title: Differential microRNA expression of R213G extracellular superoxide dismutase mice in the setting of inflammation resolution and attenuated acute lung injury

status: Public on May 29 2020

city: Aurora

first: Denis

last: Ohlstrom

state: CO

address: 12700 E. 19th Avenue

country: USA

institute: University of Colorado-Anschutz Medical Campus

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: Oxidative stress is a key contributor to the development of dysregulated inflammation in acute lung injury (ALI). A naturally occurring single nucleotide polymorphism in the key extracellular antioxidant enzyme, extracellular superoxide dismutase (EC-SOD), results in an arginine to glycine substitution (R213G) which promotes resolution of inflammation and protection against bleomycin-induced ALI. Previously we found that mice with the R213G mutation in EC-SOD have an inflammation-resolving transcriptomic profile at 7 days post-bleomycin However, the epigenetic differences between WT and R213G EC-SOD lungs have not been examined. Therefore, we used Next Generation microRNA (miR) Sequencing of lung tissue to identify dysregulated miRs 7 days after bleomycin in wild-type (WT) and R213G mice.
Methods: WT and homozygous R213G EC-SOD (rs1799895) mice received one intratracheal administration of bleomycin in phosphate-buffered saline (PBS) (100 uL at 1 U/mL) or PBS at 8-12 weeks old. Lungs were harvested and frozen. Frozen lungs were homogenized, placed in Qiazol, and RNA was isolated using the miRNeasy Mini Kit (Qiagen). Samples underwent 1x150, directional, single-end sequencing using the Illumina hiSEQ 4000 system.
Results: 1424 microRNAs were detected. Up/Down regulated microRNAs were defined as havinga FC > 1.2 and p <0.05. microRNAs "unique" to a genotype were defined as meeting the prevoius criteria in only one strain, or in both with a fold change 1.5x greater in one over the other. This method identified 92 WT and 235 R213G miRs uniquely dysregulated in their respective genotypes.

overall_design: Lung microRNA profiles of 11-week-old WT and R213G mice with intratracheal PBS (control) or bleomycin-induced lung injury from Illumina sequencing.

first: Laura

last: Hernandez-Lagunas

first: Anastacia

middle: M

last: Garcia

first: Ayed

last: Allawzi

first: Anis

last: Karimpour-Fard

first: Carmen

middle: C

last: Sucharov

first: Eva

last: Nozik-Grayck


title: Global gene expression pattern in Mouse Trophoblast Stem Cells (mTS) with or without knocking down of Tead4

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

type: Expression profiling by high throughput sequencing

summary: A TEA domain containing transcription enhancer factor, TEAD4 (TEF3) was found to be very important in the trophectoderm (at preimpantation embryos in rodent) in some earlier studies (Home et al, Saha et al, 2012). Here we report the role of TEAD4 in the TE derived mTS cells with a loss of function approach where the mTS cells under stem condition were transduced with lentiviral shRNA construct and the global gene expression was analysed with the help of a third generation sequencer.

overall_design: mTS cells under stem condition was transduced with lentiviral particles consists of scramble or shRNA against Tead4. The puromycin selected cells were passaged and then the whole cell-lysates were used to prepare RNA. RNA-seq analysis were performed using a illumina HiSeq2500 platform.

first: Soumen

last: Paul

first: Biswarup

last: Saha


title: HSD17B10 binds to NEAT1 and CCAT1 might related to inflammatory bowel disease pathogenesis

status: Public on May 31 2020

city: changsha

first: Xiangli

last: Yin

state: Hunan

address: the 2nd Xiangya Hospital

country: China

institute: the 2nd Xiangya Hospital

summary: To study the potential function of HSD17B10 in inflammatory bowel disease, we obtained HSD17B10-bound RNA in HeLa cells.

overall_design: Overexpresed HSD17B10,then get the iRIP-seq from Hela cells.

first: Ouyang

last: Chunhui


title: Identification of TEAD4 target genes in Human trophoblast stem cells (HTS) by ChIP-seq analysis.

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq profiles of TEAD4 and input in Human trophoblast stem cells (HTS) using Illumina NovaSeq 6000 Sequencing System.

first: Paul

last: Soumen

first: Ganguly

last: Avishek

first: Gunewardena

last: Sumedha


title: Transcriptome analysis of Human Trophoblast Stem cell (HTS) and TEAD4 knock down HTS cells by next generation sequencing

summary: mRNA profiles of control Human Trophoblast Stem cell (HTS) and TEAD4 knock down HTS cells were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000 platform. TEAD4 Knock down in HTS cells were confirmed by RT-PCR analysis and immuno staining.


title: Targeted transcriptome profiling of fresh paired normal and tumor tissue samples in glioblastoma patients

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

summary: Glioblastoma (GBM) is the most common and aggressive primary central nervous system malignancy, with median survival of 15 months. Glioblastoma represents extraordinarily high tumor heterogeneity and alterations in genomic, transcriptomic or methylomic levels.  To gain deeper insights into the molecular processes involved we studied transcriptome wide expression profiles using RNAseq of normal/tumor tissue pairs of 12 GBM patients and systematically analyzed the differentially expressed genes.

overall_design: Fresh paired normal and tumor tissue samples were obtained from 12 patients with GBM undergoing surgery. Immunnostaining was performed to validate the nature of both tissue groups. After RNA extraction and reverse transcription,  libraries were prepared with the Ion Ampliseq Transcriptome Human Gene Expression Kit. Templated spheres were achieved by emulsion PCR using the Ion One Touch system and sequenced with an Ion S5 semiconductor sequencer.

first: Didem

last: Seven

first: Arif

middle: B

last: Ekici

first: Andre

last: Reis

first: Bilge

last: Bilgic

first: Altay

last: Sencer

first: Aydin

last: Aydoseli

first: Nur

last: Buyru


title: RNA-seq analysis of pulmonary arterial smooth muscle cells(PASMCs)stimulated with BMP9/10

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

summary: Inactivation of BMP9/10 in mice leads to attenuated contractility of smooth muscle cells and decreased blood pressure.Treatment of de-differentiated PASMCs with BMP9/10 resulted in a strong increase of ACTA2 expression as measured by immunofluorescence and RT-PCR, indicating a switch from the de-differentiated, synthetic to a differentiated, contractile state. To further study the role of BMP9/10 in smooth muscle cells, we isolate PSAMCs and stimulate cells with or without BMP9/10 and perform the RNA-seq analysis.

overall_design: Before the stimulation, PASMCs were cultured without any supplemet for another 48 hours. Then cells were stimulated in Promocell medium without supplements with or without BMP9 (R&D 5566-BP-010) and BMP10 (R&D 6038-BP) at 1 ng/mL and 5 ng/mL respectively.

first: Stefan

last: Guenther

first: Lei

last: Wang


title: Single-cell RNA-seq: INCB059872 in wild-type murine bone marrow

status: Public on May 28 2020

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave.

institute: Vanderbilt University

summary: INCB059872 is a selective irreversible inhibitor of Lysine-Specific Demethylase 1 (LSD1) that is in phase 1 clinical trials in hematopoietic malignancies. Mice treated with INCB059872 had reduced platelet counts within 4 days of treatment. Here, we used single-cell RNA-seq to study the effects of INCB059872 on hematopoietic progenitor populations within wild-type murine bone marrow. Our results showed that INCB059872 triggered accumulation of megakaryocyte early progenitor cells with gene expression hallmarks of stem cells, which may begin to explain the thrombocytopenia observed in patients treated with LSD1 inhibitors.

overall_design: Single-cell RNA-seq of lineage-negative bone marrow from mice treated with LSD1i for 0, 4, or 6 days (3 mice per group)

first: Gretchen

last: Johnston


title: In vivo RNA-seq for for Hh Dependent genes in E7.5 mesoderm

city: Chicago

first: Alexander

last: Guzzetta

state: IL

department: Pediatrics

institute: University of Chicago

summary: Mesp1-Cre+ cells from E7.5 mouse embryos  (from the cross Mesp1-Cre/+  x  Rosa26-Gli3R-IRES-YFP/tdTomato) were sorted by FACS where wild type (tdTomato-expressing) and mutant (Gli3R + YFP co-expressing) cells were collected separately from single litters.

overall_design: Comparing Mesp1Cre sorted E7.5 mesoderm between Wt embryos embryos expressing a dominant negative Hh pathway transcriptional repressor (Gli3R). All 3 samples were litter-matched

first: Megan

last: Rowton

first: Ivan

middle: P

last: Moskowitz


title: Cross-species glucocorticoid-sensitive hippocampal gene network: developing a polygenic score associated with susceptibility to psychiatric conditions in response to adversity in humans

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

summary: The risk for psychiatric disorders is strongly affected by environmental stressors. The underlying mechanisms are inevitably multifactorial still not fully understood. Glucocorticoids (GCs), which are prominent stress mediators that affect transcriptional activity and brain morphology, are implicated in the pathophysiology of multiple forms of psychopathology.  The challenge is that of establishing the relevance of GC-related transcriptional effects for stress-related psychopathology in humans.  We addressed this issue by generating gene expression data from hippocampal dentate gyrus from macaques and rats to identify clusters of co-expressed genes sensitive to GC exposure as the basis for a biologically-informed polygenic risk score (ePRS) to investigate neuropsychiatric outcomes in humans exposed to early life adversity. We used RNA-sequencing data to identify a cluster of GC-responsive genes co-expressed in the posterior dentate gyrus (pDG) of female Cynomologus monkeys and preserved in the rat model with the homologous region (the dorsal DG).  In total 11395 SNPs derived from these genes (507 genes) were used to create an ePRS to explore the interaction with early life adversity on psychiatric phenotypes in human cohorts using the UK Biobank Resource and ALSPAC data sets. The biologically-informed ePRS significantly predicted psychotic behavior in adversity-exposed females as well as variation in brain volume.  These findings reveal that GC exposure influences a specific group of genes in pDG, largely enriched for transcription processes and pathways related to development activity. Variations in the expression of this gene network can be used in a translational manner to predict risk for neuropsychiatric conditions and brain volume alterations after early stress exposure. These results highlight the importance of hippocampal GC-related transcriptional activity as a mediator for the effects of early life adversity on mental health outcomes.

overall_design: RNA sequencing of brain regions in female macaques exposed to glucocorticoids and controls

last: O’Toole

first: Danusa

last: Arcego


title: A lysosomal hydrolase receptor, CPBF2, involve in invasion machinery of an enteric protozoan parasite Entamoeba histolytica

city: Tokyo

first: Kumiko

last: Nakada-Tsukui

address: 1-23-1, Toyama, Shinjyuku-ku

country: Japan

institute: National Institute of Infectious Diseases

summary: To know the role of lysosomal hydrolase receptors in virulecne of enteric protozoan parasite Entamoeba histolytica, eleven cysteine protease binding protein family (CPBF) proteins were specifically silenced and examined the effect on virulence-related phenotypes. Among them, CPBF2 gene silence caused defect in Matrigel invasion. To clarify transcriptomic difference in CPBF2 gene silenceing strain, RNA-seq analysis was conducted.

