse lungs, we identify several mesenchymal cell subtype changes. These include increases in Col13a1 matrix fibroblasts, mesenchymal progenitors and mesothelial cell populations and decreases in lipofibroblasts, endothelial and Pdgfrb high cell populations. Our data suggest that repetitive HBO exposure may affect biological processes in the lungs such as response to wounding, extracellular matrix, vasculature development and immune response.

overall_design: To assess the effect of repetitive HBO-exposure on mice lungs, six to eight weeks old male C57BL/6 mice (20-25 g) mice were divided into control group  and HBO group.The mice in the HBO group were subjected to the 2.5 ATA (Atmosphere Absolute) HBO once a day for 11 consecutive days, 90 min for each time, while the mice in the control group were placed in the chamber for the same duration without pure oxygen pressurization. The day after the end of thel ast exposure, lung tissues were collected to do RNA-seq. Four mouse lungs were sequenced in each group.

first: Yuan

last: Yuan

first: Yilu

last: Zhou

first: Yali

last: Li

first: Zhenglin

last: Jiang


title: Microarray expression profile analysis of long non-coding RNAs in human aldosterone-producing adenoma

status: Public on Jan 26 2020

city: Guangzhou

first: Yinghua

last: Chen

address: 1023 South Shatai  Road

department: Department of Histology and Embryology

institute: Southern Medical University

summary: To further explore the clinical significance of lncRNAs in aldosterone producing adenoma (APA), we have employed large-scale biological database based transcriptome sequencing and microarray techniques as a discovery platform to identify expression changes of lncRNAs between APA (sample3, 4, 5) and normal adrenal (NA, sample A, B, L) tissue. By microarray analysis, we selected differentially expressed LncRNAs and mRNAs, and we further constructed coding-non-coding gene co-expression networks (CNC network) based on the correlation analysis between lncRNAs and target mRNAs. These networks will subsequently help to predict lncRNAs target genes, and will provide important insights into the role of lncRNAs in APA pathogenesis.

overall_design: Microarray analysis was done in total of 6 RNA samples, consisting of 3 each from aldosterone producing adenoma (sample A,B,L) and normal adrenal tissues (sample 3,4,5) . Finally, 38,361 lncRNAs and 34,215 coding transcripts collected from databases.

first: Lichao

last: Zhang

first: Weilie

last: Hu


title: RNA-Seq on wild type and Linear Minichromosome strains arrested in metaphase

summary: Purpose: Are convergent genes at boundaries expressed?


title: Upregulated heme biosynthesis, an exploitable vulnerability in MYCN-driven leukemogenesis

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
The increased heme biosynthesis long observed in leukemia was previously of unknown significance.  Heme, synthesized from porphyrin precursors, plays a central role in oxygen metabolism and mitochondrial function, yet little is known about its role in leukemogenesis. Here we show increased expression of heme biosynthetic genes, including UROD, only in pediatric AML with high MYCN expression.  Both high UROD and MYCN expression predict poor overall survival and unfavorable outcomes in adult AML.  Murine leukemic progenitors derived from hematopoietic progenitor cells (HPCs) overexpressing a MYCN cDNA (MYCN-HPC) require heme/porphyrin biosynthesis, accompanied by increased oxygen consumption, to fully engage in self-renewal and oncogenic transformation. Blocking heme biosynthesis reduced mitochondrial oxygen consumption and markedly suppressed self-renewal. Leukemic progenitors rely on balanced production of heme and heme intermediates, the porphyrins. Porphyrin homeostasis is required because absence of the porphyrin exporter, ABCG2, increased death of leukemic progenitors in vitro and prolonged the survival of mice transplanted with Abcg2-KO MYCN HPCs. Pediatric AML patients with elevated MYCN mRNA display strong activation of TP53 target genes.  Abcg2-KO MYCN HPCs were rescued from porphyrin toxicity by p53 loss. This vulnerability was exploited to show that treatment with a porphyrin precursor, coupled with the absence of ABCG2, blocked MYCN-driven leukemogenesis in vivo thereby demonstrating, that porphyrin homeostasis is a pathway crucial to MYCN leukemogenesis.
We used microarrays to compare the global transcription profiles of hematopoietic progenitor cells from wild-type and Abcg2-ko mice that after transduction with vector-alone or vector containing MYCN gene.

