title: RNA SEQ N. gonorrhoeae strain WHO Z

city: Gold Coast

first: John

middle: Michael

last: Atack

state: QLD

address: Gold Coast Campus

department: Institute for Glycomics

country: Australia

institute: Griffith University

summary: comparison of RNA expression profiles from Neisseria gonorrhoeae strain WHO Z grown in presence of DMSO vs PBT2

overall_design: RNA isolated from triplicate cultures of Neisseria gonorrhoeae strain WHO Z grown in GC broth to mid-log, then addition of either DMSO or PBT2 and grown for further 16hrs; comparison of gene expression profiles post 16h growth by comparing DMSO grown cells vs PBT2 grown cells to determine differential gene expression influenced by presence of PBT2

first: Freda

last: Jen

middle: M

first: Michael

middle: P

last: Jennings


title: Transcription dynamics regulate poly(A) tails and expression of the RNA degradation machinery to balance mRNA levels

status: Public on Mar 10 2020

city: San Francisco

first: Binyamin

last: Zuckerman

state: California

country: USA

institute: UCSF

type: Expression profiling by high throughput sequencing

summary: To investigate the potential influence of transcription on mRNA stability in mammalian cells, we tested  the global relationship between rates of synthesis and decay of mRNAs. We estimated synthesis rates by flash 4sU labeling followed by RNA-seq, and decay rates by treating cells with Actinomycin D (ActD) for 0, 2, 4 and 6 hours and measuring half-lives of all expressed genes by MARS-seq analysis. As short-term perturbations of transcription elongation dynamics diminished mRNA stability, we next wished to examine the effect of extended transcription slowdown. To this end, we treated cells with CPT for 24 hours and profiled mRNA stability in a genome-wide manner using ActD time-course and MARS-seq.

overall_design: For synthesis rates estimation, 2 biological replicates were 4sU labeled in MCF7 cells. RNA was fragmented, biotinylated and 4sU-positive sequences were isolated using streptavidin beads. This RNA was rRNA-depleted and used for Lexogene library preparation without poly(A)-enrichment. For half life estimation, MCF7 cells were subjected to Actinomycin D (ActD) treatment for 0, 2, 4 and 6 hours. After isolation of RNA, external RNA was added as a spike to all samples. To examine effect of long CPT treatment, cells were pre-treated with 6 micromolar CPT for 24 hours, followed by the same ActD time-course.

first: Boris

last: Slobodin

first: Anat

last: Bahat

first: Urmila

last: Sehrawat

first: Igor

last: Ulitsky

first: Rivka

last: Dikstein


title: Dual RNA-seq analyses of porcine alveolar macrophage and Toxoplasma during infection process

status: Public on Mar 11 2020

city: Wuhan

first: Bang

last: Shen

address: No. 1 SHizishan St

country: China

institute: Huazhong Agricultural University

summary:
Purpose:This study was aimed to profile the transcriptome changes during Toxoplasma infection with porcine alveolar macrophages. for this purpose, Porcine alveolar macrophages (PAMs,3D4/21) were infected by Toxoplasma Me49 strain in vitro. The transcriptome changes were captured by dual RNA-seq analyses.
Methods: Transcriptomic profiles of infection samples (Me49 infected PAMs) and controls (Me49 and PAMs, respectively) were generated by deep sequencing, in triplicate, using Illumina HiseqPE150. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat (v2.0.12) followed by HTSeq (v0.6.1). The Cufflinks (v2.1.1) was used to construct and identify novel transcripts. qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, More than 30 million paired-end reads were generated for the Me49 controls and 93% of the clean reads were mapped to the Me49 reference genome. Nearly 2~3 times more reads were produced in the PAMs alone or infected PAMs samples. Among these, 60% to 80% of clean reads were mapped to the Sus Scrofa genome. In the infection groups, approximately 16% of total clean reads were aligned to the Me49 reference genome. RNA-seq data indicated the remarkable transcripts changes of both sides during infection process. More than 800 and 1800 genes (fold change ≥2 and adjusted p value <0.05) were significantly regulated in PAMS and Me49, respectively. Altered expression of 15 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. The differentially expressed genes in Toxoplasma were mainly related to metabolic process and macromolecule synthesis as reflected by enhanced activity of FASII pathway. Further analyses of differentially expressed genes in PAMs uncovered unique responses of porcine macrophages to Toxoplasma infection. These analyses provide novel insights into Toxoplasma interaction with it’s hosts.
Conclusions: Our study represents the first detailed dual analyses of porcine alveolar macrophages and Me49 with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here provide the overall transcripts changes both PAMs and Me49. The results showed the unexpected responses of PAMs to Toxoplasma infection. These widen our understanding of interactions between Toxoplasma and it’s hosts.