overall_design: Examine RNA-seq analysis of mock transfected and CPBF2 gene silenceing strain. (n=3)

first: Konomi

last: Marumo

first: Tomoyoshi

last: Nozaki


title: Development of an mPing-based Activation Tag for Crop Insertional Mutagenesis

city: Aiken

first: Nathan

last: Hancock

state: SC

address: 471 University Parkway

department: Department of Biology and Geology

institute: University of South Carolina Aiken

summary: Modern plant breeding increasingly relies on genomic information to guide crop improvement. Although some genes are characterized, additional tools are needed to effectively identify and characterize novel genes associated with crop traits. To meet this need, the mPing element from rice was developed as an activation tag designed to induce overexpression of nearby genes. Addition of promoter sequences to mPing resulted in a decrease in overall transposition rate, however, this effect was negated by using a hyperactive version of mPing called mmPing20. These mPing-based activation tags were found to induce expression of nearby reporter genes in transient assays. Transgenic soybean plants carrying mPing-based activation tags and the appropriate transposase protein expression constructs showed evidence of transposition. Expression analysis of a line that contained a heritable insertion of the mmPing20F activation tag, indicated that the activation tag induced overexpression of the nearby soybean genes. This represents a significant advance in gene discovery technology as activation tags have the potential to induce more phenotypes than the original mPing element, improving the overall effectiveness of the system.

overall_design: Two replicates of plants harboring the mPing based activation tag (T162821 and T162822) were compared with two plants not harboring the activation tag. The latter two plants consisted of an untransformed soybean plant (Thorne) and a transgenic plant containing the transposase expression construct (T1622845).

first: C

middle: N

first: Alex

last: Johnson


title: Gene expression changes in uteri of mice treated with  17beta-estradiol (E2), p-Phenoxyphenol (PhOP), or p-pentyloxyphenol (PeOP)

city: Beijing

first: Zhaobin

last: Zhang

address: Yiheyuan Road 5#

institute: Peking Univ

summary: p-Phenoxyphenol (PhOP) and p-pentyloxyphenol (PeOP) have been reported to be estrogenic in vitro. But their in vivo estrogenic activities have rarely been of concern. In this study, we  performed an immature mouse uterotrophic assay and next-generation transcriptome sequencing (RNA-seq) to study the estrogenicity of PhOP and PeOP, as well as E2.

overall_design: Uteri Gene expression of female CD-1 mice aged 24 postnatal days were measured after  3 consecutive days gavaging with  with 3 and 30 mg/kg bw/d PhOP and PeOP and 0.4 mg/kg bw/d E2,respectively.

first: Yue


title: Effect of myostatin inhibition on skeletal muscle gene expression in high fat diet-fed mice

city: Reading

first: Wouter

last: Eilers

address: Whiteknights Campus

country: United Kingdom

institute: University of Reading

summary:
Myostatin (GDF8) is a member of the TGF-beta family of proteins which is predominantly expressed in skeletal muscle and acts as a negative regulator of muscle mass. Inhibition of myostatin leads to muscle hypertrophy and  has been shown to mitigate insulin resistance in mouse models of type 2  diabetes, although the mechanisms underlying this effect are unclear. We found that myostatin inhibition by AAV-mediated overexpression of the myostatin propeptide improves skeletal muscle insulin sensitivity in mice made insulin-resistant by high fat diet feeding.
To gain insight into potential gene expression changes responsible for this effect, we performed microarray analysis on skeletal muscle samples from high fat diet-fed mice with and without myostatin inhibition.

overall_design: Male C57Bl/6 mice (n=8) were switched from regular chow to a high fat diet (HFD) at 8 weeks of age. 4 Weeks later, mice were given an intramuscular injection of AAV8 Promyo into one Tibialis Cranialis (TC) muscle, while the contralateral TC muscle was injected with saline. Mice were kept for 10 weeks post-injection before collecting the injected muscles.

first: David

last: Chambers

first: Mark

last: Cleasby

first: Keith

last: Foster


title: Phenotypic and Gene Expression Features Associated with Variation in Chronic Ethanol Consumption in Heterogeneous Stock Collaborative Cross Mice

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

summary: Of the more than 100 studies that have examined some aspect of the relationships between excessive ethanol consumption and the brain transcriptome, relatively few rodent studies have examined the effects of chronic consumption. The current study allowed 114 heterogeneous stock collaborative cross mice to freely consume 10% ethanol for 3 months (13 weeks), with a water choice. RNA-Seq data were then used to identify transcriptional differences within the central nucleus of the amygdala, a brain region known to impact ethanol preference. Average week 1 preference for consuming ethanol over water was modestly correlated with average preference for the final week of the study, and over the course of the 3-month trial, a sex-difference emerged. In females but not males, there was a significant escalation of preference from week 1 to week 13 and significant alignment of the transcriptome with average week 13 ethanol preference and consumption was found for female, but not male mice. The genes significantly correlated with preference were enriched in annotations associated with cilium movement, cilium organization, extracellular region and collagen-containing extracellular matrix. For the females, 376 of the total 415 genes that correlated with ethanol preference in the gene co-expression network were associated with a single network module that was enriched in genes with an astrocyte annotation. The key hub node in the module was the master regulator, orthodenticle homeobox 2 (Otx2). These data support an important role for the extracellular matrix and primary cilium in individual differences in ethanol preference and consumption in a genetically diverse population of mice.

overall_design: Ninety-six samples were chosen for RNA-Seq analysis, balanced for sex and quartile of ethanol preference. Samples were lost for several reasons: failed dissection, low RNA yield, poor RNA quality, failed library preparation and poor sequencing. The final group included 84 samples: 12 high preference (≥ 0.5) females, 8 high preference males, and  the remaining 64 were distributed across the preference range from 0 to < 0.5. The analysis of the RNA-Seq data focused on preference phenotype x expression correlations, beginning with the data for all 84 animals, then moving to the 43 females and 41 males in separate analyses. Correlations were calculated for week 1 average, week 13 average and the average across all weeks.

first: Robert

last: Hitzemann

first: Tamara

middle: J

last: Phillips

first: Denesa

middle: R

last: Lockwood

last: Searles


title: Establishment of coral-algal symbiosis is accompanied by extensive transcriptional repression in the symbiont

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

summary:
Background: The molecular machinery underpinning the establishment of this relationship is not well understood. This is especially true of the symbiont side, as previous attempts to understand the interaction between coral larvae and Symbiodiniaceae have focused nearly exclusively on the host
Results: The transcriptomic response of C. goreaui to the symbiotic state was complex, the most obvious feature of which was extensive and generalized downregulation of gene expression. Included in this “symbiosis-derived transcriptional repression” were a range of stress response and immune-related genes. In contrast, a range of genes implicated in metabolism were upregulated in the symbiotic state. Consistent with previous ecological studies, this transcriptomic response of C. goreaui suggests that active translocation of metabolites to the host may begin early in the colonization process, and thus that the mutualistic relationship is established at the larval stage
Conclusions: This study provides novel insights into the transcriptomic remodelling that occurs in C. goreaui during transition to a symbiotic lifestyle, with important implications for understanding the establishment of symbiosis between corals and their dinoflagellate partners.

sample_organism:
Cladocopium sp. C1
Cladocopium goreaui

overall_design: Symbiont mRNA profiles from colonized larvae after 3, 12, 48, and 72 h were generated by deep sequencing, in triplicate, using Illumina HiSeq platform

first: Natalia

last: Andrade

first: Aurelie

last: Moya

first: Cheong

middle: X

last: Chan

first: Andrew

last: Negri

middle: G

last: Bourne

first: Eldon

middle: E

last: Ball

last: Miller


title: qDRIP-seq in HeLa cells

city: Stanford

first: Karlene

middle: Anne

last: Cimprich

state: CA

address: 318 Campus Drive

institute: Stanford University

summary: R-loops are dynamic, co-transcriptional nucleic acid structures that facilitate physiological processes and cause DNA damage in certain contexts. Perturbations of transcription or R-loop resolution are expected to change their genomic distribution. Next-generation sequencing approaches to map RNA:DNA hybrids, a component of R-loops, have so far not allowed quantitative comparisons between such conditions. Here we describe quantitative differential RNA:DNA immunoprecipitation (qDRIP), a method combining synthetic RNA:DNA-hybrid internal standards with high-resolution, strand-specific sequencing. We show that qDRIP avoids biases inherent to read-count normalization by accurately profiling signal in regions unaffected by transcription inhibition in human cells, and by facilitating accurate differential peak calling between conditions. Finally, we use these quantitative comparisons to make the first estimates of the absolute count of RNA:DNA hybrids per cell and their half-lives genome-wide. Overall, qDRIP allows for accurate normalization in conditions where R-loops are perturbed and for quantitative measurements that provide previously unattainable biological insights.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Input, IP and RNase H treated samples for control knockdown conditions, DMSO, and DRB treatment in HeLa cells.

middle: A

first: Madzia

last: Crossley

first: Michael

last: Bocek

first: Stephan

last: Hamperl

first: Tomek

last: Swigut


title: Single-cell RNA-seq of AML patient bone marrow treated with INCB059872, azacitidine, or combination

first: Scott

last: Hiebert

summary: INCB059872 is a selective irreversible inhibitor of Lysine-Specific Demethylase 1 (LSD1) that is in phase 1 clinical trials in hematopoietic malignancies. We evaluated a pre-treatment bone marrow sample of a patient who showed a clinical response to INCB059872 + azacitidine treatment. Single-cell RNA-sequencing (scRNA-seq) showed that INCB059872 caused a shift in gene expression that was associated with GFI1/GFI1B regulation.

overall_design: A pre-INCB059872 treatment bone marrow sample from an AML patient was divided and treated ex vivo in duplicate with vehicle, INCB059872, AZA, or INCB059872 + AZA.

first: Johnston

last: Gretchen

first: Hiebert

last: Scott


title: A SIX1/EYA2 small molecule inhibitor disrupts EMT and metastasis

status: Public on May 30 2020

first: Heide

last: Ford

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

summary: This study identified a novel compound reverses SIX1-mediated EMT and metastasis in breast cancer

overall_design: RNA-seq was used to identify transcriptional signature that is influenced by SIX1 overexpression, and subsequently reversed by compound treatment

middle: L

first: Rui

last: Zhao

first: Hengbo

last: Zhou

last: Goodspeed

first: Matthew

middle: D

last: Galbraith


title: Expression data from human hematopoietic stem and progenitor compartments from patients with acute myeloid leukemia with complex karyotype

city: Cincinnati

first: Laura

last: Barreyro

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary:
We applied transcriptional analysis of multiple, highly fractionated stem and progenitor populations from patients with acute myeloid leukemia (AML) with complex karyotype. We isolated phenotypic long-term HSC (LT-HSC), short-term HSC (ST-HSC), and committed granulocyte-monocyte progenitors (GMP) from individual patients, and measured gene expression profiles of each population, and in comparison to their phenotypic counterparts from age-matched healthy controls.
In this dataset, we include the expression data obtained from sorted hematopoietic stem and progenitor cells from patients with AML with complex karyotype.

overall_design: Bone marrow samples from AML patients with complex karyotype. Hematopoietic stem and progenitor compartments were purified by multiparameter-high speed fluorescence-activated cell sorting (FACS) from CD34+ enriched bone marrow to isolate LT-HSC (Lin-/CD34+/CD38-/CD90+), ST-HSC (Lin-/CD34+/CD38-/CD90-), and GMP (Lin-/CD34+/CD38+/CD123+/CD45R+).

