title: Interferon-β corrects massive gene dysregulation in multiple sclerosis:  Short-term and long-term effects on immune regulation and neuroprotection

city: Chicago

first: Riyue

last: Bao

state: IL

address: 900 E 57 Street

department: Center for Research Informatics

institute: University of Chicago

summary: Background: In multiple sclerosis (MS), immune up-regulation is coupled to subnormal immune response to interferon-β (IFN-β) and low serum IFN-β levels. The relationship between the defect in IFN signalling and acute and long-term effects of IFN-β on gene expression in MS is inadequately understood. Methods: We profiled IFN-β-induced transcriptome shifts, using high-resolution microarrays on 227 mononuclear cell samples from IFN-β-treated MS Complete Responders (CR) stable for five years, and stable and active Partial Responders (PR), stable and active untreated MS, and healthy controls.  Findings: IFN-β injection induced short-term changes in 1,200 genes compared to baseline expression after 4-day IFN washout. Pre-injection after washout, and in response to IFN-β injections, PR more frequently had abnormal gene expression than CR. Surprisingly, short-term IFN-β induced little shift in Th1/Th17/Th2 gene expression, but up-regulated immune-inhibitory genes (ILT, IDO1, PD-L1). Expression of 8,800 genes was dysregulated n therapy-naïve compared to IFN-β-treated patients. These long-term changes in protein-coding and long non-coding RNAs affect immunity, synaptic transmission, and CNS cell survival, and correct the disordered therapy-naïve transcriptome to near-normal. In keeping with its impact on clinical course and brain repair in MS, long-term IFN-β treatment reversed the overexpression of proinflammatory and MMP genes, while enhancing genes involved in the oligodendroglia-protective integrated stress response, neuroprotection, and immunoregulation. In the rectified long-term signature, 277 transcripts differed between stable PR and CR patients.

overall_design: 227 samples,from 54 subjects.  27 relapsing/remitting MS (RRMS) on IFN-β therapy for 8·14 ± 0·86 years. 12 were Complete Responders to IFN-β therapy, exacerbation-free >6 months before sampling. 15 Partial R patients were stable for >6 months, and were also followed for 5 years. PR were also sampled during an exacerbation. Therapy-naïve included 10 with stable RRMS and 9 RRMS during exacerbations.  Ther were age- and sex-macthed with 8 healthy controls.

first: Xuan

last: Feng

first: Lei

last: Li

first: Florian

last: Deisenhammer

first: Barry

middle: W

last: Arnason

first: Anthony

middle: T

last: Reder


title: RGS4 Maintains Chronic Pain Symptoms in Rodent Models

status: Public on Sep 26 2019

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

type: Expression profiling by high throughput sequencing

summary: There is an imminent need for safe and efficient chronic pain medications. Regulator of G-protein signaling 4 (RGS4) is a multi-functional signal transduction protein, widely expressed in the pain matrix. Here, we demonstrate that RGS4 plays a prominentrole in the maintenance of chronic pain symptoms in male and female mice. Using genetically modified mice, we show a dynamicrole of RGS4 in recovery from symptoms of sensory hypersensitivity deriving from hindpaw inflammation or hindlimb nerveinjury. We also demonstrate an important role of RGS4 actions in gene expression patterns induced by chronic pain states in themouse thalamus. Our findings provide novel insight into mechanisms associated with the maintenance of chronic pain states anddemonstrate that interventions in RGS4 activity promote recovery from sensory hypersensitivity symptoms.

overall_design: Using a mouse line carrying a floxed RGS4 gene and adeno-associated virus (AAV) vectors expressing Cre recombinase, we downregulated RGS4 expression in the VPL-THL (ventral posterolateral thalamic nuclei)

first: Kleopatra

last: Avrampou

first: Kerri

middle: D

last: Pryce

first: Farhana

last: Sakloth

first: Li

last: Shen

first: Fiona

middle: B

last: Carr

first: Venetia

last: Zachariou


title: Expression Data from Arabidopsis ULT1 and CLF Mutants

city: Albany

first: Jennifer

middle: C

last: Fletcher

state: CA

address: 800 Buchanan Street

institute: Plant Gene Expression Center

summary:
ULT1 and CLF function antagonistically as epigenetic regulators of gene expression in Arabidopsis. We sought to identity their global downstream target genes at two stages of plant development and determine their common targets.
We used microarrays to determine the global gene expression programs regulated by ULT1 and FLC during vegetative and reproductive development and compared the overlap among target genes between the two proteins.

overall_design: Arabidopsis shoot apices from wild-type Ler, ult1-3 Ler, 35S:ULT1 Ler, and clf-2 Ler plants were collected at the vegetative and reproductive stages for RNA extraction and hybridization on Affymetrix microarrays.

first: Ludmila

last: Tyler


title: Isomorphic diffuse glioma is a distinct tumour entity with recurrent gene fusions of MYBL1 or MYB and a benign disease course

city: Regensburg

first: Annika

middle: K

last: Wefers

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

country: Germany

institute: Regensburg University Hospital

summary:
DNA methylation profiling of 26 individual isomorphic diffuse gliomas using Illumina HumanMethylation450 BeadChips or  Illumina Infinium HumanMethylation850 BeadChips.

Abstract:
The “isomorphic subtype of diffuse astrocytoma” was identified histologically in 2004 as a supratentorial, highly differentiated glioma with low cellularity, low proliferation and focal diffuse brain infiltration. Patients typically had seizures since childhood and all were operated on as adults. To define the position of these lesions among brain tumours, we histologically, molecularly and clinically analysed 26 histologically prototypical isomorphic diffuse gliomas. Immunohistochemically, they were GFAP-positive, MAP2-, OLIG2- and CD34-negative, nuclear ATRX-expression was retained and proliferation was low. All 24 cases sequenced were IDH-wildtype. In cluster analyses of DNA-methylation data, isomorphic diffuse gliomas formed a group clearly distinct from other glial/glio-neuronal brain tumours and normal hemispheric tissue, most closely related to paediatric MYB/MYBL1-altered diffuse astrocytomas and angiocentric gliomas. Half of the isomorphic diffuse gliomas had copy number alterations of MYBL1 or MYB (13/25, 52%). Gene fusions of MYBL1 or MYB with various gene partners were identified in 11/22 (50%) and were associated with an increased RNA-expression of the respective MYB-family gene. Integrating copy number alterations and available RNA sequencing data, 20/26 (77%) of isomorphic diffuse gliomas demonstrated MYBL1 (54%) or MYB (23%) alterations. Clinically, 89% of patients were seizure-free after surgery and all had a good outcome. In summary, we here define a distinct benign tumour class belonging to the family of MYB/MYBL1-altered gliomas. Isomorphic diffuse glioma occurs both in children and adults, has a concise morphology, frequent MYBL1- and MYB-alterations and a specific DNA-methylation profile. As an exclusively histological diagnosis may be very challenging and as paediatric MYB/MYBL1-altered diffuse astrocytomas may have the same gene fusions, we consider DNA-methylation profiling very helpful for their identification.

first: David

last: Capper

first: Daniel

last: Schrimpf


title: Re-programing chromatin with a bifunctional LSD1/HDAC inhibitor induces therapeutic differentiation in DIPG [RNA-seq]

city: Boston, MA

first: Jamie

last: Anastas

state: United States of America

address: 300 Longwood Ave

department: Newborn Medicine

institute: Boston Children's Hospital

summary: Histone H3 lysine 27 to methionine mutations (H3K27M) resulting in aberrant chromatin regulation are frequently observed in Diffuse Intrinsic Pontine Glioma (DIPG), a pediatric brain tumor with no cure. We conducted a CRISPR screen to determine if various chromatin regulators might be targeted to treat DIPG. Excitingly, this genetic screen reveals that co-targeting lysine specific demethylase 1 (LSD1) and histone deacetylases (HDACs) results in an enhanced growth suppressive effect in patient DIPG cells. Consistent with the genetic screen, a bifunctional inhibitor of HDACs and LSD1, Corin, inhibits DIPG growth in vitro and in xenografts. Mechanistically, Corin rescues H3K27me3 levels typically suppressed by the dominant effects of H3K27M mutations in DIPG and simultaneously increases HDAC-targeted H3K27ac and LSD1-targeted H3K4me1 at enhancers. Further studies reveal that Corin de-regulates DIPG transcription resulting in cell death, cell cycle arrest, and the induction of neuronal differentiation. These data suggest that co-targeting LSD1 and HDACs may represent a novel strategy for treating DIPG.

overall_design: RNA-seq of polyA RNA from SU-DIPGXIII cells that had been treated with 0.5 uM of the LSD1 inhibitor, JKD-1-62, the HDAC inhibitor MS-275, the dual LSD1 and HDAC inhibitor, Corin, or the vehicle control, DMSO.

first: Yang

last: Shi


title: Identification of a LIF-responsive replication-competent human β cell

status: Public on Sep 25 2019

city: Cambridge

first: Edwin

middle: Antonio

last: Rosado-Olivieri

state: MA

address: 7 Divinity Ave

department: Department of Stem Cell and Regenerative Biology

institute: Harvard University

summary: The beta (β) cell mass formed during embryogenesis is amplified by cell replication that occurs primarily during fetal and early postnatal development. Thereafter, β cells become functionally mature and their mass is maintained by a very low rate of replication.  For those few β cells that replicate in adult life, it is not known how replication is initiated, uncoupled from β cell function nor whether this occurs in a specialized subset of β cells. To explore these issues with the aim of controlling replication of mature human β cells, we capitalized on a YAP overexpression system that induces cell cycle re-entry in stem cell derived-β cells.  Singe cell RNA sequencing revealed an upregulation of components of the leukemia inhibitory factor (LIF) pathway upon cell cycle re-entry.  Experimental activation of the LIF pathway induces replication and expansion of human stem cell derived- and adult β cells in vitro and in vivo. In both stem cell derived- and adult human β cells, the expression of the LIF receptor LIFR is restricted to a subset of β cells with distinct transcriptional profiles and defines a subpopulation of β cells with increased replication rates.  Further analysis identified 15 transcription factors whose gene networks are active in replicating β cells. Overall, this study sheds light on regulatory networks that control β cell replication and reveals a heterogeneity in LIF responsiveness and replication competence.

overall_design: Single cell analysis of LacZ- and YAPS6A-overexpressing beta cells using the 10X genomics platform and bulk RNA-seq analysis of LIFR+ and LIFR- sorted beta cells.