sample_organism:
Toxoplasma gondii
Sus scrofa

platform_organism:
Toxoplasma gondii
Sus scrofa

overall_design: Dual transcript profiles of porcine alveolar macrophages and Toxoplasma were generated by deep sequencing, in triplicate, using Illumina HiseqPE150.

first: Jianmin

last: Cui


title: Single-cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2-deficient vascular progenitors into skeletal muscle

city: Cincinnati

first: Saulius

last: Sumanas

state: Ohio

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: During vertebrate embryogenesis, vascular endothelial cells originate in the lateral plate mesoderm (LPM) next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line, in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly, a cell population with the skeletal muscle signature was observed in etv2-deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites, elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2-deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors, thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally, we demonstrate that arterial progenitors co-express multiple arterial and venous markers during early stages of vasculogenesis, suggesting multi-potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular, muscle and other types of progenitors for therapeutic purposes.

overall_design: 96 cells 48 cells each

first: Andrew

last: Koenig


title: Gene expression profile of liver tissue in low-dose, repeated diethylnitrosamine (DEN)-treated rat treated with epigallocatechin gallate (EGCG)

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Background: Hepatocellular carcinoma (HCC) is increasing in incidence and treatment is often unsuccessful. Thus, prevention in high-risk patients with established cirrhosis has been proposed as an alternative strategy. It has been suggested that the increased inflammation and fibrogenesis observed during cirrhosis predisposes the liver to future malignant transformation to HCC through a “field effect”. A growing body of evidence indicates that the green tea polyphenol, (-)-epigallocatechin gallate (EGCG), can reduce inflammation and fibrogenesis during chronic liver injury. Here, we test the hypothesis that EGCG administered in the setting of cirrhosis can prevent future HCC development. Methods: A rat model of diethylnitrosamine (DEN)-induced cirrhosis was used to examine the efficacy of EGCG for inhibition of HCC formation in these cirrhotic livers. DEN (50 mg/kg) was administered weekly throughout the study while 0.02% EGCG was given in drinking water beginning at the onset of cirrhosis. At the end of the study, rats were sacrificed, livers were sectioned and stained to analyze disease progression and tumor nodules were counted. Liver function tests were performed to determine liver injury and overall liver function. Finally, genome-wide gene expression profiling on the surrounding, non-tumoral liver tissue was used to monitor the “field effect” in response to EGCG. Results: EGCG significantly (p < 0.01) prevented the development of HCC tumor nodules from on average 18.8 in vehicle controls to on average 9.1 in EGCG-treated animals. EGCG also reduced liver injury and improved liver function as assessed by serum chemistry tests. Finally, a gene expression signature predictive of poor survival and HCC development in human cirrhosis patients was reversed in response to EGCG. Conclusions: Our data are consistent with the growing body of evidence suggesting that EGCG has protective effects in liver disease. Further, our results suggest that EGCG is a potentially effective HCC prevention strategy that can be monitored using gene expression signatures.