first: Britta

last: Will

first: Daniel

middle: T

last: Starzynowski


title: Topical application of hESC-derived mesenchymal stem cell spheres accelerates wound healing in a CXCL12-CXCR4 axis-dependent manner

city: Macao

first: Renhe

last: Xu

address: Avenida de Universidade  Taipa

department: Faculty of Health Sciences

institute: University of Macao

summary: It has been reported that mesenchymal stem cells (MSC) derived from adult tissues are effective in promoting wound healing. However, the cell quality varies and cell number is limited as both depend on donations. Moreover, dissociated MSC delivered to an inflammatory lesion are subject to challenges to their survival and functions. Here we demonstrate that dropping of spheres of MSC derived from human embryonic stem cells (EMSC) onto murine dermal wound had much higher survival and efficacy than topical application of dissociated EMSC. RNA sequencing on cells isolated from the wound highlights the CXCL12-CXCR4 signalling in the EMSC sphere-mediated efficacy, which was verified via CXCL12 knockdown in EMSC and CXCR4 inhibition in target cells such as vascular endothelial cells, epithelial keratinocytes, and macrophage. Finally, we enhanced the biosafety of EMSC spheres by engineering the cells with an inducible suicide gene. Together, we propose topical application of EMSC spheres as an unlimited, quality-assured, safety-enhanced, and noninvasive therapy for wound healing and the CXCL12-CXCR4 axis as a key player in the treatment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We employed a murine model of excisional splinted skin wounds, in which contraction of skin around a wound is prevented so the wound healing effect of a treatment can be displayed and measured objectively. We directly dropped EMSCSp onto the wound surface, which promoted wound healing much faster than local delivery of EMSCDiss. EMSCSp survived longer, migrated farther, and induced more macrophage accumulation, vascular genesis and re-epithelialization in the wounds than EMSCDiss. Similar results were observed with MSC spheres derived from human bone marrow (BM-MSCSp) versus dissociated control cells. Finally, to reduce tumorigenesis concern, we transduced EMSC with a chemically inducible caspase-9 (iCasp9) and demonstrated that the engineered EMSC could be efficiently killed in vitro and eliminated in vivo post-therapy.

first: Xiaoyan

last: Wang

first: Bin

last: Jiang

first: Huiyan

last: Sun

first: Dejin

last: Zheng

first: Zhenwu

last: Zhang

first: Li

last: Yan

first: Enqin

last: Li

first: Ren-He


title: Transcriptional Profiling of Lung Macrophages from Preterm Infants Identifies Disease Related Programs

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

institute: UCSD

summary: To understand the molecular mechanisms of human lung macrophage development, function, and role in BPD pathogenesis, we conducted a clinical study using isolated tracheal aspirate macrophages from intubated preterm infants born before 30 wk gestation. One hundred twenty-eight patients intubated for respiratory distress syndrome and surfactant administration were consented for the study.

overall_design: Tracheal aspirate cells were collected from intubated preterm infants as detailed below. After instillation of 0.5 ml of normal saline into the endotracheal tube, a suction catheter was introduced into the endotracheal tube and tracheal secretions were aspirated into a sterile mucus trap. The suction catheter was subsequently rinsed with an additional 1.5 ml of sterile saline to clear any remaining aspirate from the catheter into the mucus trap. Cells were collected by centrifugation and resuspended in DMEM with 10% fetal bovine serum, penicillin, and streptomycin. Equal aliquots of resuspended cells were divided between two separate tissue culture treated plates and incubated at 37 ˚C in a humidified environment of 95% air and 5% CO2 to allow macrophage attachment. After 30 min, nonadherent cells were removed by gentle washing and fresh cell culture media was applied. Lipopolysaccharide from E. coli (strain 055:B5, gel purified, Sigma-Aldrich L2637; 250 ng/ml) was added to one of the plates and both were incubated for 4 h at 37 ˚C. After incubation, the media was removed and cells were lysed in TRIzol monophasic solution containing phenol and guanidine isothiocyanate (Thermo Fisher). RNA was isolated using standard protocols for TRIzol extraction. RNA yield and quality were measured using High Sensitivity RNA ScreenTape Analysis (Agilent Tapestation).

first: Livia

last: Zaramela

first: Gilberto

last: Hernandez

first: Uyen

last: Mai

first: Sahar

last: Taheri

first: Dharanidhar

last: Dang

first: Ashley

last: Stouch

first: Rachel

middle: M

last: Medal

first: Alyssa

last: McCoy

first: Judy

last: Aschner

first: Timothy

last: Blackwell

first: Karsten

last: Zengler

first: Lawrence

last: Prince


title: Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviors

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415 Curie Boulevard

institute: University of Pennsylvania

summary: Non-genetic factors can cause individual cells to fluctuate substantially in gene expression levels over time. Yet it remains unclear whether these fluctuations can persist for much longer than the time of one cell division. Current methods for measuring gene expression in single cells mostly rely on single time point measurements, making the duration of gene expression fluctuations or cellular memory difficult to measure. Here, we report a method combining Luria and DelbrÃ¼ckâ€™s fluctuation analysis with population-based RNA sequencing (MemorySeq) for identifying genes transcriptome-wide whose fluctuations persist for several cell divisions. MemorySeq revealed multiple gene modules that are expressed together in rare cells within otherwise homogeneous clonal populations. Further, we found that these rare cell subpopulations are associated with biologically distinct behaviors, such as the ability to proliferate in the face of anti-cancer therapeutics, in different cancer cell lines. The identification of non-genetic, multigenerational fluctuations has the potential to reveal new forms of biological memory at the level of single cells and suggests that non-genetic heritability of cellular state may be a quantitative property

overall_design: We generated clonal cell lines of WM989 (BRAFV600E melanoma), WM983b (BRAFV600E melanoma), MDA-MB-231 (triple negative breast cancer), and PC9 (EGFR del Glu746-Ala750 lung cancer) from single-cell bottlenecks. Starting with these parental, clonal cell lines (WM989-A6, WM983B-E9, MDA-MB-231-D4 and PC9-D11) we isolated a single cell, let it proliferate until reaching roughly 100-200 cells, then plated these cells into a 96 well plate at a dilution in which we expected roughly 0.5 cells per well. From these wells, we isolated ~100 subclones for further expansion, excluding wells that were seeded with more than 1 cell.  Of these, we aimed for 48 subclones from each cell line for downstream analysis. We grew the subclones until they reached a minimum of around 100,000 cells, with some reaching as high as roughly 200,000 cells. At that point, we used miRNAeasy RNA extraction kit (Qiagen 217004) to isolate RNA from each subclone, followed by library preparation using the NEBNext Poly(A) Magnetic Isolation Module and NEBNext Ultra RNA sequencing library prep kit for Illumina (NEB). For WM989-A6, WM983b-E9, and MDA-MB-231 cell lines, at the time of RNA isolation for the subclones, we also isolated 48 separate samples of 100,000 cells from the parental line and prepared these samples for RNA sequencing as controls.

first: Benjamin

last: Emert

first: Sydney

last: Shaffer


title: Transcriptome analysis of zcIs13 and zcIs13; Punc-119_ds-fzo-1 RNAi in Caenorhabditis elegans

city: Taipei City

first: Li-Tzu

last: Chen

address: No. 1, Sec. 1, Ren’ai Rd., Zhongzheng Dist.

department: Institute of Molecular Medicine

country: Taiwan

institute: National Taiwan University

summary: Mitochondrial functions across different tissues are regulated in a coordinated fashion to optimize fitness of the organism. Mitochondrial unfolded protein response (UPRmt) can be non-autonomously elicited by mitochondrial perturbation in neurons, but neuronal signals that propagate such response and its physiological significance remains incompletely understood. Here we show that in C. elegans, loss of neuronal fzo-1/Mitofusin induces non-autonomous UPRmt through multiple neurotransmitters and neurohormones, including acetylcholine, serotonin, glutamate, tyramine and insulin-like peptides. Neuronal fzo-1 depletion also triggers non-autonomous mitochondrial fragmentation, which requires autophagy and mitophagy genes. Systemic activation of UPRmt and mitochondrial fragmentation in C. elegans via perturbing neuronal mitochondrial dynamics improves resistance to pathogenic Pseudomonas infection, which is supported by transcriptomic signatures of immunity and stress response genes. We propose that C. elegans surveils neuronal mitochondrial dynamics that coordinate systemic UPRmt and mitochondrial connectivity for pathogen defense and optimized survival under bacterial infection.

overall_design: Total RNA profiles of zcIs13 and zcIs13; Punc-119_ds-fzo-1 RNAi Caenorhabditis elegans were generated by deep sequencing using Illumina Solexa technology.

first: Chun-Liang

last: Pan


title: TEAD4

city: Kansas City

first: Sumedha

last: Gunewardena

address: 2146 West 39th Avenue

institute: University of kansas medical center

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

overall_design: Refer to individual Series


title: Drop-seq of normal mammary cells pre and post- conditional reprogramming (CR)

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

summary: Normal mammary cells obtained from reduction mammoplasty samples were processed into single cells and either frozen down or established in conditional reprogramming culture conditions.  Drop-seq was performed on samples pre-and post-CR in order to characterize the conditional reprogramming culture process.

overall_design: N=3 normal mammary samples and their conditionally reprogrammed counterparts

first: Tasha

last: Thong

first: Michael

last: Brooks


title: Effect of IL-6 deficiency on gene expression in cell types of control and HD mouse striatum

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 77 Massachusetts Ave., Bldg 46-4285

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

summary: Huntington’s disease (HD) is an incurable neurodegenerative disorder that is caused by CAG trinucleotide expansions in the huntingtin gene. However, the exact molecular and cellular mechanisms underlying the pathogenesis of HD are still not well understood. Immune signaling has been hypothesized to contribute to HD pathogenesis. In this study, we used single-nucleus RNA sequencing (snRNA-seq) to access the transcriptional profiles of striatal cell types in control and R6/2 HD model mice that either had normal levels of, or were deficient for, the cytokine interleukin-6 (IL-6). Our results provide insights into the gene expression programs that are under the control of this important immune regulator in both a normal and HD model context.

overall_design: Single-cell profiling of Il6 knock-out spiny projection neurons in R62 mouse model of HD.