middle: A

last: Rosado-Oliveri

first: Idil

middle: I

last: Aigha

middle: H

last: Kenty

first: Dani

last: Swain

first: José

last: Rivera-Feliciano

first: Douglas

last: Melton


title: Cigarette smoke preparations, but not moist snuff, impair expression of genes involved in signaling and cytolytic functions in peripheral blood mononuclear cells

city: Winston-salem

first: Prasad

last: GL

state: NC

address: 401 N Main St

institute: RAISC

summary:
Cigarette smoking exerts diverse physiological effects including immune suppression. Existing US epidemiological data show that consumption of smokeless tobacco products, such as moist snuff, is less harmful relative to cigarette smoking. In efforts to understand the molecular changes due to consumption of different tobacco product classes, we have shown recently that smokers exhibit distinct peripheral blood mononuclear cells (PBMCs) gene expression patterns relative to moist snuff users and non-tobacco consumers (NTCs). To better characterize the biological effects exerted from the use of different tobacco products, a genome-wide gene expression study, using a cultured PBMC model, was performed.
Gene expression profiles from PBMCs treated with low equi-nicotine units (0.3 µg/ml) of WS-CM and a single high dose of STE (100 µg/ml) were similar to those from untreated controls.  Cells treated with medium and high equi-nicotine unit doses of WS-CM (1.0 and 3.0 µg/ml) exhibited significantly different gene expression profiles compared to the low equi-nicotine WS-CM dose and STE.  Pre-treatment with higher doses of WS-CM inhibited the expression of several pro-inflammatory genes that regulate immune responses, including IFNγ, TNFα, and IL-2.  Gene expression changes of these genes and other cytokine signaling genes were confirmed by qRT-PCR. Moreover, secretion of IFNγ, TNFα and IL-2 proteins was abolished by WS-CM pre-treatment even after 24 hours of toll like receptor stimulation. Additionally, pathway analyses revealed that higher doses of WS-CM inhibited NF-ĸβ signaling and a wide range of signaling pathways associated with immune cell differentiation and inflammatory responses, and increased  expression of genes involved in apoptosis. Collectively, our results show that pre-treatment of PBMCs with higher doses of WS-CM inhibits immune activation and effector cytokine expression and secretion, resulting in a reduced immune response, whereas STE had minimal effect.

overall_design: To understand how different tobacco products impact immune responses, we assessed transcriptomic profiles in peripheral blood mononuclear cells (PBMCs) pretreated with Whole Smoke Conditioned-Medium (WS-CM) or Smokeless Tobacco Extracts (STE), and stimulated with lipopolysaccharide, phorbol myristate and ionomycin (agonists).

first: Gang

last: Liu

first: G

middle: L

last: Prasad


title: Re-programing chromatin with a bifunctional LSD1/HDAC inhibitor induces therapeutic differentiation in DIPG

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene Expression Profiling of siRNA Knockdown and overexpression of SMYD3 in C2C12

city: Paris

first: ROBERTA

last: CODATO

address: 35 rue Hélène Brion

country: France

institute: Paris Diderot University - UMR 7216 Epigenetics and Cell Fate

summary: Members of the SMYD family of Histone Lysine Methyltransferases, including SMYD3, were shown to be involved in both cardiac and skeletal myogenesis. Currently, very little is known about their mechanisms of action and their potential target genes. To study the cellular and molecular function of SMYD3 in skeletal muscle differentiation, we used loss and gain of function approaches in C2C12 myoblasts. We used RNA sequencing (RNA-seq) to generate gene expression profiling during myogenic differentiation under SMYD3 transient knockdown by siRNAs or SMYD3 stable overexpression in C2C12. We identified multiple genes whose expression is significantly affected by Smyd3 levels, among them the key myogenic regulatory factor (MRF) Myogenin.

overall_design: For knockdown condition, C2C12 myoblasts were transfected with siRNAs against SMYD3 or control 24h before start of differentiation. For overexpression condition, we generated a stable C2C12-derived cell line (SMYD3-CL5) that expresses a HA-Flag-tagged SMYD3, and a control cell line (empty vector). For both conditions, cells were harvested for gene expression profiling when differentiation was induced (0h, confluent cells) and after 24h of differentiation in differentiation medium.  For each time point, three replicates were performed per siRNA, and two replicates were performed for the clonal cell lines overexpressing SMYD3.

first: Souhila

last: Medjkane

first: Roberta

last: Codato


title: MDA-MB-231 metastasis to human bone

status: Public on Sep 24 2019

city: Sheffield

first: Penelope

last: Ottewell

state: England

address: Medical School, Beech Hill Road

department: Oncology and Metabolism

country: United Kingdom

institute: University of Sheffield

summary: MDA-MB-231 human breast cancer cells were injected orthotopiclly into mammary glands 4 of female NOD SCID mice 4-weeks after sub-cutaneous implantation of human femoral bone chips. Primary tumour, bone chips containing metastatic deposits and naive bone chips were isolated and mRNA analysed for gene expression to determine genetic signitures associated with breast cancer bone metastasis.

overall_design: Group 1-Primary tumours that did not metastasise, Group 2-Primary tumours that metastasised to bone, Group 3- naïve human bone (patient matiched), Group 4- human bone containing metastatic deposits


title: Identify gene networks in maize and beneficial fungus Trichoderma virens that result in induced systemic resistance (ISR)

city: College Station

first: Michael

last: Kolomiets

state: Texas

address: 496 Olsen Blvd.2132 TAMU

department: Plant Pathology and Microbiology

institute: Texas A&M University

summary: ISR is the initiation of a beneficial association by certain fungi in the rhizosphere followed by the establishment of belowground-aboveground signaling communication may result in the induction of heightened host resistance to foliar and stem pathogens, as well as insect pests.

overall_design: Examination of maize and T. virens transcriptome during early and late interaction.

first: Ken-Der

last: Wang


title: Ultra-deep sequencing reveals pre-mRNA splicing as a sequence driven high-fidelity process

city: Irvine

first: Klemens

last: Hertel

address: 19182 Jamboree Rd. 811 Med Sci I, C270

department: MMG

institute: UCI

summary: Alternative splicing diversifies mRNA transcripts in human cells. While the spliceosome pairs exons with a high degree of accuracy, the rates of rare aberrant and non-canonical pre-mRNA splicing have not been evaluated at the nucleotide level to determine the quantity and identity of these events across splice junctions. Using ultra-deep sequencing the frequency of aberrant and non-canonical splicing events for three splice junctions flanking exon 7 of SMN1 were determined at single nucleotide resolution. After correction for background noise introduced by PCR amplification and sequencing steps, pre-mRNA splicing was shown to maintain a low overall rate of aberrant and non-canonically spliced events. Several previously unannotated splicing events across 3 exon|intron junctions in SMN1 were identified. Mutations within SMN exon 7 were shown to affect splicing fidelity by modulating RNA secondary structures, by altering the binding site of regulatory proteins and by changing the 5’ splice site strength. Mutations also create a truncated SMN1 exon 7 through the introduction of a de novo non-canonical 5’ splice site. The results from the ultra-deep sequencing approach highlight the impressive fidelity of pre-mRNA splicing and demonstrate that the immediate sequence context around splice sites is the main driving force behind non-canonical splice site pairing.

overall_design: HeLa cells were transfected with a library of SMN1 mini-gene (exon6-exon7-exon8) constructs with all possible mutations at every synonymous position within exon7 within a 6bp sliding window. RNA-seq reads for only these constructs were generated.

first: Derrick

middle: J

last: Reynolds


title: Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle

first: Natalia

last: Teleshova

state: NY

address: 1230 York Avenue

institute: Population Council

summary: Despite extensive studies suggesting increased susceptibility to HIV during the secretory phase of the menstrual cycle, there is limited knowledge of the molecular mechanisms involved. We aimed to explore the ectocervical and endocervical tissue transcriptomes during the proliferative and secretory phases of the cycle using RNA sequencing (RNAseq) to identify potential signatures of susceptibility to HIV. We utilized hysterectomy tissue specimens from subjects not using hormonal contraception/treatment for gynecological conditions. Ectocervical (n=10) and endocervical tissues (n=15) were used for this study. The cycle phase was determined by assessing the histopathology of hematoxylin-and-eosin stained sections of the endometrial mucosa by gynecologic pathologists. Total RNA was isolated from tissues frozen in RNAlater (Ambion) following manufacturer’s instructions (Qiagen RNeasy Fibrous Tissue Mini Kit). After extraction, the quality and the purity of the RNA were measured by the Agilent Bioanalyzer (Agilent, Santa Clara, CA). RNA was labeled and sequenced at the RU Genomics center by using Illumina TruSeq technology (75bp, >30M coverage). The data were analyzed using Ingenuity Pathway Analysis (IPA) software (QIAGEN Inc., https://www.qiagenbioinformatics.com/products/ingenuitypathway-analysis). To inquire into changes in gene expression irrespectively of p-value cut off, pre-ranked genes based on proliferative vs. secretory phase expression were subjected to Gene Set Enrichment Analysis (GSEA) against the Hallmark Gene sets (H) and Immunologic Signatures Gene sets (collection C7) from the Molecular Signatures Database (MSigDB)(http://software.broadinstitute.org/gsea/msigdb/index.jsp). Our data show menstrual cycle phase-associated changes in the transcriptomic landscape of the endocervix and ectocervix, some of which may contribute to changes in HIV susceptibility.

overall_design: 15 endocervical samples (n=8 proliferative, n=7 secretory); 10 ectocervical samples (n=5 proliferative,  n=4 secretory)


title: RNAseq data from mtDNA mutator induced pluripotent stem cells

city: Kuopio

first: Riikka

last: Hämäläinen

address: Neulaniementie 2

country: Finland

institute: university of eastern Finland

summary: RNAsequencing data from POLG D257A mutant mouse iPS (induced pluripotent stem) cells. These mice accumulate random point mutations in their mitochondrial genome and manifest progeric features. The reprogramming and phenotype of the cells is described in Hämäläinen et al. 2015, Cell reports, mtDNA Mutagenesis Disrupts Pluripotent Stem Cell Function by Altering Redox Signaling. The goal of the study was to analyze altered gene expression profiles between mutant and wt iPS cells to identify altered biological pathways responsible for the stemness and proliferation defects seem in mtDNA mutator stem cells.

overall_design: The sample set includes 5 independent mutator iPSC lines, homozygous for the POLG D257A mutation,  and 3 wt control lines derived from littermate control embryos.

first: Anu

last: Suomalainen


title: Systematic assessment of commercially available low-input miRNA library preparation kits

status: Public on Sep 27 2019

city: Oslo

first: Fatima

last: Heinicke

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: Oslo University Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: We compared the performance of six commercial kits (QIAseq, SMARTer, CATS, CleanTag, srLp, TailorMix) capable of handling <100ng total RNA input for miRNA detection sensitivity, reliability, titration response and ability to detect differentially expressed miRNAs at different amounts of synthetic miRNAs.   We observed differences in detection sensitivity between the kits, but none were able to detect the full repertoire of expected miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the majority of miRNAs.

sample_organism:
Homo sapiens
synthetic RNA

platform_organism:
Homo sapiens
synthetic RNA

overall_design:
Systematic comparison of miRNA profiles assessed in low-input synthetic miRNA samples and samples from pools of blood derived CD8 T cells of rheumatoid arthritis (RA) patients or healthy controls (HC) by six commercially available library preparation kits.