overall_design: Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg for 18 weeks. A subset of rats received either daily (5X a week) 0.02% EGCG in drinking water (n=3) or water (n=3) during weeks 13-18. Animals were sacrificed at 19 weeks after a one-week washout period to eliminate acute effects of DEN. At the time of sacrifice, the non-tumor liver tissues were collected in RNase-free tubes and snap-frozen in liquid nitrogen. Frozen tissues were stored at -80°C until RNA extraction.

first: Suguru

last: Yamada

first: Lan

last: Wei

first: Bryan

last: Fuchs


title: Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing [fCLIP-seq]

status: Public on Mar 09 2020

city: Daejeon

first: Young-suk

last: Lee

address: 1113 CMS(E16), 291 Daehak-ro, Yuseong-gu,

department: Department of Bio and Brain Engineering

country: South Korea

institute: KAIST

summary: TENT4 enzymes generate “mixed tails” on mRNAs by adding adenosines with intermittent non-adenosine residues, which protect mRNAs from deadenylation. Here we discover the extensive mixed tailing in the transcripts of two distinct DNA viruses, hepatitis B virus (HBV) and human cytomegalovirus (HCMV), and their striking similarity in the mechanism to exploit the TENT4-ZCCHC14 complex. TAIL-seq analyses of HBV and HCMV RNAs revealed that TENT4A and TENT4B are responsible for the mixed tailing and protection of viral poly(A) tails. By fCLIP-seq on HBV-producing cells, we found that the HBV posttranscriptional regulatory element (PRE) is the primary site of the TENT4 interactome. A hairpin with a CNGGN-type pentaloop in the PRE is critical for TENT4-dependent regulation. Unexpectedly, HCMV also utilizes a similar pentaloop hairpin, an interesting example of convergent evolution. We further found that the CNGGN pentaloop is recognized by the SAM domain-containing ZCCHC14 protein which in turn recruits TENT4 to stabilize viral transcripts. Altogether, our study reveals the action mechanism of PRE that has been widely used to enhance gene expression, and introduces the TENT4-ZCCHC14 complex as the key host factor and a potential target for antiviral therapeutics.

overall_design: fCLIP-seq of total RNA in HepG2.2.15 cell line

first: Dongwan

last: Kim

first: Soo-Jin

last: Jung

first: Jinah

last: Yeo

first: V

middle: N


title: Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing

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

overall_design: Refer to individual Series


title: Hematopoietic stem cell-restricted Cdx2 expression induces transformation to myelodysplasia and acute leukemia [Chip-Seq]

city: Brisbane

first: Jasmin

last: Straube

address: 300 Herston Rd

institute: QIMR Berghofer

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The caudal-related homeobox transcription factor CDX2 is ectopically expressed in the majority of patients with acute myeloid leukemia (AML). We generated an inducible transgenic mouse model whereby Cdx2 was specifically activated in HSCs. Cdx2 mice developed myelodysplastic syndrome (MDS) with progression to acute leukemia associated with stepwise acquisition of additional driver mutations.

overall_design: Cdx2 DNA binding using ChIPSeq of lineage depleted bone marrow infected with retrovirus with flagged Cdx2 construct or empty vector (EV).

first: Leanne

last: Cooper

first: Steven

middle: W

last: Lane

first: Megan

last: Bywater


title: Long-Term Gene Expression Dynamics at the Neurovascular Unit After Cerebral Ischemia/Reperfusion Injury in Mice

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: With increasing distribution of endovascular stroke therapies, transient middle cerebral artery occlusion in mice depicts a relevant patient population with recanalized M1 occlusion. This study provides a well-controlled transcriptome dataset of short and long-term transcriptomic changes at the neurovascular unit in cerebral ischemia/reperfusion injury.

overall_design: After transient middle cerebral artery occlusion for 60 minutes or sham surgery, male C57Bl/6J mice were treated according to a new post-stroke care protocol to increase survival. At 24 hours or 7 days after stroke onset, RNA from microvessel fragments was isolated and used for mRNA sequencing by DFKZ genomics and proteomics.