first: Sergio

last: Pineda


title: Functional assessment of the “two-hit” model for neurodevelopmental defects in Drosophila and X. laevis models of 16p12.1 deletion

city: State College

first: Santhosh

last: Girirajan

address: 205A Life Sciences Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: We recently identified a deletion on chromosome 16p12.1 that is mostly inherited and associated with multiple neurodevelopmental phenotypes, where severely affected probands carried an excess of rare pathogenic variants in the genome compared to mildly affected carrier parents. We hypothesized that the 16p12.1 deletion sensitizes the genome for disease, but other hits in the genetic background modulate the ultimate phenotypic trajectory. To test this model, we examined the individual contribution of 16p12.1 homologs towards neurodevelopmental, cellular and molecular phenotypes in Drosophila melanogaster and Xenopus laevis. We observed that 16p12.1 homologs affect multiple phenotypic domains, leading to developmental delay, seizure susceptibility, brain size alterations, abnormal neuronal morphology, and cellular proliferation defects. In contrast to genes within CNVs of higher de novo occurrence, such as 16p11.2 deletion, homologs of 16p12.1 genes did not interact with each other, were less connected in a human brain network, and were sensitive to variation in the genetic background. Moreover, 214 “two-hit” models in the fly eye identified additive (47%), suppressive (34.5%), and epistatic (18.5%) interactions between 16p12.1 homologs and 80 homologs of genes carrying “second-hits” in children with the deletion and genes within related neurodevelopmental pathways. In fact, homologs of the intellectual disability-associated “second-hit” gene SETD5 synergistically interacted with homologs of MOSMO, modifying brain and cellular phenotypes and leading to new neuronal defects. Our results provide functional evidence for the “two-hit” model of neurodevelopmental disorders, where multiple 16p12.1 genes sensitize the genome to developmental defects, and complex domain-specific interactions with “second-hit” genes define the final phenotypic manifestation.

overall_design: mRNA-sequencing of Drosophila neuron-specific (Elav-GAL4 driver) RNAi knockdown (whole head) for four individual 16p12.1 homologs (CDR2, MOSMO, POLR3E, UQCRC2) and two VDRC GD wild-type controls (one with Dicer2 at 25°C, and one without Dicer2 at RT). Sequencing was performed using Illumina HiSeq 2000 on three biological replicates per sample (18 total replicates).

first: Lucilla

last: Pizzo

first: Micaela

last: Lasser

first: Matthew

last: Jensen


title: RNA-seq of murine megakaryocyte progenitor cells treated with LSD1 inhibitor INCB059872

city: Nashville

first: Scott

last: Hiebert

address: 2220 Pierce Ave.

institute: Vanderbilt University

summary: INCB059872 is a selective irreversible inhibitor of Lysine-Specific Demethylase 1 (LSD1) that is in phase 1 clinical trials in hematopoietic malignancies. We identified a population of cells within murine lineage-negative bone marrow that is expanded after treatment with INCB059872. Here we sorted cells from this population (Lin- Cd41+ Cd200r3-) and performed RNA-seq to measure gene expression changes caused by INCB059872. Consistent with the thrombocytopenia observed in LSD1i-treated mice, INCB059872 reduced expression of genes associated with platelet function.

overall_design: Mice were treated for 0, 4, or 6 days with 10 mg/kg INCB059872 (2 mice per treatment group) before harvesting bone marrow and sorting megakaryocyte progenitor cells for RNA-seq.

first: Gretchen

last: Johnston


title: RNA-seq of MV-4-11 or THP-1 cells treated with LSD1 inhibitor INCB059872

summary: INCB059872 is a selective irreversible inhibitor of Lysine-Specific Demethylase 1 (LSD1) that is in phase 1 clinical trials in hematopoietic malignancies. LSD1 inhibition can induce differentiation of acute myeloid leukemia (AML), and here we have used RNA-seq to measure the transcriptional changes caused by INCB059872 in two AML cell lines.

overall_design: Cells were treated (in duplicate) for 3hr or 24hr with INCB059872 before extracting RNA for polyA-enriched RNA-seq.


title: ChIP-seq for histone acetylation and methylation in THP-1 cells treated with LSD1 inhibitor INCB059872

summary: INCB059872 is a selective irreversible inhibitor of Lysine-Specific Demethylase 1 (LSD1) that is in phase 1 clinical trials in hematopoietic malignancies. We performed ChIP-seq for histone modifications to define the earliest regulatory events associated with INCB059872 treatment. Changes in acetylation were more dramatic than changes in methylation, and these changes could be traced back to a loss of CoREST activity at GFI1-regulated targets.

overall_design: THP-1 cells were treated (in duplicate) with 25nM INCB059872 for 24 or 48 hours before crosslinking cells and performing ChIP-seq for H3K27ac or H3K4me1 and H3K4me2.


title: Effects of aronia juice consumption on the mRNA expression profile in peripheral blood mononuclear cells in subjects at cardiovascular risk

city: Belgrade

first: Aleksandra

last: Stankovic

address: Mike Petrovica Alasa 12

department: Department of Health and Environment

country: Serbia

institute: VINCA Institute of Nuclear Sciences, University of Belgrade

summary: We aimed to explore the effects of two, high-polyphenol (AMJ) and low-polyphenol (dAMJ), doses of aronia juice (including polyphenol-free placebo, PLB) and their additive effects on whole transcriptome in peripheral blood mononuclear cells (PBMC) of subjects at cardiovascular risk.

overall_design: Three-arm, crossover, randomized, double-blind, placebo-controlled intervention study

first: Ljiljana

last: Stojkovic

first: Ivan

last: Jovanovic

first: Maja

last: Zivkovic


title: Activation and inhibition of nonsense-mediated mRNA decay control the abundance of alternative polyadenylation products

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

summary: Alternative polyadenylation (APA) produces transcript 3’ untranslated regions (3’UTRs) with distinct sequences, lengths, stability, and functions. We show here that APA products include a class of cryptic nonsense-mediated mRNA decay (NMD) substrates with extended 3’UTRs that gene- or transcript-level analyses of NMD often fail to detect. Transcriptome-wide, the core NMD factor UPF1 preferentially recognizes long 3’UTR products of APA, leading to their systematic downregulation. Further, we find that many APA events consistently observed in multiple tumor types are controlled by NMD. Additionally, PTBP1, previously implicated in direct modulation of co-transcriptional polyA site choice, regulates the balance of short and long 3’UTR isoforms by inhibiting NMD. Our data suggest that PTBP1 binding near polyA sites can drive production of long 3’UTR APA products in the nucleus and/or protect them from decay in the cytoplasm. Together, our findings reveal a widespread role for NMD in shaping the outcomes of APA.

overall_design: eCLIP analysis of FLAG-PTBP1 binding in HEK-293 Flp-In TREx cell lines, with size-matched input control.

first: Nazmul

last: Haque

first: Aparna

last: Kishor

first: J


title: Gene expression changes in the conceptus following maternal exposure to PolyI:C

city: London

first: Kelly

middle: Joan

last: Baines

state: Ontario

address: 1151 Richmond St

department: Anatomy and Cell Biology

institute: The University of Western Ontario

summary: We report the global transcript changes in the rat conceptus following maternal exposure to PolyI:C

overall_design: Examination of global transcript changes in implantation sites following maternal PolyI:C exposure

first: Stephen

last: Renaud


title: PRO-seq of THP-1 cells treated with LSD1 inhibitor INCB059872

summary: INCB059872 is a selective irreversible inhibitor of Lysine-Specific Demethylase 1 (LSD1) that is in phase 1 clinical trials in hematopoietic malignancies. We used precision nuclear run-on sequencing (PRO-seq) to define early transcriptional changes associated with INCB059872 treatment. Changes in nascent transcription could be traced back to a loss of CoREST activity resulting in activation of GFI1-regulated targets.

overall_design: THP-1 cells were treated (in duplicate) with 25nM INCB059872 for 0, 6, 12, or 24hrs. PRO-seq was used to measure changes in nascent transcription.


title: Genome-wide transcriptome analysis reveals Embryonic-Stem Cell derived tenocytes resemble fetal, not adult, tenocytes

city: Herts

first: Deborah

middle: Jane

last: Guest

address: Hawkshead Lane, North Mymms, Hatfield

department: Deptartment of Clinical Sciences and Services

institute: Royal Veterinary College

summary:
Purpose:- RNA sequencing was performed on adult, fetal and embryonic stem-cell derived equine tenocytes cultured in 3D to look at which had more similar gene expression profiles.
Results:- 6,190 genes were significantly differentially expressed (DE) across the three lines of fetal, adult and ESC-tenocytes (logFC ± 2, padj <0.01). 542 of these were DE between adult and fetal tenocytes, 2,708 between fetal and ESC-tenocytes and 2,940 between adult and ESC-tenocytes. Genes which were DE between adult and fetal tenocytes were significanlty involved in cell migration and motility. Genes which were DE between the ESC-tenocytes and both adult and fetal tenocytes were in organism process and development.

overall_design: Methods:- mRNA profiles of three independent lines of adult, fetal and ESC derived tenocytes were generated by RNA sequencing, using Illumina NovaSeq6000 and Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed using the pseudoaligner Salmon and differential expression quantified using DESeq2, with batch correction applied. Gene ontology analysis was then conducted using Panther GoSlim.

first: Y

middle: Z

last: Paterson

first: A

last: Cribbs

first: M

last: Espenel

first: E

last: Smith

first: F

last: Henson

first: D


title: H3.3 nucleosome assembly mutants display a late-onset maternal effect

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Maternally inherited RNA and protein control much of embryonic development. The impact of such maternal information beyond embryonic development is largely unclear. Here we report that maternal contribution of histone H3.3 assembly complexes can prevent the expression of late-onset anatomical, physiologic, and behavioral abnormalities of C. elegans. We show that mutants lacking hira-1, an evolutionarily conserved H3.3-deposition factor, have severe pleiotropic defects that manifest predominantly at adulthood. These late-onset defects can be maternally rescued, and maternally derived HIRA-1 protein can be detected in hira-1(-/-) progeny. A screen for mutants that mimic the hira-1 mutant phenotype identified a HIRA complex component (PQN-80/UBN1) and a second H3.3 chaperone (XNP-1/ATRX). pqn-80 and xnp-1 abnormalities are also maternally rescued. Furthermore, mutants lacking histone H3.3 have late-onset defects similar to those of hira-1, pqn-80, and xnp-1 mutants. These data demonstrate that H3.3 assembly complexes provide non-DNA-based heritable information that can markedly influence adult phenotype. We speculate that similar maternal effects might explain the missing heritability of 2 late-onset human diseases, such as Alzheimer’s disease, Parkinson’s disease, and type 2 diabetes.

overall_design: Wild-type and hira-1 null nematodes at stage L1, stage L4 and adult

first: Kirk

middle: B

last: Burkhart

first: Steven

last: Sando

first: Anna

last: Corrionero

first: H

last: Horvitz


title: Treatment of MEC1, EHEB and JVM2 leukemia cell lines with fludarabine, ibrutinib and idelalisib

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

institute: Laval University

summary: UGT2B17 is a recently identified molecular marker for poor prognosis and drug response in Chronic Lymphocytic Leukemia (CLL), which is the most prevalent adult leukemia subtype in the western world. The goal of this study was to investigate transcriptome changes associated with drug-induced UGT2B17 up-regulation to identify possible upstream regulators of drug response and downstream effects of UGT induction.

overall_design: The MEC1, EHEB and JVM2 cell lines were treated with 50uM fludarabine, 5uM ibrutinib, 10uM idelalslib or DMSO control. MEC1, JVM2 and EHEB cells were treated for 48, 72 and 96h, respectively.

first: Eric

middle: P

last: Allain

first: Michèle

last: Rouleau


title: Vibrio cholerae biofilm and planktonic growth RNAseq analysis

city: Santa Cruz

first: Sinem

last: Beyhan

address: 1156 High Street

department: Microbiology and Environmental Toxicology

institute: University of California, Santa Cruz

summary: To determine transcriptome differences in Vibrio cholerae when grown as planktonic and biofilm cultures, whole-genome level transcriptional profiling was performed using RNAseq analysis. Transcriptomes of biofim and planktonic cultures were compared in this study.