Altogether five different miRNA mixes were created (denoted mix A to mix E). Mix A and Mix B consisted of the equimolar miRNA pool supplemented with the non-equimolar pool present at eight different concentration ratios between the two mixes spanning a 100 fold range. Mix C was a titration of 0.75 mix A and 0.25 mix B, while mix D was a titration of 0.25 mix A and 0.75 mix B. In the case of mixes A-D, the total miRNA concentration was 30 nM, with individual equimolar miRNAs present at 30 pM and other miRNAs ranging from 3-300 pM. Mix E consisted of the same miRNAs as mix A but at a 10-fold lower concentration.

first: Gregor

last: Gilfillan


title: Expression in the Mut- ko/ki (Mut p.M700K) and controls

status: Public on Sep 22 2019

city: Washington

first: Kimberly

last: Chapman

state: DC

address: 111 Michigan Ave NW

department: genetics

institute: Children's National

summary: Gene expression from 2 livers and 2 hearts from mouse Mut-ko/ki (MUT p.M700K) described in Forny et al JBC 2016 and 3 livers, 2 hearts from littermate controls

overall_design: Whole RNA isolated from flash frozen specimens (liver and heart from Mut-ko/ki using MirVANA (Ambion) and expression determined by Clariom S mouse arrays.

first: Patrick

last: Forny


title: Molecular profiling of physiologically-defined neuronal types

status: Public on Sep 23 2019

city: Saint Louis

first: Donghoon

last: Lee

state: MO

address: 660 S Euclid Ave, PO 8108

institute: Washington University In St. Louis

summary: We report an approach called physiological optical tagging sequencing (PhOTseq), a technique for tagging cells based on their functional properties and then harvesting them for RNA sequencing. We demonstrate that PhOTseq is capable of selecting physiologically rare ( < 0.2%) cell types and enriching them by nearly one hundred-fold.

overall_design: After calcium imaging, physiologically-distinct cell types were photo-tagged. These cells were collected by FACS and subjected to single cell RNA sequencing. We collected cells from five physiologically-distinct cell types. Non-tagged cells were also collected as controls.

first: Timothy

middle: E

last: Holy


title: Regulatory T cell depletion promotes oncogenic Kras driven pancreatic tumorigenesis.

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Regulatory T cells (Treg) are common in the tumor microenvironment in both human pancreatic cancer and in genetically engineered mouse models of the disease. Previous studies in orthotopic syngeneic models of pancreatic cancer -recapitulated in our own data- indicated that Treg depletion results CD8+ T cell-mediated tumor regression. In human patients and in mouse models, regulatory T cells accumulate during the onset of Pancreatic Intraepithelial Neoplasia (PanIN), the earliest steps of carcinogenesis. We thus generated a genetic model to investigate the role of regulatory T cells during the onset of pancreatic carcinogenesis. Unexpectedly,  depletion of Tregs during early stages of carcinogenesis led to accelerated tumor progression.

overall_design: We are using KC;Foxp3DTR mice generated by crossing KC (Ptf1a-Cre;LSL-KrasG12D) with Foxp3DTR (B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J, Jackson Laboratory). We depleted Foxp3-expressing Tregs by Diphtheria Toxin (DT) injection to determine the requirement of Tregs during oncogenic Kras induced Pancreatic Intraepithelial Neoplasia (PanIN) formation and maintenance. To investigate the mechanisms underlying the tumor-promoting effect of Treg depletion in KC; Foxp3DTR mice we performed RNA sequencing (RNAseq) for epithelial cells (DAPI-CD45-EpCAM+) and fibroblasts (DAPI-CD45-EpCAM-PDGFRα+) flow-sorted from KC and KC; Foxp3DTR pancreata.

first: Yaqing

last: Zhang

first: Marina

last: Pasca di Magliano


title: FBP2 inhibits sarcoma progression by restraining mitochondrial biogenesis

status: Public on Sep 20 2019

city: Philadelphia

first: M.

middle: Celeste

last: Simon

state: PA

address: 421 Curie Blvd

department: AFCRI

institute: University of Pennsylvania

summary: We show that expression of the gluconeogenic isozyme fructose-1,6-bisphosphatase 2 (FBP2) is silenced in a broad spectrum of soft tissue sarcoma (STS) subtypes, revealing an apparent common metabolic feature shared by diverse STS. Enforced FBP2 expression inhibits STS cell and tumor growth through two distinct mechanisms. First, cytosolic FBP2 antagonizes elevated glycolysis associated with the “Warburg effect”, thereby inhibiting sarcoma cell proliferation. Second, nuclear-localized FBP2 restrains mitochondrial biogenesis and respiration in a catalytic activity-independent manner by inhibiting the expression of nuclear respiratory factor (NRF1) and mitochondrial transcription factor A (TFAM).  Specifically, nuclear FBP2 colocalizes with the c-Myc transcription factor at the TFAM locus and represses c-Myc-dependent TFAM expression. This unique dual function of FBP2 provides a rationale for its selective suppression in STS, identifying a potential metabolic vulnerability and possible therapeutic target. This study aims to globally compare the transcriptomes from control or FBP2-expressing LPS246 cells. Total RNA was isolated from 5 sets of control cells and 5 sets of FBP2-expressing cells using RNeasy Mini Kit (Qiagen). Low-throughput library prep using Illumina truSeq stranded mRNA kit. The sequencing were performed on Illumina Platform 100SR, with 312 million raw reads/sample.

overall_design: This study set out to globally compare the liver transcriptomes from control or FBP2-expressing LPS246 cells. Total RNA was isolated from 5 sets of control cells and 5 sets of FBP2-expressing cells using RNeasy Mini Kit (Qiagen). Low-throughput library prep using Illumina truSeq stranded mRNA kit. The sequencing were performed on Illumina Platform 100SR, with 312 million raw reads/sample.

first: M

first: Peiwei

last: Huangyang


title: CREB5 promotes resistance to androgen-receptor antagonists and androgen deprivation in prostate cancer

status: Public on Sep 21 2019

city: Boston

first: Justin

last: Hwang

address: 450 Brookline Ave Dana Bldg

department: Medical Oncology

institute: Dana farber Cancer Institute

summary: Inhibition of androgen-receptor (AR)signaling is the foundation of therapeutic regimens for advanced prostate cancers. However, nearly all patientsdevelop resistance and some never respond. To identify genes that mediate resistance to androgen ablation therapy, we performed an open reading frame (ORF) expression screen of17,255 ORFs and found that the transcription factorCREB5robustly conferred resistance to androgen deprivation and AR inhibition by enzalutamide. CREB5 overexpressionincreased enzalutamide-resistance 45-fold, enhanced resistance of tumor xenografts. CREB5 expression was also essential for enzalutamide-resistance patient-derived organoids. In clinical mCRPC, CREB5is frequently amplified and itsoverexpression positively correlated with castration resistance gene signatures including those of MYC and cell cycle. Mechanistically, CREB5 directly interacted at AR binding sites andenhanced site-specific AR bindingin enzalutamide. This dysregulated expression of 393 AR target genes including MYC and CDK1.These observations identifyCREB5asadriver of enzalutamide-resistance in a subset of advancedprostate cancer.

overall_design: To perform ChIpseq  (H3K27Ac, AR, FoxA1 or CREB5 antibody), ATAC seq or RNAseq in LNCaP cells expressing either luciferase or CREB5 after treatment either enzalutamide or DMSO control.

first: Ji-Heui

last: Seo

first: Xintao

last: Qui


title: Re-programing chromatin with a bifunctional LSD1/HDAC inhibitor induces therapeutic differentiation in DIPG [ChIP-seq]

first: Jamie

last: Anastas

overall_design: We performed ChIP-seq using antibodies to H3K27me3, H3K27ac, and H3K4me1 modified histones in SU-DIPGXIII diffuse intrinsic pontine glioma cells after one week of treatment with either DMSO (control) or a dual inhibitor of LSD1 and HDACs 1-3 (Corin).

first: Yang

last: Shi


title: MicroRNA expression profiles do not distinguish between primary and recurrent well-differentiated liposarcoma

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

country: Netherlands

institute: Erasmus University Medical Center

summary: Well-differentiated liposarcoma (WDLPS) recurs in approximately one-third of the patients. The molecular relationship between primary tumor and recurrent tumors is barely studied, but is important to reveal potential drivers of recurrence. Here we investigated the biology of recurrent WDLPS using 27 paired primary and recurrent WDLPS samples. MicroRNA expression profiles were determined using TaqMan® Low Density Array (TLDA)-cards. In the supervised clustering analyses, no clear clustering separating the primary from the recurrent tumors, based on differentially expressed microRNAs was observed. The clustering was also not based on tumor localization, time to recurrence, age or status of the resection margins. Subgroup analysis for tumors localized in the extremity or retroperitoneum also did not yield a clear distinction between primary and recurrent WDLPS. In conclusion, microRNA expression profiles do not distinguish between primary and recurrent WDLPS and no putative common drivers for recurrence could be identified.

overall_design: In order to identify common alterations in miRNA expression levels that may drive well-differentiated liposarcoma (WDLPS) recurrence, the miRNA expression profiles of 27 paired tumor samples were determined. Each sample pair consisting of a primary tumor and matching first recurrent WDLPS from patients that were treated with surgery only.

first: Melissa

last: Vos

first: Ruben

last: Boers

first: Anne

last: Vriends

first: Joachim

first: Patrica

middle: F

last: van Kuijk

first: Winan

last: van Houdt

first: Geert

last: van Leenders

first: Michal

last: Wagrodzki

first: Wilfred

last: van IJcken

first: Joost

last: Gribnau

first: Dirk

last: Grünhagen

first: Cornelis

last: Verhoef

first: Stefan

last: Sleijfer


title: Expression data from stroke patients blood samples

status: Public on Sep 19 2019

city: Barcelona

first: Elena

last: Palà

address: Pg Vall d’Hebron 119-129

country: Spain

institute: Institut de Recerca Hospital Vall d’Hebron

summary: Ischemic stroke can be classified depending on its etiology as cardioembolic (CE), large-vessel atheroesclerotic (LAA), lacunar, other or cryptogenic. Our aim was to identify gene expression changes that could differentiate CE and LAA stroke in order to guide the optimal secondary treatment .

overall_design: Blood from 26 ischemic stroke patients (18 CE and 8 LAA) was collected into EDTA tubes within the first 4.5h after the onset of neurological symptoms. After centrifugation, buffy coat was mixed with RNAlater solution and preserved at -80°C until RNA isolation. In order to obtain a common signature and to avoid interindividual variability, equal amounts of RNA from individual samples were pooled based on their stroke etiology and according to clinical characteristics: 18 CE strokes were divided among 7 different pools and 8 LAA strokes among 4 pools.

first: Teresa

last: García-Berrocoso

first: Joan

last: Montaner

first: Israel

last: Fernández-Cadenas


title: Understanding the stromal composition of fat-associated lymphoid clusters of the omentum using single-cell transcriptomics

status: Public on Sep 18 2019

city: Edinburgh

first: Cecile

last: Benezech

address: 47 Little france Crescent

department: Centre for Cardiovascular Sciences

institute: University of Edinburgh

summary: We profile the transcriptome of over 4000 murine single cells from the stromal non-endothelial fraction of the omentum. We uncover that the omentum is composed of 2 populations of fibroblasts which differentially express Ccl11 and Ccl19 and three populations of mesothelial cells.  One of these mesothelial populations were distinguised by the expression of inflammatory genes and the other one by the expression of anti-viral genes.  This study unveil the complexcity of the stromal niche in the omentum and revealed the adaptation of the mesothelium to FALCs function.