overall_design: We analyzed a total of 8 samples; duplicates of hematopoietic progenitors in the following conditions: WT + Vector, WT + MYCN, Abcg2-ko + Vector, Abcg2-ko + MYCN

first: Yu

last: Fukuda

first: Gerard

last: Grosveld

first: John

last: Schuetz


title: Silencing of ultra-conserved long non-coding RNA Uc.291 causes delay of keratinocyte differentiation

status: Public on Jan 08 2020

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier, 1

department: Dept. of Exp. Medicine and Surgery

country: Italy

institute: University of Rome "Tor Vergata"

summary: Development of the skin includes a complicated program of cellular differentiation. Here, we study the role of Uc.291, a long non-coding RNA derived from ultra-conserved region, upregulated in suprabasal layer of the skin and during in vitro differentiation of keratinocytes. Depletion of Uc.291 causes delay of keratinocyte differentiation with decreased levels of the expression of epidermal differentiation complex (EDC) genes.

overall_design: To investigate the effect of Uc.291 depletion on keratinocyte differentiation, we used microarray expression profiling to identify the genes with altered expression. Human normal epidermal keratinocytes (HEKn) were transiently knocked-down by RNA interference and induced to differentiate for 3 days.

first: Emanuele

last: Panatta


title: Gene expression analysis of Influenza vaccine response in Young and Old - Year 4

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: We profiled gene expression from a stratified cohort of subjects to define influenza vaccine response in Young and Old

overall_design:
Differential gene expression by human PBMCs from Healthy Adults receiving Influenza Vaccination (Fluvirin, Novartis). Healthy adults (older >65, younger 21-30 years) were recruited at seasonal Influenza Vaccination clinics organized by Yale University Health Services during October to December of 2013 – 2014 seasons. With informed consent, healthy individuals were recruited as per a protocol approved by Human Investigations Committee of the Yale University School of Medicine. Each subject was evaluated by a screening questionnaire determining self-reported demographic information, height, weight, medications and comorbid conditions. Participants with acute illness two weeks prior to vaccination were excluded from study. Blood samples were collected into BD Vacutainer Sodium Heparin tube at four different time points, once prior to administration of vaccine and three time points after vaccination on days 2, 7 and 28. Peripheral Blood Mononuclear Cells (PBMC) were isolated from heparinized blood using Histopaque 1077 in gradient centrifugation. About 1.0x10^7 freshly isolated PBMC were lysed in Triso and immediately stored in -80C. Total RNA in aqueous phase of Trisol - Chloroform was isolated in an automated QiaCube instrument using miRNeasy according to manufacturer’s instructions. Integrity of RNA samples were assessed by Agilent 2100 BioAnalyser Samples were processed for cRNA generation using Illumina TotalPrep cRNA Amplification Kit and subsequently hybridized to Human HT12-V4.0 BeadChip at Yale Center for Genomic Analysis (YGCA).

The current data set, together with GSE59654, GSE59635, GSE59743, and GSE101710, represents subsets of the same overall study

first: Albert

middle: C

last: Shaw

first: Subhasis

last: Mohanty

first: Steven

last: Kleinstein

first: Sui

last: Tsang

first: Stefan

last: Avey


title: Transcriptional profiling of OT-1 cells during in vitro memory formation after high- or low-affinity priming

status: Public on Jan 06 2020

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: To understand the impact of TCR affinity during priming on memory formation, we performed transcriptional profiling of OT-1 cells at different time points after stimulation with high- or low-affinity ligands. Our findings indicate that low-affinity stimulaation is associated with earlier memory formation.

overall_design: We stimulated purified OT-1 T cells with high-affinity N4 or low-affinity Q4 peptides, icw anti-CD28. After 30h cells were washed and cultured with IL-15 or IL-2 for an additional 5 days. RNA was isolated at T0, T30, T72 and T140.

first: Felix

last: Wensveen


title: Tri-cultures of HGSOC cells replicate tissue remodelling observed in biopsies.

status: Public on Jan 01 2020

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

summary: We built novel tri-cultures of HGSOC cells with human primary omental adipocytes and fibroblasts which replicated tissue remodelling and matrisome production observed in biopsies. RNAseq analysis showed that tri-cultures reproduced the prognostic matrisome signature.