first: Roxane-I

last: Kestner

first: Franziska

last: Mayser

first: Rajkumar

last: Vutukuri

first: Lena

last: Hansen

first: Robert

last: Brunkhorst

first: Kavi

last: Devraj

first: Waltraud

last: Pfeilschifter


title: Expression data from brain-regions of mice in varying CIE and drinking states

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

summary:
Persistent changes in brain gene expression are hypothesized to underlie thealtered neural signaling producing abusive consumption in AUD. To identify brain regional gene expression networks contributing to progressive ethanol consumption, we performed microarray and scale-free network analysis of expression responses in a C57BL/6J mouse model utilizing chronic intermittent ethanol by vapor chamber (CIE) in combination with limited access oral ethanol consumption.
The interaction of CIE and oral consumption was studied with Affymetrix microarrays. Gene expression was studied in medial prefrontal cortex, nucleus accumbens, hippocampus, bed nucleus of the stria terminalis, and central nucleus of the amygdala. Brain region expression networks were analyzed for ethanol-responsive gene expression, correlation with ethanol consumption and functional content using extensive bioinformatics studies.

overall_design: Male C57BL6/J mice were selected for chronic intermittent ethanol (CIE) delivered by vapor chamber with limited access ethanol drinking. Mice were divided into four groups: CIE with limited access drinking, CIE without limited access drinking, air by vapor chamber with limited access drinking, air by vapor chamber without limited access drinking. After four cycles of CIE and drinking, mice were sacrifice and five brain regions (medial prefrontal cortex, nucleus accumbens, hippocampus, central nucleus of the amygdala, and bed nucleus of the stria terminals) were harvested for RNA extraction and and hybridization on Affymetrix microarrays.

middle: F

first: Maren

middle: L

last: Smith

first: Howard

middle: C

last: Becker

first: Marcelo

last: Lopez

first: Aaron

middle: R

last: Wolen


title: Viral hijacking of the TENT4-ZCCHC14 complex protects viral RNAs via mixed tailing [TAIL-seq]

first: Young-suk

last: Lee

overall_design: HepG2.2.15 cells and HFF cells were knocked down of control or TENT4

first: Dongwan

last: Kim

first: Soo-Jin

last: Jung

first: Jinah

last: Yeo

first: V


title: Seminal plasma promotes decidualization of endometrial stromal fibroblasts from women with and without inflammatory disorders in a manner dependent on IL11 signaling

first: Nadia

last: Roan

address: 1650 Owens Street

institute: University of California at San Francisco

summary: SP promotes decidualization of eSF from women with and without inflammatory disorders (polycystic ovarian syndrome (PCOS), endometriosis) in a manner that is not mediated through semen amyloids and that is associated with a potent transcriptional response including induction of IL11, a cytokine important for SP-induced decidualization.

overall_design: This is a cross-sectional study involving samples treated with vehicle alone versus treatment with SP or SP constituents. SP was tested for the ability to promote decidualization in eSF from women with or without PCOS or endometriosis (n=9). The role of semen amyloids and fractionated SP in mediating this effect and in eliciting transcriptional changes in eSF was then studied. Finally, the role of IL11, a cytokine with a key role in implantation and decidualization, was assessed for its role in SP-facilitated decidualization.

first: Ashley

last: George

first: Karen

middle: S

last: Jang

first: Mette

last: Nyegaard

first: Jason

last: Neidleman

first: Trimble

last: Spitzer

first: Guorui

last: Xie

first: Joseph

last: Chen

first: Eytan

last: Herzig

first: Anders

last: Laustsen

first: Erika

middle: G

last: Marques de Menezes

first: Sahar

last: Houshdaran

first: Christopher

middle: D

last: Pilcher

first: Philip

middle: J

last: Norris

first: Martin

last: Jakobsen

first: Warner

last: Greene

first: Linda

last: Giudice


title: RNA memories: trans-generational epigenetic inheritance of RNA-mediated gene silencing