overall_design: Single-cell transcriptomic data are presented from the pooled omentum of 3 unchallenged mice. Cell were sorted as CD45-Ter119-CD41-CD31-Gp38+

first: Peter

last: Smith

first: Jordan

middle: R

last: Portman

first: Beth

last: Henderson

first: Ross

last: Dobie

first: Neil


title: Retrograde inhibition by a specific subset of interpeduncular α5 nicotinic neurons regulates nicotine preference.

status: Public on Sep 11 2019

city: New York

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

summary: Translational profiling of specific populations in the MHb-IPN circuit allow identification of neurons in the relatively uncharacterized circuit. Here we use bac Cre drivers  to direct expression of a Cre-iducible EGFP-tagged ribosomal protein to access translating mRNAs. We describe unique and complementary subsets of Chrna5 cells with differential response to nicotine treatment.

overall_design: Polysome-bound mRNAs from TRAP IPs were compared to whole tissue mRNAs for baseline profiling. To determine nicotine-regulated genes, mRNAs from TRAP IPs from saccharin-treated mice were compared to IPs from nicotine-treated mice. For IPN, BAC Cre driver mice were crossed with Cre-inducible TRAP mice to generate double trangenic bacTRAP mice, while single transgenic bacTRAP mice were used for the MHb. Data was collected from ChAT neurons in the MHb and frm Chrna5, Amigo1 and Epyc neurons in the IPN. We collected at least 3 replicates per condition, with the exception of nicotine-treated IPN cells from Epyc-Cre mice and nicotine-treated MHb ChAT cells, which were collected in duplicate. Males and females were pooled for each sample unless otherwise indicated.

first: Jessica

last: Ables

first: Beatriz

last: Antolin-Fontes

first: Cuidong

last: Wang

first: Ines

last: Ibanes-Tallon

first: Nathaniel

last: Heintz


title: RNA sequencing revealed nasal epithelium-initiated pathways contributing to influenza damage and complications

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: RNA sequencig study for influenza response

overall_design: Whole transcriptome study of In vitro differentiated nasal epithelial cells treated with influenza over timepoints.

first: Anand

last: Kumar Andiappan


title: The global IL-1α gene expression response in p65 enhancer mutant HeLa cells.

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: Conversion of cytokine-driven changes in chromatin topology into gene regulatory circuits during inflammation still remains unclear. Here, we analyzed the expression profiles of HeLa cells carrying microdeletions of p65-binding sites in two enhancers regulating the IL-1α-inducible IL8 and CXCL1-3 genes within the extended chemokine locus on human chromosome 4.

overall_design: Gene expression study in HeLa cells with IL-1α treatment

first: Axel

last: Weber

first: Michael

last: Kracht


title: The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 (ATAC-Seq)

summary: The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the chromatin accessibilty at the genome-wide level by ATAC-seq experiments.

overall_design: ATAC-seq in KB cells  under different treatment conditions


title: Characterization of  IL-1α–responsive enhancers and of IL-1α -mediated changes in chromatin topology.

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

overall_design: Refer to individual Series


title: The RNA-binding protein HuR is a negative regulator in adipogenesis [Ribo-seq_RNA-seq_matched]

status: Public on Sep 09 2019

first: Lei

last: Sun

address: 8 College Road

institute: Duke-NUS

summary: Human antigen R (HuR) protein, a RNA binding protein (RBP), has been reported to  regulate essential steps in RNA metabolism and immune response in a variety of cell types,  but its function in metabolism remains unclear. This study identifies HuR as a major  repressor during adipogenesis. Knockdown and overexpression of HuR in primary adipocyte  culture enhances and inhibits adipogenesis in vitro, respectively. Fat-specific knockout of  HuR significantly enhances adipogenic gene program in all three major adipose tissues  including epidydimal, inguinal white and brown adipose tissue, accompanied with systemic  glucose intolerance and insulin resistance. Conversely, transgenic overexpression of HuR in  adipose tissue prevents the HFD induced obesity by repressing adipogenesis.  Mechanistically, HuR may inhibit adipogenesis by recognizing and modulating the stability of  hundreds of adipocyte transcripts, including the mRNA of Insig1, a negative regulator during  adipogenesis. Taken together, our work establishes HuR as a novel posttranscriptional  regulator of adipogenesis and provides a new insight into how RNA processing contributes  to adipocyte development.

overall_design: 8 samples were included. Duplicate of epididymal white fat from control and huR knockout animals were harvested for matched RNA-seq and RIBO-seq.

first: Yen

last: Lim


title: The RNA-binding protein HuR is a negative regulator in adipogenesis


title: The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 (ChIP-Seq)

summary: The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the genome-wide binding of CTCF by ChIP-seq experiments.

overall_design: ChIP-seq in KB cells with CTCF antibody under different treatment conditions


title: The RNA-binding protein HuR is a negative regulator in adipogenesis [RNA-seq]

overall_design: 16 samples were included. Triplicate of epididymal and inguinal white fat and duplicate of brown fat from control and HuR knockout animals are comparied


title: ZRANB2 and SYF2 mediated splicing programs converging on ECT2 are involved in breast cancer cell resistance to doxorubicin

status: Public on Sep 15 2019

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

summary: We explored the regulation of alternative splicing in a cell model of breast cancer resistance to doxorubicin, and the impact of the depletion of two splicing factors (ZRANB2 and SYF2) in this context.

overall_design: We analyzed by RNA-seq, alternative splicing regulation between doxorubicin-resistant and sensitive cells, and between resistant cells with ot without depletion of either ZRANB2 or SYF2 (2 independent siRNAs for each, all conditions in triplicate).

first: Martin

last: DUTERTRE

first: Iris

last: TANAKA

first: Alina

last: CHAKRABORTY

first: Olivier

last: SAULNIER

first: Clara

last: BENOIT-PILVEN

first: Sophie

last: VACHER

first: Eric

last: LAM

first: Ivan

last: BIECHE

last: DELATTRE

first: Didier

last: AUBOEUF

first: Stéphan

last: VAGNER


title: Early Cold Stress Responses in Post-meiotic Anthers from Tolerant and Sensitive Rice Cultivars

status: Public on Sep 07 2019

city: Rosario

first: Nahuel

middle: Damian

last: Gonzalez-Schain

state: Santa Fe

address: Ocampo y Esmeralda

department: Biofisica del reconocimiento molecular

country: Argentina

institute: Instituto de Biologia Molecular y Celular de Rosario

summary:
Background: Rice grain production is susceptible to a changing environment that imposes both biotic and abiotic stress conditions. Cold episodes are becoming more frequent in the last years and directly affect rice yield in areas with a temperate climate. Rice is particularly susceptible to cold stress during the reproductive phase, especially in anthers during post-meiotic stages which, in turn, affect pollen production. However, a number of rice cultivars with a certain degree of tolerance to cold have been described, which may represent a good breeding resource for improvement of susceptible commercial varieties. Plants experiencing cold stress activate a molecular response in order to reprogram many metabolic pathways to face these hostile conditions.
Results: Here we performed RNA-seq analysis using cold-stressed post-meiotic anther samples from a cold-tolerant, Erythroceros Hokkaido (ERY), and a cold-susceptible commercial cultivar Sant´Andrea (S.AND). Both cultivars displayed an early common molecular response to cold, although the changes in expression levels are much more drastic in the tolerant one. Comparing our datasets, obtained after one-night cold stress, with other similar genome-wide studies showed very few common deregulated genes, leading to the conclusion that molecular responses in cold-stressed anthers strongly depend on conditions and the duration of the cold treatments. Cold-tolerant ERY exhibits specific molecular responses related to ethylene metabolism, which appears to be activated after cold stress. On the other hand, S.AND cold-treated plants showed a general downregulation of photosystem I and II genes, supporting a role of photosynthesis and chloroplasts in cold responses in anthers, which has remained elusive.
Conclusions: Our study revealed that a number of ethylene-related transcription factors, as putative master regulators of cold responses, were upregulated in ERY providing promising candidates to confer tolerance to susceptible cultivars. Our results also suggest that the photosynthesis machinery might be a good target to improve cold tolerance in anthers. In summary, our study provides valuable candidates for further analysis and molecular breeding for cold-tolerant rice cultivars.

overall_design: In order to compare the early molecular responses to cold-stress from tolerant ERYTHROCEROS HOKKAIDO and susceptible SANT´ANDREA cultivars, anthers were isolated from one day cold (8°C) or control (24°C)-treated panicles specifically coinciding with post-meiotic stages. Three biological replicates from each treatment were processed.

last: González-Schain

first: Roig-Villanova

last: Irma

middle: M

last: Kater


title: Single cell RNAseq analysis of Cxcl12-tdTomato+ bone marrow stromal cells after marrow ablation, Day 14

status: Public on Sep 06 2019

city: Houston

first: Noriaki

last: Ono

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

summary: A single cell transcriptional profile of murine CXCL12-abundant reticular stromal cells isolated from ablated bone marrow

overall_design: Lineage-marked Cxcl12-iCreER+ cells were FACS-isolated from ablated femurs of Cxcl12-iCreER; R26R-tdTomato mice at 14 days after bone marrow ablation, with tamoxifen injection at 7 days before ablation. 18,000 cells were loaded onto 10X Genomic Chromium Single Cell Expression Solution version 2 platform. cDNA was sequenced by Illumina HiSeq 4000.


title: Multiscale gene expression profiling of 1 cm root tips of control and submerged Oryza sativa, Medicago truncatula, Solanum lycopersicum and Solanum pennellii seedlings

city: Atlanta

first: Roger

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

summary: Climate change has increased the frequency and intensity of floods that impact global agricultural productivity. To better understand the response mechanisms and evolutionary history of gene family member regulation across angiosperm phyla, we studied the rapid submergence response of rice, the legume Medicago truncatula, and two Solanum species, domesticated tomato (S. lycopersicum cv. M82) and its dryland-adapted wild relative S. pennellii. Response to hypoxic conditions was measured by analyzing transcriptional and post-translational regulation in root tips of each species. This was achieved by the use of Nuclei Tagged in specific Cell Types (INTACT) and Translating Ribosome Affinity Purification to obtain chromatin and sub-populations of gene transcripts. (1) Chromatin accessibility was evaluated by coupling INTACT with ATAC-seq (assay for Transposon-Accessible Chromatin). (2) INTACT was used to capture nuclear RNA (nRNA). (3) Polyadenylated mRNA (polyA RNA) was obtained by standard oligo(dT) selection. (4)  Ribosome-associated polyA mRNA (polyA RNA) was obtained by use of Translating Ribosome Affinity Purification (TRAP).  Ribosome footprinting (Ribo-seq) was accomplished by using TRAP to capture ribosome protected fragments after RNAseI digestion. Samples evaluated include the apical root tip (four species) and shoot region (Solanum species only) under control conditions and after 2 h of submergence

sample_organism:
Medicago truncatula
Solanum lycopersicum
Solanum pennellii
Oryza sativa Japonica Group

overall_design:
5 genotypes (Oryza sativa, Medicago truncatula-hairy root, Solanum lycopersicum, Solanum lycopersicum-hairy root and Solanum pennellii ), 2 conditions (control and 2 hour-submerged tissue grown on petri dishes with 1X MS, 1 % [w/v] Sucrose, pH 5.8). 4 bioreplicates of 4 RNA pools (total mRNA, rRNA degraded nuclear RNA, TRAP-RNA, Riboseq-RNA) and ATAC-seq. Up to two tissues (root tip and shoot apical meristem).