overall_design: RNA sequencing on 1) 3D-tricultures of HGSOC malignant cells, omental fibroblasts and adipocytes with (n = 2) or without (n = 2) TGFβRI + GLI1/2 inhibitors, or on adipocyte-only gels (n = 1), or co-cultures of HGSOC malignant cells and omental fibroblasts (n = 2); and 2) on two HGSOC malignant cell lines grown in monolayer (n = 2-3) and as spheroids (n = 2-3).

first: Robin

last: Delaine-Smith

first: Beatrice

last: Malacrida

first: Frances

last: Balkwill


title: Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [END-seq]

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: During V(D)J recombination RAG proteins introduce DNA double strand breaks (DSBs) adjacent to conserved recombination signal sequences (RSS) that contain either 12- or 23-nucleotide spacer regions. Coordinated cleavage following the “12/23” rule predicts that DSBs at variable (V) gene segments should not exceed the level of breakage at joining (J) segments, thereby ensuring that V regions do not engage in undesirable recombination events with one another. Here we report abundant RAG dependent DSBs at a multitude of V gene segments within the Ig locus independent of V-J rearrangement.  We discover that a large fraction of V gene segments are flanked not only by a bone-fide 12 spacer, but also an overlapping, 23 spacer flipped RSS. These compatible pairs of RSS mediate recombination and deletion inside the V cluster even in the complete absence of J gene segments, and support a novel recombination center (RC) independent of the conventional J-centered RC. We propose a model that explains V gene segment usage by taking into account not only the probability of V-to-J rearrangement but also the surprisingly frequent, evolutionarily conserved intra-V cluster recombination events. These findings shed light on the diverse molecular strategies that shape the primary antigen receptor repertoires.

overall_design: END-seq profile in abelson-transformed pre-B cells, primary bone marrow pre-B cells, and thymocytes.

first: Kenta

last: Shindoa

first: Andres

last: Canela

first: David

last: Shchatz

first: Ferenc

last: Livak

first: André

last: Nussenzweig


title: GABPα and CREB1 binding to double nucleotide polymorphisms of their consensus motifs and cooperative binding to the ETS-CRE motif (ACCGGAAGTGACGTCA).

city: Bethesda

first: Charles

last: Vinson

state: MD

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

summary: Previously, cooperative binding to DNA between the bZIP domain of CREB1 and the ETS domain of GABPα was observed for the composite ETS-CRE motif (A0C1C2G3G4A5A6G7T8G9A10C11G12T13C14A15).  Single nucleotide polymorphisms (SNPs) at the beginning and end of the ETS motif (ACCGGAAGT) increased cooperative binding.  Here, we use a microarray containing all double nucleotide polymorphisms (DNPs) of the ETS-CRE motif to explore GABPα and CREB1 binding to their canonical motifs and their cooperative binding to the ETS-CRE motif.  For GABPα, binding to SNPs predicted binding the DNPs.  In contrast, CREB1 binding to DNPs showed cooperativity.  Similar results were observed for other ETS and bZIP family members.  Cooperative binding between GABPα and CREB1 was typically weaker than expected except for DNPs containing A7 and SNPs at the beginning of the ETS motif.

overall_design: Protein binding microarray (PBM) experiments were performed for the DNA binding domain of GABPa and CREB1.  Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded custom Agilent microarrays (He et al., G3 2015) in order to determine their cooperative binding preferences to composite DNA motifs.

first: Nima

last: Assad


title: Immune surveillance of cellular homeostasis by NOD1/2 via sensing cytosolic sphingosine-1-phosphate (S1P)

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Chronic inflammation is associated with disruption of cellular homeostasis, yet the underlying mechanisms remain elusive1. Nucleotide-binding oligomerization domain-containing protein 1/2 (NOD1/2) are intracellular pathogen recognition receptors that activate innate immune responses via sensing bacterial peptidoglycans2-4. We demonstrate that NOD1/2 sense not only microbe-specific molecular patterns but also perturbation of cell homeostasis, and thereby cause inflammation. Host generation of sphingosine-1-phosphate (S1P) via the hydrolysis pathway is essential for NOD1/2 signaling upon such stress. Cytosolic delivery of S1P activates NOD1/2 dependent NF-κB activation and inflammation. Finally, we demonstrate that S1P directly binds to and activates NOD1/2. In sum, we describe a hitherto unknown role of NOD1/2 by revealing that they initiate innate immune responses by surveillance of cellular homeostasis through sensing of cytosolic S1P. Our findings provide a novel link between host cytosolic S1P and NOD1/2 mediated immune activation upon perturbation of cellular homeostasis and thus form the basis for future intervention strategies targeting the S1P-NOD1/2 axis.