city: cambridge

first: Eric

last: Miska

address: tennis court road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

type: Non-coding RNA profiling by high throughput sequencing

summary: Trans-generational epigenetic inheritance (TEI), which functionally intersects RNA with histone modification, recently forced a reinterpretation of the interplay between gene expression and selective pressures. Our groups integrate genetic, genomic, dynamic imaging, biochemistry and proteomic technologies to provide a functional mechanistic understanding of the interplay of TEI and the RNA interference (RNAi) phenomena in the nematode C. elegans. We discovered a family of proteins (the nuclear Argonaute-interacting proteins or NIPs), which controls the strength, inheritance and gene target specificity of nuclear RNAi. Loss of NIP-1 and NIP-2 in the soma leads to an enhancement of nuclear RNAi activities without affecting cytoplasmic RNAi. Loss of NIP-3 in the germline disables TEI and leads to a profoundly impaired response to transposable genomic elements (viral-like sequences). The genome of nip-3 mutants becomes de-stabilized; spontaneous visible mutations arise at high frequency due to an unbridled mobilization of a subset of transposable elements. Surprisingly, silencing of a distinct subset of transposable elements is coincidentally enhanced. Finally, expression imaging revealed an eminent role for the maturing male germline in TEI. This data supports a model wherein NIPs determine the potency and stability of TEI by gating and sorting small RNAs (which provide specificity) towards germline and somatic nuclear RNAi and epigenetic machineries. Our work further implies that this  molecular machinery evolved to atone an animal’s epigenetic memory to preserve a species’ integrity in face of genetic pathogens.

overall_design: Examination of three novel candidates in transgenerational epigenetic inheritance in the nematode C. elegans.

first: Thomas

last: Duchaine

middle: A

first: Mihail

last: Sarov


title: Activin-A limits Th17 pathogenicity and autoimmune neuroinflammation via CD39 and CD73 ectonucleotidases and Hif1-α -dependent pathways

status: Public on Mar 06 2020

city: Athens

first: Anastasia

last: Kotanidou

address: 45 Ipsilantou Str

department: 1st Department of Critical Care Medicine and Pulmonary Services

country: Greece

institute: Evangelismos Hospital, National and Kapodistrian University of Athens

summary: In multiple sclerosis (MS), Th17 cells are critical drivers of autoimmune central nervous system (CNS) inflammation and demyelination. Th17 cells exhibit functional heterogeneity fostering both pathogenic and non-pathogenic, tissue-protective functions. Still, the factors that control Th17 pathogenicity remain incompletely defined. Here, using experimental autoimmune encephalomyelitis (EAE), an established mouse MS model, we report that therapeutic administration of activin-A ameliorates disease severity and alleviates CNS immunopathology and demyelination, associated with decreased activation of Th17 cells. In fact, activin-A signaling through activin-like kinase (ALK)4 receptor represses pathogenic transcriptional programs in Th17-polarized cells, while it enhances anti-inflammatory gene modules. Whole genome profiling and in vivo functional studies revealed that activation of the ATP-depleting CD39 and CD73 ectonucleotidases is essential for activin-A-induced suppression of the pathogenic signature and the encephalitogenic functions of Th17 cells. Mechanistically, aryl hydrocarbon receptor, along with STAT3 and c-Maf, are recruited to promoter elements on Entpd1 and Nt5e (encoding CD39 and CD73, respectively) and other anti-inflammatory genes, and control their expression in Th17 cells in response to activin-A. Notably, we show that activin-A negatively regulates the metabolic sensor, hypoxia-inducible factor-1 and key inflammatory proteins linked to pathogenic Th17 cell states. Of translational relevance, we demonstrate that activin-A is induced in the CNS of individuals with MS and restrains human Th17 cell responses. These findings uncover activin-A as a novel critical controller of Th17 cell pathogenicity that can be targeted for the suppression of autoimmune CNS inflammation.

overall_design: RNA-sequencing libraries were generated for Th17 or act-A-Th17 cells using the Illumina’s TruSeq RNA Library Preparation Kit v2 and the sequencing was implemented with HiSeq 2000 by the European Molecular Biology Laboratory.