Please note that [1] the Sample titles indicate RNA population tissue and species as following:
INRNA: Nuclear RNA
TOT: Poly A RNA
TRA: Polysomal PolyA RNA
RS: Ribo-seq RNA
OS: Oryza Sativa
MT: Medicago truncatula
SL: Solanum lycopersicum M82
SP: Solanum pennellii
ROOT: 1 cm root tip
SHOOT: Shoot apex

[2] The processed data generated from multiple samples is linked as Series supplementary files and is inidicated in the corresponding sample description field.

first: Mauricio

last: Reynoso

first: Germain

last: Pauluzzi

first: Julia

last: Bailey-Serres

first: Kaisa

last: Kajala

first: Siobhan

last: Brady

first: Donnelly

last: West

first: Kristina

last: Zumstein

first: Neelima

last: Sinha

first: Marko

last: Bajic


title: The RNA-binding protein HuR is a negative regulator in adipogenesis [RIP-seq]

first: Lei

last: Sun

overall_design: RNA immunopercipitation was performed from control and knock epididymal white fat

first: Yen

last: Lim


title: Sestrin prevents skeletal muscle atrophy

status: Public on Sep 05 2019

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

summary: We identify sestrins, a family of stress-inducible metabolic regulators, as protective factors against muscle wasting. Sestrin expression decreases during inactivity and its genetic deficiency exacerbates muscle wasting; conversely, sestrin overexpression suffices to prevent atrophy.

overall_design: RNAseq analysis: total RNA from tibialis anteror TA muscles 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 3-4 samples per condition, using Illumina Hiseq 2500.  RNAseq analysis was done in two sets. Sets are indicated in the sample and file names (Set1 and Set2).

first: Jessica

last: Segales

first: Pura

last: Munoz-Canoves


title: Brain metastasis-related microRNAs in patients with advanced breast cancer

status: Public on Sep 04 2019

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

summary: The combination of serum miRNAs could be a classifier for predicting the development of brain metastasis in breast cancer patients

overall_design: Serum microRNA profiles and clinical characteristics of 79 woman with breast cancer

first: Jun

last: Sato

first: Akihiko

last: Shimomura

first: Junpei

last: Kawauchi

first: Juntaro

last: Matsuzaki

first: Yusuke

last: Yamamoto

first: Hiromi

last: Sakamoto

first: Makoto

last: Ohno

first: Yoshitaka

last: Narita

first: Takahiro

last: Ochiya

first: Kenji

last: Tamura


title: Response of Hepatocytes to CCl4 Injury and Yap/Taz Knockout

status: Public on Sep 01 2019

first: Rory

last: Kirchner

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

summary: Assessment of Hepatocytes in response to Yap/Taz knockout and also CCl4 injury

overall_design: Hepatocytes from male mouse livers (2-3 months old) was FACS sorted from control (5), Yap/Taz Knockout (4), CCl4 injury (5) Yap/Taz knockout with CCl4 injury

first: Dean

last: Yimlamai


title: Single cell RNAseq analysis of Cxcl12-tdTomato+ bone marrow stromal cells after marrow ablation, Day 7

first: Noriaki

last: Ono

summary: A comparative single cell transcriptional analysis of murine CXCL12-abundant reticular stromal cells isolated from ablated and control bone marrow

overall_design: Lineage-marked Cxcl12-iCreER+ cells were FACS-isolated individually from ablated and contralateral control femurs of Cxcl12-iCreER; R26R-tdTomato mice at 7 days after bone marrow ablation, with tamoxifen injection at 7 days before ablation. 6,500~14,000 cells were loaded onto 10X Genomic Chromium Single Cell Expression Solution version 2 or 3 platform. cDNA was sequenced by Illumina HiSeq 4000 or NovaSeq 6000.


title: Global changes in gene expression of larval zebrafish

status: Public on Aug 28 2019

city: BEIJING

first: Bo

last: Chen

state: BEIJING

address: TianTan XiLi No. 1, Dong-cheng District, Beijing

country: China

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences

summary: We employed  DNA microarray to figure out the possible mechanism of BBR on zebrafish NAFLD model

overall_design: AB strain zebrafish (Danio. rerio)  were kept under standard laboratory conditions with a 14-h light/10-h dark cycle at a temperature of 28.5±1°C. Embryos and larvae were maintained in embryo medium to 5 dpf without feeding. Zebrafish larvae were fed with control diet (AP100, 30mg/100 fish/day) or high cholesterol diet (HCD, 180mg AP100 plus 4% cholesterol/100fish/day) or HCD plus berberine (5μM) for 10 days.


title: Total RNA sequencing in human biofluids and extracellular vesicles using SMARTer technology

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

summary: Transcriptome profiling has emerged as a powerful tool to investigate the biomarker potential of human biofluids. However, despite an enormous interest in extracellular nucleic acids, total RNA sequencing methods to quantify RNA content outside cells are rare. Here, we evaluate the performance of the SMARTer Stranded Total RNA-Seq method in human platelet-rich plasma, platelet-poor plasma, urine, conditioned medium, and extracellular vesicles from these biofluids.

overall_design:
Total RNA sequencing in human biofluids (plasma and urine) and extracellular vesicles.

**Submitter declares that the raw data are unavailable because of patient privacy concerns.**

first: Hetty

last: Helsmoortel

first: Jo

last: Vandesompele


title: Histone concentration times the cell cycle and transcription in early development.

status: Public on Aug 30 2019

city: Princeton

first: Amanda

last: Amodeo

state: NJ

address: Carl Ichan Laboratory, Washington Rd

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: This study measures transcriptomic differences due to overexpression (via Slbp RNAi) or knockdown (via abo mutation) of histones in precisely staged Drosophila melanogaster embryos spanning the maternal to zygotic transition.

overall_design: This study was conducted as 3 different RNA-seq experiments; a) Slbp v/s WT single embryo broad timecourse comparison b) abo v/s WT single time point pooled embryo comparison and c) abo v/s WT single embryo timecourse comparison  For Slbp (single embryo) comparison: 5 replicates each of Slbp and WT pre-nuclear cycle (NC) 9 embryos; 4 replicates of Slbp and 6 replicates of WT NC13; 5 replicates of WT NC14 embryos. Slbp NC13 Replicates 1 and 2  and WT NC13 Replicate 1 were also sequenced multiple times i.e. technical replicates. For abo single time-point (40 pooled embryo) comparison: 3 replicates each of abo and WT at NC14. For abo timcourse (single embryo) comparison: 2 replicates of abo unfertilized (NC0) and 3 replicates of WT NC0; 3 replicates each of abo and WT at NC10, NC11, NC12, NC13 and NC14. The abo time course libraries were sequenced over 4 lanes in 2 different in different batches to get the necessary read depth i.e. technical replicates.

first: Sudarshan

last: Chari


title: 4h vs. 16h Microarray in synchronized murine (m) GLUTag cells

status: Public on Aug 29 2019

city: Toronto

first: Patricia

middle: Lee

last: Brubaker

state: ON

address: Rm 3366 MSB 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

summary: Analysis of mGLUTag transcriptome at 4h and 16h after synchronization. This analysis identified secretory pathways as upregulated, matching protein data suggesting GLP-1 secretion is rhythmic due to the rhythmic expression of SNARE proteins and other regulators of secretion.

overall_design: Total RNA obtained from synchronized mGLUTag cells at 4 and 16h, n = 3 for each time point

first: Andrew

last: Biancolin

first: Alexandre

last: Martchenko

first: Emilia

last: Mitova

first: Everan

last: Michalchyshyn

first: Jennifer

last: Chalmers

first: Alessandro

last: Doria

first: Josyf

last: Mychaleckyj

first: Alice

last: Adriaenssens

first: Frank

last: Reimann

first: Fiona

last: Gribble

first: Manuel

last: Gil-Lozano

first: Brian

last: Cox


title: Kallikrein-mediated cytokeratin 10 degradation is required for VZV propagation in skin

city: London

first: Ryan

last: O'Shaughnessy

address: 4 Newark Street

institute: Queen Mary University of London

summary: Varicella Zoster Virus (VZV) is a skin-tropic virus that infects epidermal keratinocytes and causes chickenpox. Although common, VZV infection can be life-threatening particularly in the immunocompromised. Therefore, understanding VZV-keratinocyte interactions is important to find new treatments beyond vaccination and anti-viral drugs. In VZV- infected skin, Kallikrein 6 (KLK6), and the ubiquitin-ligase MDM2 are up-regulated concomitant with Keratin 10 (K10) down-regulation. MDM2 binds to K10 targeting it for degradation via the ubiquitin-proteasome pathway. Preventing K10 degradation reduced VZV propagation in culture and prevented epidermal disruption in skin explants. K10 knockdown induced expression of the nuclear receptor subfamily 4, group A, member 1 (NR4A1) and enhanced viral propagation in culture. NR4A1 knockdown prevented viral propagation in culture, reduced LC3 levels and increased LAMP2 expression. We therefore describe a novel drug-able pathway whereby MDM2 ubiquitinates and degrades K10 increasing NR4A1 expression allowing VZV replication and propagation.

overall_design: 12 samples: 3 uninfected, 3 VZV infected, 3 VZV infected treated with Nutlin-3, 3 uninfected treated with nutlin-3. VZV infected samples were infected with the pOka strain of the VZV virus. Uninfected are the reference in this analysis.

first: Dan

last: Depledge


title: Sex chromsomes affect gene expression of autoantigen specific CD4+ T cells

status: Public on Aug 21 2019

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

summary: To determine the role of sex chromsomes in sex differences of autoimmune disease, we used high throughput RNA sequencing to analyze the transciptomes of autoantigen specific CD4+ T cells from XX and XY- mice using the “four core genotypes” mouse model.

overall_design: Female mice from the "four core genotypes" mouse model (XX and XY-) were gonadectomized at 4-6 weeks old and subsequently immunized with MOG 35-55 peptide emulsified in complete fraunds adjuvant, suppplemented with myobacterium tuberculosis H27Ra for 10 days. Auxillary, brachial, and inguinal draining lymph nodes were collected and processed into single cell suspensions. Cells were stiumulated with  MOG 35-55 and IL-12 for 36 hours. Stimulated cells were sorted for CD4+ T cells using the EasySep Mouse CD4+ T cell isolation kit (STEMCELL), and RNA was isolated for analysis by high throughput RNA sequencing.

first: Lisa

last: Golden

first: Noriko

first: Rhonda

last: Voskuhl


title: RNA-seq of Aspergillus fumigatus infected to HL-60 derived macrophage-like cells for 0,1, and 2 hours.