overall_design: Microarray experiments were performed as single-color hybridizations according the recommendation of Agilent Technologies. Quality control and quantification of total RNA amount was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies), an AATI Fragment Analyzer (Advanced  Analytical)  and a NanoDrop 1000 spectrophotometer (Kisker).

first: Gang

last: Pei

first: Joanna

last: Zyla

first: January

last: Weiner

first: Anca

last: Dorhoi

last: Kaufmann


title: Expression data of Jmjd2a and Jmjd2c-regulated genes in plasma cell differentiation

city: Taipei

first: Kuo-Hsuan

last: Hung

address: 128 Academia Road, Section 2

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Base on the privious studie from our lab, we found the histone demethylases, Jmjd2a and Jmjd2c are upregulated in stimulated primary B cells, depletion of Jmjd2a and Jmjd2c in stimulated B cells resulted in failed activation of B cells. Owimg to the essential functions of Jmjd2a and Jmjd2c, We here applied loss of function approach, such as siRNA, to study the how Jmjd2a and Jmjd2c regulate plasma cell differentiation.

overall_design: Splenic B220+ B cells from total splenocytes were isolated, and treated with Tfh-derived signals. The cells were transfected with sicontrol, siJmjd2a or siJmjd2c to deplete Jmjd2a or Jmjd2c. Collected the cells and lysed the cells directly by adding TRIZOL at day 0, day 1, and day 3 after stimulation.

first: Kou-I

last: Lin


title: Whole-transcriptome analysis of tumor tissues of lung adenocarcinoma reveals molecular changes under the influence of IFN-γ

city: Wuhan

first: yi

last: gao

state: Hubei

address: No.1095 Jie Fang Avenue

department: Thoracic surgery

institute: Tongji Hospital

summary: IFN-γ is a critical cytokine which regulates both innate and adaptive immune. Ample evidences have elucidated the mechanisms of IFN-γ mediated antitumor effects, including driving T Helper Type 1 (Th1) polarization, activating cytotoxic lymphocyte (CTL) and natural killer T cells, upregulating major histocompatibility complex class I expression (MHC Class I) in tumor cells, and inhibiting tumor cells proliferation, inducing tumor cells apoptosis. Despite the multiple effects in cancer immune elimination phase (also known as cancer immune surveillance), IFN-γ also effectuates antitumor immunity and protumorigenic activities throughout the cancer immunoediting process including elimination phase and escape phase. One of the most important mechanism elucidating the dual effect of IFN-γ in immunoediting is IFN-γ induced PD-L1 expression in cancer cells. To obtain a detailed molecular appreciation of what was going on in tumor microenvironment under the influence of IFN-g, we performed global gene expression analysis using the Agilent oligonucleotide microarray system.

overall_design: First, we evaluated the IFN-γ expression in a uniform cohort of patients with IIIA lung adenocarcinoma from our patient archive. IFN-g expression was assessed by means of RT-PCR. The median DCt value from tested specimens was set as breakpoint, IFN-g expression below median DCt value was considered as low IFN-g group (IFN-g-) whereas above median DCt value was the high IFN-g group (IFN-g+). Then, we analyzed PD-L1 expression by IHC staining of biopsy specimens in whole slides. PD-L1 expression was quantified by multiplying the staining intensity scores by the percentage of positive cells. Biopsy specimens from 12 lung adenocarcinoma patients were included to perform the Agilent oligonucleotide microarray system. Six of biopsy specimens contain high levels of IFN-g while others expressing IFN-g at low or undetectable levels. Furthermore, we divided IFN-g+ group into two subgroups according to PD-L1 expression, three IFN-g+ specimens expressing PD-L1 (IFN-g+PD-L1+) but others not (IFN-g+PD-L1-).

first: Yi

last: Gao

first: Lequn

last: Li

first: Xiangning

last: Fu


title: ChIP-Seq of Jmjd2a and Jmjd2c in B220+ B cells

summary: Here we reported the Jmjd2a and Jmjd2c are co-targeted at the essential genes of mouse activating B220+ B cells. B cell activation programs transcription networks that subsequently induce plasma cell differentiation, but how histone demethylases participating in this process remains elusive. We found that histone demethylases Jmjd2a and Jmjd2c are expressed in Tfh-mediated signals stimulated mouse spelenic B220+ B cells. we then perform ChIP-seq by using anti-Jmjd2a and anti-Jmjd2c antibodies to identified the genes regulated by Jmjd2a and Jmjd2c and required for correct activation.