overall_design: Three biological replicates of wild-type V. cholerae A1552 smooth variant grown under planktonic or biofilm conditions were used for this study.

first: Ana

last: Gallego-Hernandez

first: Jinhwan

middle: H

last: Park

first: Jennifer

middle: K

last: Teschler

first: Fitnat

last: Yildiz


title: UPF1 regulatory loop variant RNA-Seq and RIP-Seq

first: J. Robert

last: Hogg

summary: HEK-293 Trex cells containing stable tetracycline-inducible transgenes driving overexpression of CLIP-tagged UPF1 isoforms 1 and 2 or GFP were used for total RNA-seq. In addition, CLIP-UPF1 isoforms were affinity purified, and bound RNA was subjected to high-throughput sequencing.

overall_design: Paired-end high-throughput RNA sequencing of Total RNA from cells expressing CLIP-tagged UPF1 isoform 1, UPF1 isoform 2, or GFP and RNA associated with affinity-purified CLIP UPF1 isoforms 1 and 2.

first: Sarah

last: Fritz

first: J

middle: R


title: Autophagy maintains intestinal stem cell integrity

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: The intestinal epithelium is continuously renewed by a pool of intestinal stem cells expressing Lgr5. We show that deletion of the key autophagy gene Atg7 affects the survival of Lgr5+ intestinal stem cells. Mechanistically, this involves defective DNA repair, oxidative stress, and altered interactions with the microbiota. This study highlights the importance of autophagy in maintaining the integrity of intestinal stem cells.

overall_design: Intestinal stem cells and their direct transit amplifying progenitors from individual Lgr5-EGFP-IRES-CreERT2 (WT) or Atg7(fl/fl);Lgr5-EGFP-IRES-CreERT2 (Atg7KO) mice treated with tamoxifen were enriched by sorting CD24(low)/EGFP(High) or CD24(low)/EGFP(Low) populations, respectively. RNA was extracted using the RNeasy Micro Kit (Qiagen), reverse transcribed with the Ovation Pico System V2 (Nugen), then the resulting cDNA was fragmented and labeled with biotin using the Encore Biotin Module kit (Nugen). cDNA from 3-4 EGFP(high) and EGFP(low) samples was hybridized to GeneChip® Mouse Gene 2.0 ST (Affymetrix), scanned with a GCS3000 7G, and analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files).

first: Coralie

last: Trentesaux

first: Marie

last: Fraudeau

first: Caterina

last: Pitasi

first: Julie

last: Lemarchand

first: Sébastien

last: Jacques

first: Angéline

last: Duche

first: Emmanuelle

last: Maillard

first: Karine

last: Bailly

first: Christine

last: Perret

first: Béatrice

last: Romagnolo


title: TFIID enables RNA polymerase II promoter-proximal pausing

city: Boulder

first: Dylan

middle: J

last: Taatjes

state: CO

address: Campus Box 596

department: Biochemistry

institute: University of Colorado Boulder

summary: RNA polymerase II (pol II) transcribes all protein-coding and many non-coding RNAs in the human genome.  Pol II transcription initiation is governed by the Pre-Initiation Complex (PIC), which contains TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, pol II, and Mediator.  After initiation, pol II enzymes typically pause after transcribing less than 100 bases, and paused polymerases represent a common regulatory intermediate. Accordingly, paused pol II has been implicated in enhancer function, development and homeostasis, and diseases ranging from cancer to viral pathogenesis. Precisely how pol II promoter-proximal pausing is enforced and regulated remains unclear; however, protein complexes such as NELF and DSIF increase pausing whereas the activity of CDK9 (P-TEFb complex) correlates with pause release. To address specific mechanistic questions about pol II pausing and its regulation, we reconstituted human pol II promoter-proximal pausing in vitro, entirely with purified factors (no extracts).  As expected, NELF and DSIF increased pol II pausing in vitro, whereas P-TEFb promoted pause release.  Unexpectedly, the PIC alone was sufficient to reconstitute pol II pausing, suggesting that pausing is an inherent property of the PIC.  In agreement, pol II pausing was lost upon replacement of the TFIID complex with TATA-binding protein (TBP); moreover, pausing was dependent upon TFIID subunits TAF1 and TAF2. TAF1/2 bind genomic DNA downstream of the pol II initiation site, invoking a “complex interaction” model for pausing.  Consistent with this model, PRO-Seq experiments revealed increased transcription upon acute depletion (t=60 min) of TAF1 and TAF2 in human cells, and pol II pausing was disrupted at thousands of genes.  Similar results were obtained in TAF1-depleted Drosophila S2 cells.  Collectively, these data establish the general transcription factor TFIID as a genome-wide regulator of pol II promoter-proximal pausing.

overall_design: Examination of pol II pausing by persicion run-on nucelar sequencing (PROseq) in HCT116 and S2 cells where TAF1 is knocked down vs. control.

first: Charli

last: Fant

first: Cecilia

last: Levandowski

first: Zachary

last: Maas

first: John

last: Moir


title: Expression data from benign prostatic hyperplasia samples and normal controls

city: Wuhan

first: Xiao

last: He

state: Hu Bei

address: Donghu Road 169

department: Zhongnan Hospital

institute: Wuhan University

summary: To further development of our gene expression signature for benign prostatic hyperplasia, we conducted expression profiles of BPH and normal samples.

overall_design: Five prostate samples obtained from surgical excision with benign prostatic hyperplasia (BPH) and three prostate samples obtained from donation of young man with brain death.

first: He

last: Xiao

first: Xinhua

last: Zhang


title: Exaggerated BMP4 signalling alters human airway basal progenitor cell differentiation to cigarette smoking-related phenotypes [array]

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Airway remodelling in chronic obstructive pulmonary disease (COPD) originates, in part, from smoking-induced changes in airway basal stem/progenitor cells (BCs). Based on the knowledge that bone morphogenetic protein 4 (BMP4) influences epithelial progenitor function in the developing and adult mouse lung, we hypothesised that BMP4 signalling may regulate the biology of adult human airway BCs relevant to COPD.
BMP4 signalling components in human airway epithelium were analysed at the mRNA and protein levels, and the differentiation of BCs was assessed using the BC expansion and air-liquid interface models in the absence/presence of BMP4, BMP receptor inhibitor and/or small interfering RNAs against BMP receptors and downstream signalling.

overall_design:
The study demonstrates that in cigarette smokers, BMP4 is up-regulated in ciliated and intermediate undifferentiated cells and BMP4 receptor BMPR1A is enriched in BC. In vitro, mediated by BMPR1A/Smad signaling, BMP4-induced BC to acquire a COPD-like abnormal phenotypes, characterized by decreased capacity to differentiate into the normal mucociliary epithelium, generating a hypoplastic squamous metaplasia. In summary, smoking-induced exaggerated BMP4 signaling promotes COPD-relevant airway epithelial remodeling by inducing abnormal phenotypes in human airway BC progenitor cells. Targeting of BMP4 signaling in airway BC may represent a novel approach to prevent/treat COPD-associated airway disease.
Array profiling of 208 samples (small airway epithelium cells at various collection times from COPD smokers and nonsmokers).

first: Wu-Lin

last: Zuo

first: Jing

last: Yang

first: Jacqueline

last: Salit

first: Mahboubeh

last: Rostami

first: Jason

middle: G

last: Mezey

first: Sarah

last: O'Beirne

first: Robert

last: Kaner

first: Ronald

last: Crystal


title: The transcriptional response of C. elegans to statins: general and p38 dependent responses

city: Haifa

first: Amir

last: Sapir

state: Israel

address: Abba Khoushy Ave 199

country: Israel

institute: University of Haifa

summary: We sought to decipher the general transcriptional response of C. elegans to statins and the p38-dependent portion of this global transcriptional response.

overall_design: Wild-type and worms lacking the p38 pathway exposed to 0 and 1mM fluvastatin for 9 hours beginning from larval stage four


title: Transcriptomic data of MCF7 cells adapted to culture in media containing different sugars (glucose or fructose) and cultured in 2D on plastic

city: Southampton

first: Jeremy

middle: Paul

last: Blaydes

state: Hampshire

address: Southampton General Hospital, Tremona Road

department: Faculty of Medicine

institute: University of Southampton

summary: We report the single-cell RNA sequencing data obtained from MCF7 breast cancer cells cultured in standard DMEM with 25 mM glucose, or adapted to culture in DMEM with 10 mM fructose to reduce glycolysis, and cultures in 2D on plastic

overall_design: Examination of transcriptomic changes in MCF-7 breast cancer cells mammospheres in response to restriction of glycolysis

first: Matthew

last: Rose-Zerilli


title: Translational regulation of RANKL by CPEB2 regulates mammary gland development and luminal tumorigenesis

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

type:
Other
Expression profiling by array

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

overall_design: Refer to individual Series


title: Gene Expression Study of Innate Immune Response of Chicken Intraepithelial lymphocyte natural killer cells to very virulent Infectious Bursal Disease Virus (vvIBDV)

city: Serdang

first: Boo

last: Sook Yee

state: Selangor

address: Universiti Putra Malaysia

department: Institute of Bioscience

country: Malaysia

institute: Universiti Putra Malaysia

summary:
BACKGROUND:Infectious bursal disease is an acute immunosuppressive viral disease which significantly affect the economic in poultry industrial. Infectious bursal disease virus (IBDV) infection was known to destroy B lymphocytes, activate macrophage and T lymphocytes, but there are limited studies on the impact of IBDV infection on chicken intraepithelial Natural killer (IEL-NK) cells.
RESULTS: The main objective of this study is to determine the innate immune response of chicken IEL-NK cells towards very virulent IBDV (vvIBDV) infection. Specific pathogen free (SPF) chickens were infected with vvIBDV for 0, 1 and 3 dpi. The IEL-NK cells were isolated and enriched from total IEL cells using the 28.4+ antibodies. The transcriptome sequencing was conducted in HiSeq2500 system and approximately 62 to 71 million paired-end reads generated per sample. The differential expression analysis was performed on the RNA-Seq data. On dpi 1, there are 838 genes up-regulated and 277 genes down-regulated. On dpi 3, there are 516 genes up-regulated whereas 750 genes down-regulated. According to pathway analysis, the differential expressed (DE) genes related to innate immune response are involved in several pathways such as cytokine-cytokine receptor, toll-like receptor and apoptosis pathway.
CONCLUSION: The IEL-NK cells were de-activated after infected by vvIBDV through the down-regulation of several genes activate the NK cells such as IL18, TLR4 and TLR7/8. The IEL-NK cells were de-activated through up-regulation of expression for TGFB3 which inhibit the activation and function of NK cells by repressing the mTOR pathway. Meanwhile, the infection of vvIBDV induced apoptosis in IEL NK cells by increasing the expression level of some genes promote apoptosis such as CASP2, CASP8 and TLR3.