status: Public on Aug 15 2019

city: Sungbuk-gu

first: HYEWON

last: SEO

state: Seoul

address: Anam-dong

country: South Korea

institute: Korea university

summary:
Purpose : The goals of this study are to compare transcriptome profiling (RNA-seq) of Aspergillus fumigatus infected to macrophage-like cells for 0, 1 and 2 hours.
Method : HL-60 cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum (FBS) and 1% Gibco™ Antibiotic-Antimycotic at 37°C with 5% CO2. To induce the differentiation of HL-60 cells into macrophage-like cells, HL-60 cells were stimulated with 50 nM 12-o-tetradecanoylphorbol-13-acetate (PMA) for 2 days. A total of 10^3 A.fumigatus conidia were transferred to 5 × 10^4 differentiated HL-60 cells in RPMI 1640 medium supplemented with 5% FBS. After incubating for 0, 1, and 2 hrs, the sample tubes were vigorously agitated with TRIzol® (Invitrogen) containing glass beads to extract total RNA of alive A.fumigatus. ). Libraries were prepared from 2 µg of total RNA using a SMARTer Stranded RNA-Seq Kit (Clontech Laboratories, Inc., USA). Isolation of mRNA was performed using a Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria). The isolated mRNAs were used for cDNA synthesis and shearing, following the manufacturer’s instructions. Indexing was performed using the Illumina indexes 1-12. An enrichment step was carried out using PCR. Subsequently, libraries were checked using the Agilent 2100 bioanalyzer (DNA High Sensitivity Kit) to evaluate the mean fragment size. Quantification was performed using the library quantification kit with a StepOne Real-Time PCR System (Life Technologies, Inc., USA). High-throughput sequencing was performed as paired-end 100 bp sequencing using a HiSeq 2500 (Illumina, Inc., USA). mRNA-seq reads were mapped using the TopHat software (Cole Trapnell et al., 2009) tool to obtain an alignment file.

overall_design: A.fumigatus conidia were infected into macrophage-like cells for 0,1 and 2hours and total RNA of A.fumigatus was extracted respectively. Their transcriptome expression patterns were compared by RNA-seq.

first: Cheol-Won

last: Yun

first: Hyewon

last: Seo

first: Suzie

last: Kang

first: Yong-Sung

last: Park


title: Comparative gene expression in NCI-H716 cells grown in different glucose concentrations

status: Public on Aug 27 2019

city: Charlottesville

first: Joe

state: VA

institute: University of Virginia

summary: We performed RNA-Seq whole transcriptome analysis of H716 cells grown in two glucose concentrations.

overall_design: 1 replicate each of H716 cells grown in  5.5 mM (low) glucose and 25 mM (high) glucose.

first: Josyf

first: Alessandro

last: Doria


title: Comprehensive Annotations of Human Herpesvirus 6A and 6B Genomes Reveals Novel and Conserved Genomic Features

status: Public on Aug 13 2019

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Human herpesvirus 6 (HHV-6) A and B are highly ubiquitous betaherpesviruses, infecting the majority of the human population. Like other herpesviruses, our understanding of their protein coding potential is far from complete. Here we use ribosome profiling and RNA-seq to experimentally define the HHV-6 translation products and to follow their temporal expression. We identified hundreds of new open reading frames (ORF)s, including many upstream ORFs (uORF)s and internal ORFs (iORF)s, generating a complete atlas of HHV-6 translation products.  Integrating data from human cytomegalovirus we uncover numerous uORFs and iORFs that are conserved between beta herpesviruses and we show uORFs are specifically enriched in late viral genes. We also identified three highly abundant viral long non coding RNAs (lncRNA)s and we show one of these lncRNAs generate a non-polyadenylated stable intron that is conserved between all sequenced beta herpesviruses. Overall, this work uncovers the full complexity of the HHV-6 family genomes and highlights novel features that are conserved between beta herpesviruses, providing a resource for future functional studies.

sample_organism:
Homo sapiens
Human herpesvirus 6 (strain GS)
Human herpesvirus 6 strain Z29

overall_design: Ribosme profiling and RNA-seq along HHV-6A and HHV-6B infection

first: Yaara

last: Finkel

first: Dominik

last: Schmiedle

first: Julie

last: Tai-Schmiedle

first: Aharon

last: Nachshon

first: Michal

last: Schwartz


title: Difference of GATA4 and beta-catenin pulldown chromatin immunoprecipitated DNA in HePG2i cells line with and without DOX induced GATA4 expression

city: guangzhou

first: Feng

last: Lu

address: 601 huangpu avenue west

institute: Jinan university

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of HePG2i cell line with and without DOX induced GATA4 expression by obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA.

overall_design: Examination the difference of GATA4 and beta-catenin pulldown chromatin immunoprecipitated DNA in HePG2i cell line with and without DOX induced.

first: Liang

last: Cheng


title: Next Generation Sequencing Facilitates Quantitative Analysis of HePG2i cell line with and without DOX induced GATA4 expression Transcriptomes

status: Public on Aug 09 2019

summary: HePG2i cell line mRNA profiles of DOX induced GATA4 expression and non-DOX induced were generated by deep sequencing, in triplicate, using Illumina HiSeq 10000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

overall_design: HePG2i cell line mRNA profiles of DOX induced GATA4 expression and non-DOX induced were generated by deep sequencing, in triplicate, using Illumina HiSeq 1000.


title: Generation of Blastocyst-like Structures from Extended Pluripotent Stem Cells

status: Public on Aug 03 2019

city: Shenzhen

first: gene

last: E

address: Julong Street

institute: egene

summary: A single mouse blastomere from until 8-cell embryo can generate an entire blastocyst. Whether blastomere-like extended pluripotent stem cells (EPS cells) retain a similar generative capacity remains unknown. Here, we established a 3D differentiation system that enabled the generation of blastocyst-like structures from EPS cells (EPS-blastoids) through lineage segregation and self-organization. EPS-blastoids resembled blastocysts in morphology and cell lineage allocation. EPS-blastoids formation recapitulated key morphogenetic events during preimplantation and early postimplantation development in vitro. Upon transfer, some EPS-blastoids underwent implantation, induced decidualization, and generated live, albeit disorganized, tissues in utero. Single cell and bulk RNA-sequencing analysis revealed that EPS-blastoids contained all three blastocyst cell lineages and shared transcriptional similarity with natural blastocysts. We also provide proof-of-concept that EPS-blastoids can be generated from somatic cells via cellular reprograming. EPS-blastoids provide a unique platform for studying early embryogenesis, and pave the way to generate viable synthetic embryos using cultured cells.

overall_design: To exaimine the similarity and difference between EPS-blasotids and nature blastocysts (control)

first: Ronghui

last: Li

first: Yang

last: Yu

first: Juan

last: Carlos

first: Izpisua

last: Belmonte


title: Robust hepatitis E virus infection and transcriptional response in human hepatocytes

status: Public on Aug 10 2019

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

summary: In this study, we established a protocol based on the HEV genotype 3 p6 (Kernow C-1) and the human hepatoma cell lines HepG2 and HepG2/C3A with different media conditions to produce HEV cell culture-derived particles (HEVcc) with viral titers between 10e5 to 10e6 FFU/mL. Viral titers could be further enhanced by an HEV variant harboring a mutation in the RNA-dependent RNA polymerase. These HEVcc particles were infectious in primary human hepatocytes. RNA sequencing studies of HEV infected primary human hepatocytes demonstrated a temporally structured transcriptional defense response. In conclusion, this robust cell culture model of HEV infection provides a powerful tool for studying viral-host interactions that should facilitate the discovery of antiviral drugs and vaccines for this important zoonotic pathogen.

overall_design: Primary human hepatocytes (PHH) were inoculated with cell culture-derived HEV particles and changes in transcriptional profiles were assessed using RNAseq.

first: Martina

last: Friesland

first: Eike

last: Steinmann


title: RNA-Seq of embryonic, adult lacrimal gland and lacrimal gland stem cells

status: Public on Aug 06 2019

city: Guangzhou

first: Yan

last: Zhang

state: Guangdong

address: No.132, East Outer Ring Road，Guangzhou Higher Education Mega Center

department: School of Life Sciences

institute: Sun Yat-sen University

summary: The transcriptional expression analysis of 17.5, 19.5 days embryonic lacrimal gland (LG), adult lacrimal gland, lacrimal gland stem cells (LGSCs) P2 cultured for 5, 7, 10, 14 days and LGSCs P6, P10, P20 cultured for 7 days, respectively.

overall_design: mRNA of E17.5 LG, E19.5 LG, adult LG, LGSCs P2 cultured for 5, 7, 10, 14 days and LGSCs P6, P10, P20 cultured for 7 days from C57BL/6 mice were sequenced to generate the gene expression in triplicate.

first: Sa

last: Xiao


title: PIWI-piRNA pathway mediated transposon repression in Hydra somatic stem cells

status: Public on Aug 07 2019

city: Davis

first: Celina

last: Juliano

address: 149 Briggs Hall

department: MCB

institute: University of California Davis

summary: Transposable elements (TEs) can damage genomes, thus organisms employ a variety of mechanisms to repress TE expression. The PIWI-piRNA pathway is a small RNA pathway that represses TE expression in the germline of animals. Here we explore the function of the pathway in the somatic stem cells of Hydra, a long-lived freshwater cnidarian. Hydra have three stem cell populations, all of which express PIWI proteins; endodermal and ectodermal epithelial stem cells are somatic, whereas the interstitial stem cells have germline competence. To study somatic function of the pathway we isolated piRNAs from Hydra that lack the interstitial lineage and found that these somatic piRNAs map predominantly to TE transcripts and display the conserved sequence signatures typical of germline piRNAs. Three lines of evidence suggest that the PIWI-piRNA pathway represses TEs in Hydra epithelial stem cells. First, epithelial knockdown of the Hydra piwi gene hywi resulted in upregulation of TE expression. Second, degradome sequencing revealed evidence of PIWI-mediated cleavage of TE RNAs in epithelial cells using the ping-pong mechanism. Finally, we demonstrated a direct association between Hywi protein and TE transcripts in epithelial cells using RNA immunoprecipitation. Altogether, our data reveal that the PIWI-piRNA pathway represses TE expression in the somatic cell lineages of Hydra, which we propose contributes to the extreme longevity of the organism. Furthermore, our results, in combination with others, suggest that somatic TE repression is an ancestral function of the PIWI-piRNA pathway.

overall_design: Differential gene expression analysis (mRNA-seq) comparing hywi knockdown and wildtype Hydra. Analysis of tissue/cell lineage specific piRNA expression. Degradome sequencing for homeostatic Hydra and epithelialized Hydra.

first: Bryan

last: Teefy

first: Stefan

last: Siebert


title: Genome-wide DNA demethylation of HML58-3 (a derivative cell line of HCT116) after treatment of DAC, OR-2003, and OR-2100

status: Public on Aug 01 2019

city: Tokyo

first: Naoko

last: Hattori

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

institute: National Cancer Center

summary: A derivative cell line of HCT116, HML58-3, was established to detect DNA demethylating agents [Okochi-Takada E, Epigenetics. 2018;13:147-55.]. HML58-3 cells were treated with DNA demethylating agents (DAC, OR-2003, and OR-2100). Genome-wide DNA methylation was analyzed using the Infinium Human MethylationEPIC BeadChip.

overall_design: Bisulfite converted DNA from the 4 samples were hybridized to the Infinium Human MethylationEPIC BeadChip.