overall_design: Examination the genes which are regulated by two different histone demeltylases, Jmjd2a and Jmjd2c in Tfh-mediated signals stimulated B220+ B cells by ChIP-seq.

first: Kuo-I


title: Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire

first: Yaakov

last: Maman


title: Global transcriptional analysis identifies a novel role for SOX4 in tumor-induced angiogenesis

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: The expression of the transcription factor SOX4 is increased in many human cancers, however, the pro-oncogenic capacity of SOX4 can vary greatly depending on the tumor-type. Both the contextual nature and the mechanisms underlying the pro-oncogenic SOX4 response remain unexplored. Here, we demonstrate that in mammary tumorigenesis, the SOX4 transcriptional network is dictated by the epigenome and is enriched for pro-angiogenic processes. We show that SOX4 directly regulates endothelin-1 (ET-1) expression and thereby promotes tumor-induced angiogenesis both in vitro and in vivo. Furthermore, in breast tumors, SOX4 expression correlates with blood vessel density and size, and predicts poor-prognosis in breast cancer patients. Our data provide novel mechanistic insights into context-dependent SOX4 target gene selection, and uncover a novel pro-oncogenic role by promoting tumor-induced angiogenesis. These findings establish a key role for SOX4 in promoting metastasis through exploiting diverse pro-tumorigenic pathways.

overall_design: Examination of 3 histone marks, RNAPII and SOX4 in HMLE-S4 cells with and without doxycyclin treatment


title: Expression data from single atoh7 positive retinal cells

city: Ames

first: Jeff

last: Trimarchi

state: IA

address: 2437 Pammel Drive

department: Genetics, Development and Cell Biology

institute: Iowa State University

summary: This study aimed to characterize the transcriptomes of a subset of retinal progenitors cells expressing Atoh7.

overall_design: We examined 11 single cells and compared them to single cells previously profiled in GSE9811 and GSE9812. These samples have been included in this series so that this series contains all samples analyzed in the study.

first: Rebecca

last: Chowdhury

first: Lauren

middle: A

last: Laboissonniere

first: Jillian

last: Goetz

first: Laura

last: Ellson

first: Andrea

last: Wester

first: Amy

last: Mayse

first: Shanea

last: Janes

first: Constance

last: Cepko

first: Jeffrey


title: Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [ChIP-seq]

overall_design: ChIP-seq profile in Abelson-transformed mouse Pre-B cells.

first: Kenta

last: Shindoa

first: Andres

last: Canela

first: David

last: Shchatz

first: Ferenc

last: Livak

first: André

last: Nussenzweig


title: Bayesian Correlation is a robust similarity measure for single cell RNA-seq data

status: Public on Dec 31 2019

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

institute: University of Bern

summary: Single-cell analysis of the transcriptome deepens our understanding of an individual cell's contribution to its microenvironment. Using single-cell analysis to study complex biological processes requires state-of-the-art computational tools. Assessing similarity is highly important for bioinformatics algorithms in order to determine correlations  between  biological information. Similarity can appear by chance, particularly for low expressed entities. This is especially relevant in single cell RNA-seq (scRNA-seq) because the read counts obtained are lower compared to bulk RNA-sequencing and therefore classic bioinformatics tools are insufficient to obtain reproducible results. Recently, a Bayesian correlation scheme, that assigns low correlation values to correlations coming from low expressed genes, has been proposed to assess similarity for bulk RNA-seq and miRNA. This Bayesian method uses a prior distribution before using empirical evidence. Our goal was to extend the properties of this Bayesian correlation scheme to scRNA-seq data. We assessed 3 ways to compute similarity. First, we computed the similarity of each pair of genes over all cells. Second, we identified specific cell populations and computed the correlation in those specific cells. Third, we computed the similarity of each pair of genes over all clusters, by including the total mRNA expression in those cells. To study the effect of the number of cells on the method, we did not rely on simulated data, we generated 4 scRNA-seq mouse liver cell libraries with a varying number of input cells. Results: We show that Bayesian correlations are more reproducible than Pearson correlations in all the scenarios studied. Compared to Pearson correlations, Bayesian correlations have a smaller dependence on the number of input cells. We demonstrate that the Bayesian correlation algorithm assigns high similarity values to genes with a biological relevance in a specific population. Significance: Our results demonstrate that Bayesian correlation is a robust similarity measure for scRNA-seq datasets. The Bayesian method allows researchers to study similarity between pairs of genes without discarding low expressed entities and to minimize biasing the results by fake correlations. Taken together, using our method of Bayesian correlation the reproducibility of scRNA-seq experiments is increased significantly.