overall_design: The RNA-Seq data for 3 groups of samples (uninfected chicken, chicken infected by vvIBDV for 1 day and chicken infected by vvIBDV for 3 days) in triplicate was generated using HiSeq2500

middle: S

last: Yee

first: Yeap

last: Keong


title: Primitive endoderm stem cell lines in mice

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary:
A blastocyst consists of three distinctive cell types: epiblast (EPI), trophoblast (TB), and primitive endoderm (PrE). Stem cell lines representing EPI and TB (embryonic stem (ES) cells and trophoblast stem (TS) cells) have been derived and they contribute to epiblast derivatives and trophoblast derivatives of stem cell-blastocyst chimeras, respectively. Although derived from PrE, extraembryonic endoderm (XEN) cells contribute to only a limited part of parietal endoderm (PE) but rarely to other PrE derivatives. Here we describe the establishment of primitive endoderm stem (PrES) cell lines in mice.
PrES cells were derived and maintained in a serum-free media containing CHIR99021, FGF4, heparin, and PDGF-AA. RNA-seq analysis revealed that the transcriptome of PrES cells is globaly different from XEN cells: PrES cells express not only endoderm markers (Dab2, Gata4, Gata6, Sox17, etc.), but also pluripotent markers (Pou5f1, Cdh1, Nanog, Zfp42, etc.), and resembles in vivo founder PrE. PrES cells were rapidly and efficiently incorporated into PrE after blastocyst injection and efficiently contributed to all PrE derivatives, including PE, VE (visceral endoderm), and MZE (marginal zone endoderm) in chimeras. Importantly, PrES cells rescued embryonic lethality of PrE-depleted blastocysts by complementing all PrE derivatives. PrES cells thus not only contribute to understanding of the mechanisms of PrE specification but also provide a critical resource for artificial embryo reconstitution by stem cells alone.

overall_design: mRNAs were extracted from ES, TS, XEN and PrES stem cell

first: Yasuhide

last: Ohinata

middle: A

first: Haruhiko

last: Koseki


title: Translational regulation of RANKL by CPEB2 regulates mammary gland development and luminal tumorigenesis (RIP-seq)

summary: Here we show that the RNA-binding protein CPEB2 controls synthesis of RANKL, thereby modulating epithealial proliferation, differentiation and breast cancer outcome

overall_design: RNA-immunoprecipitation sequencing of CPEB2-associated mRNAs in WT and CPEB2-KO mammary epithelial cells

first: Rosa

last: Pascual

first: Raul

last: Mendez


title: Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites [ChIP-chip]

status: Public on May 27 2020

city: Lexington

first: Sharyn

middle: E

last: Perry

state: KY

address: 1405 Veterans Dr.

department: Plant and Soil Sciences

institute: University of Kentucky

type: Genome variation profiling by genome tiling array

summary:
ABSCISIC ACID INSENSITIVE3 (ABI3) is a transcription factor that is a member of the B3 domain family and is involved in seed development. To understand how it controls development, we mapped genome-wide binding sites by ChIP-chip and combined this data with transcriptomic data obtained by microarrays.
Ran Tian, Fangfang Wang, Qiaolin Zheng, Venus Niza, A. Bruce Downie and Sharyn E. Perry (2020)

overall_design: ABI3 was expressed by its native promoter and included a C-terminal 10x c-myc tag. This transgene was able to rescue the abi3-5 mutant. A second transgene (35S:AGL15) allowed establishment of stable somatic embryo cultures. ChIP was performed using anti-c-myc antibody (Myc-Tag (9B11) Mouse mAb; Cell Signaling 2276S) on tissue expressing ABI3-myc (three biological replicates) and on three controls of tissue without c-myc antibody.


title: Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites

type: Genome binding/occupancy profiling by genome tiling array


title: Translational regulation of RANKL by CPEB2 regulates mammary gland development and luminal tumorigenesis (Affymetrix Microarrays)

overall_design: Mouse array in duplicates of freshly sorted mammary epithelial populations: myoepithelial (Epcam_low and CD49f_high) and luminal (Epcam_high and CD49f_low). The sorted luminal subpopulations were non-clonogenic luminal (Sca1+CD49b-), ductal progenitors (Sca1+CD49b+) and alveolar progenitors (Sca1-Cd49b+).

first: Pascual

last: Rosa

first: Mendez

last: Raul


title: Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites [gene expression]

summary:
ABSCISIC ACID INSENSITIVE3 (ABI3) is a transcription factor that is a member of the B3 domain family and is involved in seed development. To understand how it controls development, we mapped genome-wide binding sites by ChIP-chip and combined this data wi
Ran Tian, Fangfang Wang, Qiaolin Zheng, Venus Niza, A. Bruce Downie and Sharyn E. Perry (2020)

overall_design: Developing abi3-5 and Ler seeds were collected at 15-16 days after flowering (daf), and flash frozen for RNA extraction. In addition, 14-15 daf seeds of these genotypes were removed from the siliques and placed on moist blotter paper for 24 hours and then flash frozen for RNA extraction.


title: Chromatin state maintains human myeloid leukemia by regulating m6A demethylase ALKBH5 expression [Slam-seq]

city: Zhengzhou

first: Jiazhen

last: Wang

address: 156 Jinshui East Road

institute: Henan University of Chinese Medicine

summary: ALKBH5 is the RNA N(6)-methyladenosine (m6A) demethylase. To understhand the function and mechnism of ALKBH5 in human acute myeloid leukemia, we compared the RNA decay rate in wild-type and ALKBH5-knock-down THP1 cells.

overall_design: SLAM-seq in wild-type or ALKBH5 knock-down THP1 cells

first: Yicun

last: Li

first: Peipei

first: Guoqiang

last: Han

first: Haojian

last: Zhang


title: Transcriptomic analysis of tumor infiltrating CD8+ T cells during PDAC progression

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: CD8+ T cells are master effectors of anti-tumor immunity and their presence at tumor sites correlates with favorable outcomes. However, metabolic constraints imposed by the tumormicroenvironment can dampen their ability to control tumor progression. We will analyze the transcriptional profile of CD8+ T cells infiltrating murine tumors during progression in a pre-cinical model pancreatic ductal adenocarcinoma (PDA).

overall_design: Total RNA extraction from CD45+CD3+CD8+ T cells sorted from blood or pancreas of WT B6 mice or KC mice at different time points (4, 13, 20, 0r 30 weeks after birth).

first: Luigi

last: Nezi

first: Teresa

last: Manzo

first: Giulio

last: Draetta


title: Chromatin state maintains human myeloid leukemia by regulating m6A demethylase ALKBH5 expression [Ribo-seq]

summary: ALKBH5 is the RNA N(6)-methyladenosine (m6A) demethylase. To understhand the function and mechnism of ALKBH5 in human acute myeloid leukemia, we compared the translational efficiency in wild-type and ALKBH5-knock-down THP1 cells.

overall_design: Ribo-seq in wild-type or ALKBH5 knock-down THP1 cells


title: Expression data from HeLa cell treated with Bisphenol S and Mono-ethylhexyl phthalate

city: Seoul

first: Jun-Seok

last: Lee

address: 39-1 Hawolgok-dong Seungbuk-gu

country: South Korea

institute: Korea Institute of Science and Technology (KIST)

summary:
Bisphenol S and mono-ethylhexyl phthalate are widely used in the industry of making plastic, mailing envelopes, tickets, etc. Humans are exposed to these compounds by skin contact, inhalation, and food ingestions. However, the molecular mechanisms of these compounds' adverse effects are still unclear. We address the molecular and cellular mechanisms underlying Bisphenol S and mono-ethylhexyl phthalate effects on HeLa cells.
Here microarray analysis was performed to identify distinct classes of up- or down-regulated genes and their connections to the different metabolic pathways.

overall_design: 13 samples were analyzed. We compared samples treated by bisphenol S and mono-ethylhexyl phthalate for 2 and 24 hours with the concentration of both compounds 4 µM, 20 µM, and 100 µM (1 normal sample, 6 samples treated by bisphenol S, and  6 samples treated by mono-ethylhexyl phthalate). Genes with the absolute value of log(fold-change)  ≥1.5 were selected.

first: Mamunul

middle: M

last: Haque

first: Taras

last: Voitsitskyi


title: Chromatin state maintains human myeloid leukemia by regulating m6A demethylase ALKBH5 expression


title: Human blastocysts diagnosed using Next-generation Sequencing with mosaicism demonstrate distinct transcriptomic profiles compared to euploid or aneuploid embryos

city: Manhattan

first: Tenzin

middle: C

last: Lhakhang

address: 550 First Avenue

institute: NYU School of Medicine

summary: Objective: To determine if embryos diagnosed as mosaic using Next-generation sequencing (NGS) have distinct gene expression profiles compared to embryos diagnosed as euploid or aneuploid. Materials and methods: Fifteen blastocysts were diagnosed as mosaic with NGS including 7 full mosaic monosomies, 5 partial mosaic monosomies, 2 full mosaic trisomies, and 1 partial mosaic trisomy.  Three NGS diagnosed euploid embryos, and 25 aneuploid embryos (9 NGS, 14 aCGH, 2 Single Nucleotide Polymorphism array) were used as comparisons.  Replicate samples were available for all euploid and full aneuploid embryos.  Aneuploid embryos were chosen if their aneuploid chromosome corresponded with one of the mosaic embryos.  Complementary DNA from the samples was created using the SMATer v4 Ultra Low Kit. RNA-seq library preparation followed by sequencing on the Illumina HiSeq 2500 with 50 nucleotide length paired end reads was performed.  The STAR/2.5 aligner was used to align the reads against the hg19 ensemble reference transcriptome. Differentially expressed genes (DEGs) were calculated using DES-seq2/3.5, and p values <0.05 were considered significantly differentially expressed. Pathway analysis was performed on the top DEGs among all of the mosaic embryos with p<0.05 considered significant. Main results: The 15 mosaic embryos had transcriptomic profiles which were distinct from full aneuploid embryos involving the same chromosome.  Mosaic embryos had fewer DEGs compared to aneuploid embryos of the same chromosome when using euploid embryos as controls. Mosaic embryos were grouped on principal component analysis (PCA) and distinguishable from euploid and aneuploid embryos.  Pathways involving cell proliferation, differentiation, and apoptosis were the most disrupted from the presence of a mosaic cell line.

overall_design: Descriptive study of 43 blastocysts that underwent preimplantation genetic testing for aneuploidy (PGT-A) with either NGS or array Comparative Genomic Hybridization (aCGH) which were donated for IRB approved research.

first: Susan

last: Maxwell

first: Yael

last: Kramer

first: Yutong

first: Fang

first: Adriana

last: Heguy

first: Aristotelis

last: Tsirigos

first: James

last: Grifo

first: Frederick

last: Licciardi


title: A primary Chlamydia trachomatis genital infection of Rhesus macaques identifies new immunodominant B-cell antigens

city: Irvine

first: Arlo

middle: Zan

last: Randall

state: CA

address: 1 Technology Drive, Suite E309

institute: Antigen Discovery Inc

summary: To identify immunodominant antigens that elicit a humoral immune response following a primary genital infection, rhesus monkeys were inoculated cervically with Chlamydia trachomatis serovar D. Serum samples were collected and probed with a protein microarray expressing 864/894 (96.4%) of the open reading frames of the C. trachomatis serovar D genome. The antibody response was analyzed in 72 serum samples from 12 inoculated monkeys. The following criteria were utilized to identify immunodominant antigens: proteins found to be recognized by at least 75% (9/12) of the infected monkeys with at least 15% elevations in normalized signal intensity from week 0 to week 8 post infection. All infected monkeys developed Chlamydia specific serum antibodies. Eight proteins satisfied the selection criteria for immunodominant antigens: CT242 (OmpH-like protein), CT541 (mip), CT681 (ompA), CT381 (artJ), CT443 (omcB), CT119 (incA), CT486 (fliY), and CT110 (groEL). Of these, three antigens, CT119, CT486 and CT381, were not previously identified as immunodominant antigens using non-human primate sera. In conclusion, these immunodominant antigens can now be tested for their ability to identify individuals with a primary C. trachomatis genital infection and to design a vaccine strategy to protect against a primary infection with this pathogen.