last: Iida

first: Toshikazu

last: Ushijima


title: RNA seq on SP specific CD8+ T cells, Ly49+ and Ly49-CD8+ T cells from MOG and MOG + SP immunized mice and DNA sequencing for multiple rounds of the pMHC-yeast display selection for TCR6, TCR7 and FluTCR

status: Public on Aug 08 2019

city: Stanford

first: Ricardo

last: Fernandes

address: 279 Campus Drive

department: Molecular and Cellular Physiology

institute: Stanford University

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

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: The involvement of motor neuron specific miR-218 in human ALS

first: Eran

last: Hornstein

address: 234 Herzl St.

institute: Weizmann Institute of Science

summary: Motor-neuron specific microRNA-218 (miR-218) was recently put in the spotlight because of its striking roles in mouse development. However, miR-218 relevance to human motor neuron disease was not yet explored. Here, we demonstrate by neuropathology that miR-218 is abundant in healthy human motor neurons. However, in amyotrophic lateral sclerosis (ALS) motor neurons miR-218 is downregulated and its mRNA targets are reciprocally upregulated (de-repressed). We further identify the potassium channel Kv10.1 as a new miR-218 direct target that controls neuronal activity. In addition, we screened thousands of ALS genomes and identified six rare variants in the human miR-218-2 sequence. Intriguingly, miR-218 gene variants fail to regulate neuron activity, suggesting the importance of this small endogenous RNA for neuronal robustness. The underlying mechanisms involve inhibition of miR-218 biogenesis and reduced processing by DICER. Therefore, miR-218 activity uncovers a previously unappreciated facet of motor neuron specificity that may be particularly susceptible to failure in human ALS, contributes to a view of ALS as a disease with a prominent RNA component and suggests that miR-218 is a potential therapeutic target for motor neuron disease.

overall_design: mRNA profiles were generated from primary motor neuorn transduced with lentiviruses encoding miR-218 overexpression (OE), miR-218 knockdown (KD), or control lentiviruses (empty) . Experiments were performed in duplicates

first: Irit

last: Reichenstein


title: Mesenchymal proteases and tissue fluidity remodel the extracellular matrix during airway epithelial branching in the embryonic avian lung

status: Public on Aug 12 2019

first: Celeste

last: Nelson

address: 303 Hoyt Laboratory

department: Chemical & Biological Engineering

summary: Reciprocal signaling between an epithelium and its surrounding mesenchyme is common during morphogenesis. These epithelial-mesenchymal interactions are particularly evident in tissues that undergo branching morphogenesis, such as the airway epithelium of the lung. Here, we found that reciprocal interactions between the epithelium and mesenchyme drive remodeling of the extracellular matrix (ECM) during morphogenesis of the embryonic chicken lung. RNA-Seq analysis revealed changes in the expression of genes associated with integrin signaling and ECM remodeling. Consistently, we found that prior to branching, the basement membrane is a spatially uniform sheath that wraps the airway epithelium. After branch initiation, however, the basement membrane is significantly depleted from the tip of extending branches. Culturing embryonic lung explants revealed that this basement membrane thinning is mediated by matrix metalloproteinase-2 (MMP2), which is expressed in the mesenchyme. Inhibiting MMP activity suppresses branch extension but has no effect on branch initiation. As branches extend, we found that tenascin-C (TNC) accumulates in the mesenchyme several cell diameters away from the branch tip. Despite its pattern of accumulation, this mesenchymal ECM protein is expressed exclusively by airway epithelial cells, which activate focal adhesion kinase (FAK) to induce TNC expression. We found that branch extension coincides with the deformation of adjacent mesenchymal cells into elongated geometries, which correlates with an increase in the fluidity of the mesenchyme at branch tips. This local increase in mesenchymal movement transports TNC from the epithelial surface into the mesenchyme. These data reveal novel epithelial-mesenchymal interactions that direct ECM remodeling during airway branching morphogenesis.

overall_design: Three biological repilcates from two different stages of chicken lung development (E5 and E6, a total of six samples) were used in this analysis. Fold changes in transcript levels between E5 and E6 lungs were generated referencing transcript counts in E5 lungs.

first: James

middle: W

last: Spurlin


title: The effect of MSR1 knockout in macrophages in a co-culture system with BMSCs

status: Public on Jul 24 2019

city: Nanjing

first: Shujie

last: Zhao

address: longmian street

institute: Department of Orthopedic, The First Affiliated Hospital of Nanjing Medical University

summary: To investigate the altered gene expression levels in MSR1 knockout and wild type macrophages in co-culture with BMSCs. Each group had a biological repeat (n=3). Results provide insight into the role of MSR1 in macrophages in a co-culture system.

overall_design: Three MSR1 KO macrophages versus three MSR1 WT macrophages

first: Guoyong

last: Yin


title: RNA-Seq of Chromochloris zofingiensis in response to nitrogen deprivation

status: Public on Jul 31 2019

city: Beijing

first: Jin

last: Liu

address: No. 5 Yiheyuan Rd

department: Department of Energy and Resources Engineering

institute: Peking University

summary: Chromochloris zofingiensis, featured by the capability of simultaneously synthesizing triacylglycerol (TAG) and astaxanthin, is emerging as a leading candidate alga for production uses. In order to better understand the oleaginous mechanism of this alga, we conducted a multi-omics analysis by systematically integrating the time-resolved transcriptomes, lipidomes, and metabolomes in response to nitrogen deprivation. The data analysis unraveled the distinct mechanism of TAG accumulation, which involved the coordinated stimulation of multiple biological processes including supply of energy and reductants, carbon reallocation from protein and starch, ‘pushing’ and ‘pulling’ carbon to TAG synthesis. Unlike in the model alga Chlamydomonas, the de novo fatty acid synthesis in C. zofingiensis was promoted, together with the enhanced turnover of both glycolipids and phospholipids, supporting the drastic need of acyls for TAG assembly. Moreover, genome-wide analysis identified many key functional enzymes and transcription factors with engineering potential for TAG modulation. Two genes encoding glycerol-3-phosphate acyltransferase (GPAT), the first committed enzyme for TAG assembly, were found in the genome of C. zofingiensis; in vivo functional characterization revealed that the extrachloroplastic GPAT instead of the chloroplastic one plays a central role in TAG synthesis. These findings illuminate distinct mechanism of oleaginousness of C. zofingiensis and pave a way toward rational manipulation of this alga as an emerging model for trait improvements.

overall_design: Whole-cell mRNA profiles of Chromochloris zofingiensis at 5 time points (0, 3, 6, 12, and 24 h) of nitrogen deprivation (ND), in triplicate

first: Zheng

last: Sun

first: Xuemei

last: Mao

first: Henri

last: Gerken

first: Xiaofei

last: Wang

first: Wenqiang

last: Yang


title: CircMYBL2 Regulates FLT3-ITD FLT3AML Translation in AML

status: Public on Jul 09 2019

first: Wen-Tao

address: No. 135, Xingang Xi Road

institute: sun yat sen university

summary: CircMYBL2 is more highly expressed in AML patients with FLT3-ITD mutations than in those without the FLT3-ITD mutation. We found that circMYBL2 knockdown specifically inhibits proliferation and promotes the differentiation of FLT3-ITD AML cells in vitro and in vivo. We used the ribosome profiling and RNA-seq libraries sequenced with Illumina HiSeq 2500 to identify the mRNA that circMYBL2 targeted. Interestingly, we found that circMYBL2 significantly influences the protein level of mutant FLT3 kinase, which contributes to the activation of FLT3-ITD-dependent signaling pathways. Mechanistically, circMYBL2 enhanced the translational efficiency of FLT3 kinase by increasing the binding of PTBP1 to FLT3 mRNA. Moreover, circMYBL2 knockdown impaired the cytoactivity of inhibitor-resistant FLT3-ITD-positive cells, with a significant decrease in FLT3 kinase expression, followed by the inactivation of its downstream pathways. In summary, we are the first to reveal a circRNA that specifically influences FLT3-ITD AML and regulates FLT3 kinase levels through translational regulation, suggesting that circMYBL2 may be a potential therapeutic target for FLT3-ITD AML.

overall_design: Sh-NC and sh-circMYBL2 MOLM-13 cells used

first: Yue-Qin

last: Chen

first: Yu-Meng


title: Effects of sunlight on anthocyanin accumulation and associated co-expression gene networks in developing grape berries

status: Public on Jul 13 2019

first: Luming

last: Zou

state: PR

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

institute: University of Chinese Academy of Sciences

summary: Using RNA sequencing, we produced a spatiotemporal transcriptome based on 65 samples. Then, we constructed a weighted gene co-expression network of these three Vitis species and defined 17 modules which were correlated to anthocyanins concentrations, developmental stages and species.

sample_organism:
Vitis labrusca
Vitis cinerea
Vitis acerifolia

overall_design: V. Acerifolia and V. Cinera were sunlight-independent anthocyanins accumulation grapes while V. Labrusca were sunlight-dependent grape. We constructed a co-expression network to explore sunlight dependent and sunlight-independent anthocyanins accumulation in grape fruits.

first: Gan-Yuan

last: Zhong


title: Siah2 control on tumor environment

status: Public on Jul 18 2019

city: San Diego

first: Brian

middle: Patrick

last: James

state: CA

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Understanding mechanisms underlying anti-tumor immunity is pivotal for improving immune-based cancer therapies. Here we demonstrate that growth of inoculated BRAF mutant melanoma cells was inhibited in Siah2-/- mice, up to a complete loss. Melanoma grown in Siah2-/- mice exhibited increased proinflammatory immune components, signified by enhanced intra-tumoral activated T cells, along with decreased expression of Ccl17 and Ccl22, and decreased Foxp3 expression. A marked reduction in Treg proliferation was associated with inhibition of Treg cell cycle progression. Correspondingly, G1 cell cycle arrest in Siah2-/- Tregs coincided with elevated expression of the cyclin dependent kinase inhibitor p27, a Siah2 substrate. Growth of PD1-unresponsive melanoma was effectively inhibited up to complete tumor rejection in Siah2-/- mice subjected to PD1 blockade, highlighting synergy between PD1 inhibition and Siah2 loss. Siah2 regulation of Treg recruitment and cell cycle progression effectively controls melanoma development and confers synthetic lethality when combined with anti-PD1 therapy.

overall_design: 5  melanoma tumors grown in WT mice and 5 melanoma tumors grown in siah2 knock out mice were analyzed

first: Marzia

last: Scortegagna

first: Tongwu

last: Zhang

last: Brian

first: Ze’ev

last: Ronai


title: Siah2 control of T-regulatory cells limits anti-tumor immunity

status: Public on Jul 17 2019

city: Rockville

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

summary:
The NanoString analysis of 784 genes expressed by 24 immune cell types in the melanoma cell at 11 days after injection were performed. The Nanostring analysis uncovered marked difference in key immune regulatory networks associated with
T, DC, NC and macrophage function

overall_design: Yumm1.5 tumor cells were injected into WT or Rnf5-/- mice. Tumor were collected at day 10 and RNA were isolated from the tumor. Then Nanostring nCounter assay for immune genes were performed

first: Ze'ev


title: Large particle fluorescence-activated cell sorting enables high quality single cell RNA-sequencing and functional analysis of adult cardiomyocytes

status: Public on Jul 02 2019

city: Baltimore

first: Suraj

last: Kannan

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

summary: The use of single cell RNA sequencing (scRNA-seq) remains limited in cardiac pathology owing to technical difficulties associated with the isolation of single adult cardiomyocytes (CMs). Here, we investigated the capability of large-particle fluorescence-activated cell sorting (LP-FACS) for isolation of viable single adult CMs. We found that LP-FACS readily outperforms conventional FACS for isolation of structurally competent CMs, including large CMs. Additionally, LP-FACS enables isolation of fluorescent CMs from mosaic models. Importantly, the sorted CMs allow generation of high-quality scRNA-seq libraries. Unlike CMs isolated via previously utilized fluidic or manual methods, LP-FAC-isolated CMs generate libraries exhibiting normal levels of mitochondrial transcripts. Moreover, LP-FACS isolated CMs remain functionally competent and can be studied for contractile properties.