overall_design: 4 single cell RNA-seq liver samples with Parenchymal and non-parenchymal cells were sequenced from the same animal varying the number of input cells: 1000, 2000, 5000 and 10000.

first: Theodore

last: Perkins

first: Noelle

last: Dommann

first: Nicolas

last: Melin

first: Adrian

last: Keogh

first: Deborah

last: Stroka

first: Guido

last: Beldi


title: The Chromatin Remodelling Contributions of Snf2l in Cerebellar Granule Neuron Differentiation [RNA-Seq]

city: Ottawa

last: Picketts

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

summary: Snf2l and the closely related protein, Snf2h, play a critical role in embryonic and post-natal brain development. Murine models lacking functional Snf2h or Snf2l point to complementary activities of these remodelers; Snf2h cKO mice present with a significantly reduced cerebellum, while Snf2l Ex6DEL cerebella are larger than their wild-type counterparts. Granule neuron progenitors (GNPs) isolated from Ex6DEL cerebella display delayed cell cycle exit and hindered terminal differentiation compared to wild-type littermates. Moreover, loss of Snf2l activity results in widespread transcriptome shifts which underlie the Ex6DEL GNP differentiation phenotype. In particular, key transcription factors (TFs) are differentially expressed without Snf2l remodelling activity. We confirm that ERK pathway activation is misregulated in Ex6DEL GNPs, possibly in response to elevated fibroblast growth factor 8 (Fgf8) expression in these cultures. We find that Snf2l activity maintains the chromatin landscape throughout GNP differentiation, as Ex6DEL cultures have a global increase in chromatin accessibility. We suggest that Snf2l-mediated chromatin condensation is responsible for proper regulation of gene expression programs in GNP differentiation.

overall_design: Assess modifications in chromatin accessibility upon loss of Snf2l activity (Ex6DEL)

first: Laura

middle: R

last: Goodwin

first: Matías

last: Alvarez-Saavedra

first: Stephen

last: Rennick


title: The Chromatin Remodelling Contributions of Snf2l in Cerebellar Granule Neuron Differentiation

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

overall_design: Refer to individual Series


title: Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [HTGTS]

first: Yaakov

last: Maman

overall_design: HTGTS profile in abelson-transformed pre-B cells, primary splenic B cells, bone marrow B cells, and human PBMC B cells.


title: Affymetrix Gene Expression profiles of murine LAMTOR2-deficient hematopoietic progenitor cells

city: Hannover

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

summary: LAMTOR2, a member of the Ragulator complex, controls endosomal signaling. Here, we show that postnatal Mx1-Cre-driven deletion of LAMTOR2 in mice resulted in the development of a cell-intrinsic myeloproliferation characterized by splenomegaly, accumulation of myelomonocytoid cells, and depletion of long-term hematopoietic stem cells. LAMTOR2-deficient hematopoietic progenitors exhibited a myeloid-skewed gene expression signature as well as an enhanced GM-CSF-mediated colony formation and activation of ERK signaling. In contrast, disruption of LAMTOR2 resulted in decreased G CSF-mediated STAT3 signaling and impaired granulocytic differentiation. LAMTOR2-defective cells showed aberrant multivesicular body formation, consistent with delayed degradation of activated cytokine receptors. Our study reveals a critical role of LAMTOR2 in regulating cytokine signaling during hematopoietic differentiation.

overall_design: LAMTOR2-deficient and wild-type hematopoietic progenitor cells (LSK: Lin- Sca1+c kit+; Granulocyte-Macrophage-Progitors/GMP: Lin-Sca1-c-kit+CD34+FcγR+) were sorted from mouse bone marrow 14 days after administration of pIpC. Deletion of Lamtor2 was confirmed by PCR Analysis. Total RNA  was extracted from sorted LSK and GMP of three C57BL/6J Mx-Cre Lamtorwt/wt  and three C57BL/6J Mx-Cre Lamtor2f/f mice.

last: Kotlarz