overall_design: A total of 15 rhesus monkeys were involved in tis Chlamydia trachomatis challenge study and a total of 72 sera from them were analyzed. Subjects were infected in the cervix with C. trachomatis serovar D and sera samples were taken throughout the course of infection. At baseline (week 0) 6 subjects received 10^7 IFU and 6 subjects received 10^5 IFU, and 3 subjects received SPG  as controls. Sera samples were taken for all 15 subjects at weeks 0, 4, and 8. Samples were also taken at weeks 14, 18 and 23 for a subset of 9 of the subjects (7 of these 9 received 10^5 IFU at week 14).

first: Andy

last: Teng

first: Xiaowu

last: Liang

first: Sukumar

last: Pal

first: Alice

middle: F

last: Tarantal

first: Joseph

last: Fike

first: Peter

last: Barry

first: Luis

last: de la Maza


title: Transcriptiomics profiling of brown adipose tissue of adipocyte-specific Beclin1 knockout mice

status: Public on May 26 2020

first: Yeonho

last: Son

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: Adipose mRNA profiles of wildetype and Beclin1 knockout (tamoxifen-induced Adipoq-CreER/Beclin1(floxed/floxed)) mice were generated by deep sequencing.

overall_design: Brown adipose tissue mRNA profiles of wild type (WT) and Beclin1-/- mice were generated by deep sequencing. Three biological replicates were analyzed for each of 2 conditions (two genotypes)

first: Yun-Hee

last: Lee


title: DNA damage invokes mitophagy through a pathway involving Spata18

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Mitochondria are vital for cellular energy supply and intracellular signaling after stress. Here, we aimed to investigate how mitochondria respond to acute DNA damage with respect to mitophagy, which is an important mitochondrial quality control process. Our results show that mitophagy increases after DNA damage in primary fibroblasts, murine neurons, and C. elegans neurons. Our results indicate that modulation of mitophagy after DNA damage is independent of the type of DNA damage stimuli used and that the protein Spata18 is an important player in this process. Knockdown of Spata18 suppresses mitophagy, disturbs mitochondrial Ca2+ homeostasis, affects ATP production, and attenuates DNA repair. Importantly, mitophagy after DNA damage is a vital cellular response to maintain mitochondrial functions and DNA repair.

overall_design: mt-keima mice (N=5 per group) were subjected to either sham-treatment or whole body irradiation (6 Gy, delivered at a rate of 0.74 Gy/min), and euthanized  48h later, and cerebellum, cerebrum, heart, licer tissue dissected out for RNA extraction and microarray analysis.

first: Xiuli

last: Dan

first: Mansi

last: Babbar

first: Anthony

last: Moore

first: Noah

last: Wechter

first: Jingyan

last: Tian

first: Joy

last: Mohanty

first: Deborah

middle: L

last: Croteau

first: Vilhelm

last: Bohr


title: Chromatin state maintains human myeloid leukemia by regulating m6A demethylase ALKBH5 expression [RNA-Seq]

first: Jiazhen

last: Wang

summary: ALKBH5 is the RNA N(6)-methyladenosine (m6A) demethylase. To under sthand the function and mechnism of ALKBH5 in human acute myeloid leukemia, we compared the m6A profiling in wild-type, ALKBH5-knock-down, and ALKBH5 rescue THP1 cells.

overall_design: RNA-seq in wild-type or ALKBH5 knock-down, or ALKBH5 rescue THP1 cells

first: Yicun

last: Li

first: Peipei

first: Shaoguang

first: Haojian

last: Zhang


title: The small regulatory RNA Lpr10 regulates the expression of RpoS in Legionella pneumophila

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

summary: Legionella pneumophila (Lp) is a waterborne bacterium able to infect human alveolar macrophages, causing a severe pneumonia known as Legionnaires’ disease. In water, Lp grows inside ciliates and ameoba. Lp is able to survive for several months in water, while searching for host cells. In Lp, the sigma factor RpoS is important for survival in water. Several small regulatory RNAs (sRNA) are known to regulate the expression of RpoS in other bacteria. A previous transcriptomic study showed that RpoS positively regulates the sRNA Lpr10 in Lp. Microarray analysis was performed to investigate the genes regulated by Lpr10.

platform_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: Legionella pneumophila strains KS79 (WT), ∆lpr10, and complemented strain (∆lpr10 + plpr10) were grown in AYE broth at 37°C with shaking. When post-exponential phase was reached, RNA was extracted from triplicate samples.

first: Jospeh

last: Saoud

first: Marie-Claude

last: Carrier

first: Eric

last: Massé


title: Bulk RNA Sequencing Analysis on the Effects of SIX2 Knock Down on Stem Cell Derived Beta cells.

city: St. Louis

first: Jeffrey

last: Millman

state: MO

address: 700 Rosedale Avenue

institute: Washington University in St. Louis

summary: We reveal that SIX2 regulates important transcriptomic aspects of stem cell derived beta cells

overall_design: Bulk RNA sequencing of stage 6 SC-Beta cells treated lentivirus targeting GFP (control) and SIX2

first: Leonardo

last: Velazco-Cruz


title: Expression data from MCF-7 cells treated with 0, 50 and 100 uM Oxyresveratrol

city: Liverpool

first: Sarayut

last: Radapong

address: 2 Hatton Garden

institute: Liverpool John Moores University

summary: We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: MCF-7 cells were seeded at 2.5 x 10^5 cells/well in 6-well plates for 24 h, then they were treated with Oxyresveratrol at the concentrations of 0, 50, and 100 μM for 24 h. Total RNA of each sample was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany)


title: Effect of lipoprotein(a) on Arterial Endothelial Cells

city: Amsterdam

last: Kroon

address: Meibergdreef 9

department: Experimental Vascular Medicine

country: Netherlands

institute: Amsterdam UMC, location AMC

summary: Human Arterial Endothelial Cells (HAECs; Lonza) were incubated with either 5mg/dl or 100mg/dl isolated lipoprotein(a) for 6 hours. Next, RNA was isolated (RIN>9) and processed for NGS. NGS details: Sequencing of RNA (rRNA depleted), HiSeq4000, Paired-End, 150 bp

overall_design: Examination of the inflammatory and metabolic effects of lipoprotein(a) on arterial endothelium (HAECs). Additional information can be found in the manuscript of Schnitzler et al. Circ Res. 2020

first: Johan

last: Schnitzler


title: Distinct mitochondrial defects trigger the integrated stress response depending on the metabolic state of the cell

city: Boston

first: Eran

last: Mick

address: 185 Cambridge st

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Mitochondrial dysfunction is associated with activation of the integrated stress response (ISR) but the underlying triggers remain unclear. We systematically combined acute mitochondrial inhibitors with genetic tools for compartment-specific NADH oxidation to trace mechanisms linking different forms of mitochondrial dysfunction to the ISR in proliferating mouse myoblasts and in differentiated myotubes. In myoblasts, we find that impaired NADH oxidation upon electron transport chain (ETC) inhibition depletes asparagine, activating the ISR via the eIF2α kinase GCN2. In myotubes, however, impaired NADH oxidation following ETC inhibition neither depletes asparagine nor activates the ISR, reflecting an altered metabolic state. ATP synthase inhibition in myotubes triggers the ISR via a distinct mechanism related to mitochondrial inner-membrane hyperpolarization. Our work dispels the notion of a universal path linking mitochondrial dysfunction to the ISR, instead revealing multiple paths that depend both on the nature of the mitochondrial defect and on the metabolic state of the cell.

overall_design: RNA-sequencing was performed on 96 RNA samples isolated from mouse C2C12 myoblasts or myotubes acutely treated with a panel of small-molecule mitochondrial inhibitors. Some of the cells were expressing a suite of genetic tools for compartment-specific oxidation of the NADH/NAD+ ratio. Most of the experimental conditions were assayed and sequenced in triplicate.

first: Denis

middle: V

last: Titov

first: Owen

last: Skinner

first: Rohit

last: Sharma

first: Alexis

last: Jourdain

first: Vamsi

last: Mootha


title: Chromatin state maintains human myeloid leukemia by regulating m6A demethylase ALKBH5 expression [m6A-seq]

first: Jiazhen

last: Wang

overall_design: m6A-seq in wild-type or ALKBH5 knock-down, or ALKBH5 rescue THP1 cells

first: Yicun

last: Li

first: Peipei


title: Exaggerated BMP4 signalling alters human airway basal progenitor cell differentiation to cigarette smoking-related phenotypes [RNA-Seq]

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary:
Airway remodelling in chronic obstructive pulmonary disease (COPD) originates, in part, from smoking-induced changes in airway basal stem/progenitor cells (BCs). Based on the knowledge that bone morphogenetic protein 4 (BMP4) influences epithelial progenitor function in the developing and adult mouse lung, we hypothesised that BMP4 signalling may regulate the biology of adult human airway BCs relevant to COPD.
BMP4 signalling components in human airway epithelium were analysed at the mRNA and protein levels, and the differentiation of BCs was assessed using the BC expansion and air-liquid interface models in the absence/presence of BMP4, BMP receptor inhibitor and/or small interfering RNAs against BMP receptors and downstream signalling.

overall_design:
The study demonstrates that in cigarette smokers, BMP4 is up-regulated in ciliated and intermediate undifferentiated cells and BMP4 receptor BMPR1A is enriched in BC. In vitro, mediated by BMPR1A/Smad signaling, BMP4-induced BC to acquire a COPD-like abnormal phenotypes, characterized by decreased capacity to differentiate into the normal mucociliary epithelium, generating a hypoplastic squamous metaplasia. In summary, smoking-induced exaggerated BMP4 signaling promotes COPD-relevant airway epithelial remodeling by inducing abnormal phenotypes in human airway BC progenitor cells. Targeting of BMP4 signaling in airway BC may represent a novel approach to prevent/treat COPD-associated airway disease.
RNA-Seq profiling of 71 samples (large airway basal cells and large airway epithelium cells at various collection times from COPD smokers, smokers, and nonsmokers).

first: Wu-Lin

last: Zuo

first: Jing

last: Yang

first: Jacqueline

last: Salit

first: Mahboubeh

last: Rostami

first: Jason

last: Mezey

first: Sarah

last: O'Beirne

first: Robert

last: Kaner

first: Ronald

last: Crystal


title: Genome-wide map of RNA-Seq in fission yeast Schizosaccharomyces pombe

city: Winston Salem

first: David

last: de la Cerda

state: NC

address: 1834 Wake Forest Rd

department: Biology

institute: Wake Forest University

summary: RNA-Seq from 3 different strains of fission yeast Schizosaccharomyces pombe.