overall_design: Here, we include raw and processed data from two separate experiments performed to assess LP-FACS isolation of cardiomyocytes. For the multichamber study, we isolated single adult (~3 months old) CMs using LP-FACS from various chambers of the heart. For the live/fixed study, we isolated ventricular CMs both pre- and post-ethanol fixation via LP-FACS.

first: Matthew

last: Miyamoto

last: Lin

first: Renjun

last: Zhu

first: Sean

last: Murphy

first: David

last: Kass

first: Peter

last: Andersen

first: Chulan

last: Kwon


title: Dual RNA-seq analysis of Mycobacterium tuberculosis-infected lung macrophages reveals cell-lineage specific host-pathogen dynamics

city: Ithaca

first: Davide

last: Pisu

state: NY

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

summary:
Background: Dissecting the in-vivo host-pathogen interplay is crucial in understanding the molecular mechanisms governing control or progression of the infection. While Dual RNA-seq offers significant advantages over traditional approaches in the analysis of intracellular infections, to date technical challenges have restricted the application of this technology predominantly to tissue culture infection models. We addressed this problem by developing new protocols which allowed us to perform, for the first time, Dual RNA-seq on Mycobacterium tuberculosis-infected and ontogenetically distinct macrophages isolated directly from murine lungs.

Results: Through analysis of the Mtb transcripts specifically induced during infection of alveolar and interstitial macrophages, we first identified an in-vivo signature, a set of 180 genes uniquely upregulated by Mtb in mouse lung macrophages.  Furthermore, comparative analysis of transcripts from both Mtb and the two macrophage lineages uncovers that alveolar macrophages exhibit an M2-like polarization profile and promote bacterial growth through increased access to iron and fatty acids, while the interstitial macrophages exhibit a pro-inflammatory profile and restrict bacterial growth through iron sequestration and higher levels of nitric oxide.

Conclusions: Our study reports a new bacterial transcripts enrichment protocol which enabled us to perform dual-RNA seq at the infected cell level, providing a comprehensive look at the divergent transcriptional signatures that characterizes survival of Mtb in the two major myeloid cells. The data re-emphasizes the significance of nutritional immunity for in vivo control of infection via an unbiased interrogation of both host and pathogen transcriptomes.  Our approach provides a new tool to probe bacterial physiology at the host cell level in an in-vivo environment and therefore has a broad impact in understanding infections of intracellular pathogens.

sample_organism:
Mycobacterium tuberculosis
Mus musculus

platform_organism:
Mycobacterium tuberculosis
Mus musculus

overall_design: Examination of the transcriptional profile of both Mtb and the host cell in 2 different myeloid lineages isolated directly from the mouse lungs.

first: Lu

last: Huang

first: Jennifer

last: Grenier

middle: G

last: Russell


title: Gene expression profile of esophageal squamous cell carcinoma

status: Public on Jun 26 2019

city: Rio de Janeiro

first: Pedro

last: Nicolau Neto

state: RJ

address: 37 Andre Cavalcanti Street

department: PCM

country: Brazil

institute: INCA

summary: The goal was to identify the differently expressed genes between esophageal tumor and nonmalignant surrounding mucosa

overall_design: 15 paired ESCC samples and matched nonmalignant mucosa were analyzed

middle: P

last: Nicolau-Neto

first: Paulo

last: Santos


title: Gene expression profiling of the cancer stem cells of cervical cancer vs the bulk population

status: Public on Jun 19 2019

city: Chandigarh

first: Shifa

last: Javed

state: Outside US

address: Sector 12, Chandigarh, India

department: Cytology and GynecPathology

country: India

institute: Postgraduate Institute of Medical Education and Research

summary: To identify the differentially expressed genes in the cancer stem cells as compared to bulk tumor population

overall_design: Organism : Homo sapiens, Agilent's Human Gene Expression  8x60k Array (AMADID: 039494)

first: Radhika

last: Srinivasan

first: Rashmi

last: Bagga

first: Shalmoli

last: Bhattacharyya

first: Bipin

last: Chand


title: A TCF-1-centered transcriptional network drives an early binary effector versus exhausted CD8+ T cell fate decision

status: Public on Jul 01 2019

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

country: USA

institute: University of Pennsylvania

summary: We processed single cell RNA-Sequencing using 10X Genomics platform to study the population dynamics of LCMV antigen specific CD8+ T cells during early phase of acute and chronic infection.

overall_design:
P14 cells of Naïve, D8 p.i. ofLCMV- Armstrong, LCMV-Clone13 and LCMV-Clone13+GK1.5(△CD4)

Cell barcodes ending in -1 are Naive,-2 are D8Arm,-3 are D8Cl13 and -4 are D8Cl13_aCD4 in the barcodes file supplied.

first: Zeyu

last: Chen

last: Wherry


title: Responses to hydric stress in the seed-borne necrotrophic fungus Alternaria brassicicola

status: Public on Jun 29 2019

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

summary: In this study, we gained further insights into the mechanisms involved in the seed infection  process by analysing the transcriptomic responses of germinated spores of A.brassicicola exposed to water stress.

overall_design: Sorbitol and desiccation treatments were compared to non-treated cultures at two time points 0.5 h, 2 h and 1 h, 4 h, respectively. Three biological replicates were analyzed per comparison using the dye-switch method.

first: G

last: N’Guyen

first: T

last: Guillemette

first: C

last: Campion

first: S


title: Early response to loss of Argonaute proteins in embryonic stem cells activates the Tgf-ß/Smad Transcriptional Network [smallRNA-Seq]

status: Public on Jun 01 2019

city: LOS ANGELES

first: Jesse

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

summary: Argonaute (Ago) proteins, which act in post-transcriptional gene regulation directed by small RNAs, are vital for normal stem cell biology. Here we report the genomic characterization of stable Ago-deficient mouse embryonic stem cells (mESC) and determine the direct, primary and system level response to loss of Ago-mediated regulation. We find mESCs lacking all four Ago proteins are viable, do not repress microRNA (miRNA)-targeted cellular RNAs, and show distinctive gene network signatures. Profiling of RNA expression and epigenetic activity in an Ago mutant genetic series indicates that early responses to Ago loss are driven by transcriptional regulatory networks, in particular the Tgf-ß/Smad transcriptional network. This finding is confirmed using a time course analysis of Ago depletion and Ago rescue experiments. Detailed analysis places Tgf-ß/Smad activation upstream of cell cycle regulator activation, such as Cdkn1a, and repression of the c-Myc transcriptional network. The Tgf-ß/Smad pathway is directly controlled by multiple low-affinity miRNA interactions with Tgf-ß/Activin receptor mRNAs and receptor-mediated activation is required for Tgf-ß/Smad target induction with Ago loss. Our characterization reveals the interplay of post-transcriptional regulatory pathways with transcriptional networks in maintaining cell state and likely coordinating cell state transitions.

overall_design: Small RNA seq from Ago mutant series


title: Early response to loss of Argonaute proteins in embryonic stem cells activates the Tgf-ß/Smad Transcriptional Network  [mRNA-Seq: DicerDgcr8_KOs]

overall_design: mRNA seq from stable genetic Dicer and Dgcr8 mutant mouse embryonic stem cells.


title: Molecular analysis of population and De Novo transcriptome sequencing of Thai medaka, Oryzias minutillus (Teleostei: Adrianichthyidae)

status: Public on Jul 08 2019

city: Bangkok

first: Arin

last: Ngamniyom

address: 114 Sukumvit 23

department: Major in Environment, Faculty of Environmental Culture and Eco-tourism

country: Thailand

institute: Srinakharinwirot University

summary: We report the transcriptome sequencing of Thai medaka

overall_design: by deep sequencing, in triplicate, using Illumina HiSeq 2500


title: Annexin A3 is necessary for artery-vein alignment in the mouse retinas (RNA-seq analysis of isolated retinal endothelial cells from Anxa3;Tie2-cre mutant mice)

city: New Orleans

first: Stryder

last: Meadows

state: LA

address: 6400 Freret

department: Cell and Molecular Biology

institute: Tulane University

summary: Annexin A3 (Anxa3) is a member of the calcium-regulated, cell membrane binding family of Annexin proteins. We previously confirmed that Anxa3 is expressed in the endothelial lineage in vertebrates and that loss of Anxa3 in Xenopus laevis leads to embryonic blood vessel defects. However, the biological function of Anxa3 in mammals is completely unknown. In order to investigate Anxa3 vascular function in mammals, we generated an endothelial cell specific Anxa3 conditional knockout mouse model (Anxa3f/f;Tie2-Cre).

overall_design: To uncover genes affected by the loss of Anxa3, and which could potentially be associated with AV crossovers, we performed RNA-sequencing experiments on isolated retinal endothelial cells (iREC) from Anxa3f/f and Anxa3f/f;Tie2-Cre P7 pups.Six samples were analyzed, 3 samples were Anxa3fl/fl (WT/control) and 3 samples were Anxa3fl/fl;Tie2-cre (MUT/experimental)

first: Katie

last: Huang

first: Angela

last: Crist

first: Nehal

last: Patel

first: Avery

last: Blanks

first: Kelsey

last: Carter

first: Ondine

last: Cleaver


title: Early response to loss of Argonaute proteins in embryonic stem cells activates the Tgf-ß/Smad Transcriptional Network [mRNA-Seq: AgoTimeRescueGenetic]

overall_design: mRNA seq from stable genetic Ago mutant mouse embryonic stem cells and conditional (TT-FHAgo2) Ago2 expressing mouse embryonic stem cells .


title: Genome-wide profilings of chromatin accessibility and transcriptomes during different stages of G0 in fly wings

status: Public on May 31 2019

city: Salt Lake City

first: Bruce

last: Edgar

state: UT

address: 2000 Cir of Hope Dr.

department: Department of Oncological Sciences

institute: University of Utah

summary: Cell cycle exit is usually enforced during terminal differentiation in various organisms and tissues. To understand how this is achieved molecularly, we exained the genome-wide profiles of chromatin accessibility and transcriptomes at normal development stages of fly wings as well as situations where we uncoupled cell cylce exit from terminal differentiation with genetic manipulations. We found that developmentally programmed, temporal changes in chromatin accessibility at a small subset of critical cell cycle genes act to enforce cell cycle exit during terminal differentiation.

overall_design: FAIRE-Seq and RNA-Seq on wildtype ( L3, 6h, 18h, 24h, 36h and 44h APF) and genetically manipulated (flp control, E2F1+DP, CycD+Cdk4+E2F1+DP at 24h and 44h APF) fly wings

first: Yiqin

last: Ma

first: Laura

last: Buttitta