overall_design: Examination of RNA expression profiles in three different strains of Schizosaccharomyces pombe.

first: Ke

last: Zhang


title: Ribosome-bound lncRNAs between SW620 and SW480

city: Guangzhou

first: Guang-Rong

last: Yan

state: Guangdong

address: 63 Duobao Road

institute: Biomedicine Research Center, the Third Affiliated Hospital of Guangzhou Medical University

summary: The differential ribosome-bound lncRNAs between SW620 and SW480 were investigated by RNA-seq.

overall_design: The ribosome-bound mRNA and lncRNA expression profiles between SW620 and SW480 cell lines were generated by RNA-sequencing (RNA-seq), using an Illumina Hiseq 4000 platform.

first: Song

last: Zhu


title: ALKBH5 regulates AML development and LSC as an m6A eraser

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

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

overall_design: Refer to individual Series


title: Sequencing of mRNA in AML cells upon ALKBH5 knockdown

summary: To identify the potential mRNA targets of ALKBH5, we conducted RNA-seq of mRNA samples enriched from AML cells with ALKBH5 knockdown

overall_design: AML cells (herein is NOMO1 and MOLM13) were transduced  with lentivirus expressing shRNAs, then selected with puromycin for 4 days. Polyadenylated RNAs (poly(A) RNAs) were extracted with FastTrack MAG Maxi mRNA isolation kit (Life technology) and randomly fragmented with RNA fragmentation reagents (Ambion). Final library preparation was constructed with TruSeq Stranded mRNA Sample Prep Kit (Illumina) and the library was quantified by BioAnalyzer High Sensitivity DNA chip. The RNA-seq was conducted on the Illumina HiSeq 2500.

first: Chao

last: Shen

first: Lei

last: Dong


title: Sequencing of RNA fragments immunoprecipitated by anti-Flag in ALKBH5 overexpression NOMO1 cells

summary: To identify the direct mRNA targets of ALKBH5, we conducted RIP-seq with total RNA samples  from ALKBH5 overexpression NOMO1 cells

overall_design: AML cells (herein is NOMO1) were transduced  with lentivirus expressing ALKBH5 CDS with 3xFlag, then GFP positive cells were sorted out after puromycin selection. ALKBH5 overexpression cells were UV crosslinked then harvested for lysis. anti-Flag antibody (Sigma-Aldrich) was used to immunoprecipitate ALKBH5 protein binding RNAs. Immunoprecipitated samples were subjected to Proteinase K digestion (ThermoFisher). Total RNA was extracted from both input and immunoprecipitated RNA using TRIzol followed by Direct-zol RNA Miniprep (Zymo). RNA was then fragmented using the Bioruptor Pico sonication device. Libraries for high-throughput sequencing were constructed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), and were quantified by BioAnalyzer High Sensitivity DNA chip. RIP-seq libraries were sequenced on the Illumina HiSeq 4000 sequencing system.


title: Differential transcriptional networks in pneumonia and COPD exacerbation - the BioInflame study

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

summary:
PBMCs were isolated from patients suffering from Community Acquired Pneumonia (CAP) or acute exacerbating chronic obstructive pulmonary disease (AECOPD) or from healthy donors. RNA was extracted from these samples.
400 ng RNA per sample were then reverse transcribed with the Life Technologies miR RT kit with megaplex primers. Reverse transcribed RNA was then loaded on the human Taqman Low Density Array (TLDA) Cards and run according to manufacturer´s recommendations

overall_design: microRNA profiles were used to in silico build a biomarker network to discrimintate CAP and AECOPD


title: Transcriptomic analysis of hepatic genes in high-fat diet treated wild type and Sesn3 knockout mice

city: Indianapolis

first: Xiaocheng

middle: Charlie

state: IN

address: 635 Barnhill Drive, MS1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: RNA-seq was performed on mRNA samples purified from the liver of wild type (WT) and Sesn3 knockout (KO) mice.

overall_design: Two genotypes (WT and KO) were used for this study. Each genotype had three liver mRNA samples.


title: Lymphoma subpopulations in an Anaplastic Large Cell Lymphoma mouse model

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary:
To examine the existence of lymphoma initiating cells, we used an anaplastic large cell lymphoma mouse model. Established NPM-ALK+ lymphomas contained a heterogeneous cell composition ranging from mature T-cells to undifferentiated hematopoietic stem cells.
To investigate the underlying mechanisms and activated pathways of lymphoma initiating cells we used gene expression analyses. These analyses unmasked stem-cell-like transcriptional regulation exclusively of the DN3/DN4 lymphoma T-cell subpopulation.

overall_design: Single cell solutions of three murine lymphomas were sorted for different T-cell markers. Resulting lymphoma T-cell subpopulations were used for RNA extraction and hybridization on Affymetrix microarrays. Healthy LSK cells were used as controls.

first: Lena

last: Illert

first: Stefanie

last: Kreutmair

first: Melanie

last: Boerries


title: Epstein-Barr virus positive gastric cancer involves enhancer activation through ATF3

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: ATF3 binding sites on the genome and histone modification arround the ATF3 binding sites were analized by ChIP-seq. Regulation of gene expression by ATF3 on active enhacer regions were analyzed by knocked down of ATF3.

overall_design: Human gastric cancer cell lines MKN7 (MKN7_WT), Epstein-barr virus infected MKN7 (MKN7_EB), NCC24 and SNU719 were transfected ATF3 targeted or non-targeted shRNA lentivirus (shATF3 or shNON respectively) followed by drug selection with puromycin for 2 days. Total RNA was extracted after the drug selection for RNA-seq. MKN7_WT cells were treated with 30 micro mol/L of CDDP for 2 days to induce ATF3 followed by ChIP.

first: Yuta

last: Asakawa

first: Atsushi

last: Okabe

last: Kaneda


title: Sequencing of mRNA in AML cells upon ALKBH5 knockdown and actinomycin D treatment for different time

summary: To evaluate the effects of ALKBH5 KD on the mRNA stability, we conducted RNA-seq of mRNA samples enriched from AML cells with ALKBH5 knockdown and actinomycin D treatment for different time

overall_design: AML cells (herein is NOMO1) were transduced  with lentivirus expressing shRNAs and selected with puromycin for 4 days. The infected cells were then treated with actinomycin D for different time. Polyadenylated RNAs (poly(A) RNAs) were extracted with FastTrack MAG Maxi mRNA isolation kit (Life technology) and randomly fragmented with RNA fragmentation reagents (Ambion). Final library preparation was constructed with TruSeq Stranded mRNA Sample Prep Kit (Illumina) and the library was quantified by BioAnalyzer High Sensitivity DNA chip. The RNA-seq was conducted on the Illumina HiSeq 2500.


title: Comparative transcriptomic analysis of subcutaneous adipose tissue from local pig breeds

city: Évora

first: André

middle: Filipe Barreto

last: Albuquerque

address: Rua Ramalho Ortigao, 15

country: Portugal

institute: Universidade de Évora

summary: The aim of this work was to explore the genome function of AL and BI pig breeds to better understand the underlying physiological mechanisms associated with body fat accretion and lean muscle tissue deposition and therefore, meat quality of these breeds. Dorsal subcutaneous fat samples were collected at slaughter from adult AL and BI pigs (n=4 for each genotype) with ~150kg body weight. Total RNA was obtained and sequenced for transcriptome analysis and a bioinformatic analysis using the DESeq2 R package was implemented.  A total of 458 differentially expressed genes (q-value<0.05) were identified, with 263 found overexpressed in AL and 195 in BI, including 47 novel genes. Several key genes involved in de novo fatty acid biosynthesis, elongation and desaturation were consistently found upregulated in AL such as acly, fasn, me1, elovl6 and scd. A functional enrichment analysis of the candidate genes was performed using Ingenuity Pathway Analysis, which revealed GH signalling, HOTAIR regulatory pathway, AMPK and IGF-1 signalling among the top canonical pathways associated to the BI. Potential upstream regulators such as SCAP, MED1, SREBF2 and PPARG were found activated in AL, suggesting increased adipogenesis and cholesterol synthesis. Regulators found in the BI included INSIG1, INSIG2 and FOXO1 associated with lipogenesis inhibition, and MEF2C and PDGFB, related to myogenesis, cell proliferation and differentiation.

overall_design: Comparation of the transcriptomic data in adipose tissue of the two main Portuguese pig breeds

first: José

last: Martins


title: LOC90024-encoded small protein SRSP regulates mRNA splicing

summary: The mRNA transcriptome profiling and splicing profiling mediated by LOC90024 and LOC90024-encoded small protein SRSP were investigated by RNA-seq.

overall_design: The mRNA profiles and mRNA splicing profiles of colon cancer cells HCT-116 (NC), HCT-116 with stably expressing LOC90024 ORF for encoding small protein SRSP (ORF), and HCT-116 with stably expressing 5'UTR-ORFmut in which start code ATG for encoding SRSP was mutataed to ATT (MUT), were generated by RNA-sequencing (RNA-seq), in triplicate, using Illumina Novaseq6000.

last: Meng

first: Min


title: GCN2 adapts the proteome to scavenging-dependent growth

status: Public on May 25 2020

city: Princeton

first: Michel

last: Nofal

state: NJ

address: Washington Road

department: LSI

institute: Princeton University

summary: We report the transcriptional and translational changes that occur upon leucine deprivation +/- GCN2.

overall_design: KRPC-A cells (Gcn2 WT and KO) are switched to amino acid-replete or leucine-free medium for one hour, then cells were lysed and genetic material prepared for analysis


title: Analysis of gene expression upon deletion of Yap/Taz in the posterior palatal shelves prior to elevation in mouse

city: San Francisco

first: Alice

middle: Fitzgerald

last: Goodwin

address: 513 Parnassus Ave, HSE1506

department: Orofacial Sciences

institute: UCSF School of Dentistry

summary: The goal of this RNA-Sequencing experiment was to determine gene targets of Yap/Taz in the posterior palatal shelves prior to elevation at E14.5 in mouse.

overall_design: RNA extracted from the posterior palatal shelves of Yapfl/fl;Tazfl/fl control and Yapfl/fl;Tazfl/fl;Col2Cre mutant embryos at E14.5 was analyzed by RNA-Seq.


title: RNA-seq of intrahepatic Sox9EGFP populations

city: Atlanta

first: Adam

middle: D

last: Gracz

state: GA

address: 615 Michael St. NE

department: Medicine

institute: Emory University

summary: Cellular heterogeneity in the biliary epithelium is poorly understood, and genetic biomarkers for identifying distinct biliary epithelial cell (BEC) subpopulations are limited. Here, we utilized a Sox9EGFP transgene to study cellular heterogeneity in intrahepatic BECs. Male Sox9EGFP mice were fasted overnight, and livers were dissociated to obtain single cells. Gallbladders and extrahepatic ducts were excluded by dissection. Sox9EGFP populations were isolated by FACS into four distinct populations: GFPnegative, GFPsublow, GFPlow, and GFPhigh. We conducted RNA-seq and differential gene expression analysis to identify genes shared between and unique to each population.

overall_design: Differential expression analysis of 3 Sox9EGFP+ populations and Sox9EGFP- cells isolated from mouse liver

first: Jesse

middle: R

last: Raab