first: Georgina

last: Xanthou

first: Dimitris

last: Konstantopoulos


title: Raptor is required for β-cell metabolic coupling and repressing an α cell program before onset of hyperglycemia

status: Public on Mar 05 2020

city: Shanghai

first: Qinglei

last: Yin

address: Ruijin Second Road No.197

institute: Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary:
Raptor deficient mice showed diabetic phenotype, to dissect the effect of hyperglycemia, we isolated euglycemic 2-week-old β cells to perform microarray.
To determine the influence of Raptor deficiency on β cells independent of hyperglycemia, we hace employed whole transcriptome expression profiling as a discovery platform to identify differentially expressed genes compared with wild type controls.
We isolated mice islets, then disgested them into single cells by 0.25% EDTA,  and sorted for GFP by FACS.

overall_design: Raptor regulated gene expression in β cells from knockout mice was measured at 2 weeks after birth. Age-matched wild type mice were set as controls.

first: Qidi

last: Wang

first: Guang

last: Ning


title: High throughput RNA sequencing of hepatocellular carcinoma and pre tumor samples from Tdg fl/-; UBC-cre/ERT2+ mice livers and their age/sex matched Tdg fl/fl controls livers

city: London

first: Haider

middle: Muhammad

last: Hassan

state: Ontario

address: 800 Commissioners Road

department: Biochemistry and Oncology

country: Canada

institute: Western University

summary: We isolated whole livers from male TDG knockout livers (4-month post tamoxifen injection) and HCC, along with their age matched male control livers. RNA was extracted from the  samples as per RNAzol manufacturer guidelines with DNase treatment. RNA was then analyzed by bioanalyzer and subjected to sequencing using the Illumina NextSeq 500 platform.

overall_design: High throughput transcriptomic analysis of HCC and pre tumor livers from TDG knockout mice and their age/sex matched controls. The pre-tumor samples were isolated from mice that were aged 4-months post tamoxifen. The livers and HCC samples were kept in RNAzol and at -80 degrees celsius until the RNA extraction. RNA was extracted from the liver samples as per RNAzol manufacturer guidelines. Only the male mice livers were sequened. After the RNA sequencing was performed, the gene lists were generated using cufflinks. The p-value and FDR/q-value cutoff of 0.05 was used for downstream analysis. Fold change cutoff of 1.5 was used for gene overlaps. Pathway analysis of the overlapping genelists was performed using the KEGG and REACTOME databases.


title: Assessment of DNA methylation patterns in chimpanzee skeletal tissues

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

summary: The aim of this study was to characterize the genome-wide DNA methylation profiles of chimpanzee trabecular bone samples (n=4), identify how they relate to aspects of femur bone morphology, and assess how these epigenetic patterns relate to those in other primate taxa. The Illumina Infinium MethylationEPIC array was used to assess genome-wide methylation patterns.

overall_design: Bisulphite converted DNA from the 4 chimpanzee bone samples were hybridized to the Illumina Infinium MethylationEPIC array.


title: A Network of Sputum MicroRNAs is Associated with Neutrophilic Airway Inflammation in Asthma

status: Public on Mar 04 2020

city: New Haven

first: Jose

middle: Luis

last: Gomez

state: CT

address: 300 Cedar Street

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University

summary:
Background: MicroRNAs are potent regulators of biologic systems that are critical to tissue homeostasis.  Individual microRNAs have been identified in airway samples. However, a systems analysis of the microRNA-mRNA networks present in the sputum that contribute to airway inflammation in asthma has not been published.

Methods: We conducted a genome-wide analysis of microRNA and messenger RNA (mRNA) in the sputum from patients with asthma and correlated expression with clinical phenotypes. Weighted gene correlation network analysis (WGCNA) was implemented to identify microRNA networks (modules) that significantly correlate with clinical features of asthma and mRNA expression networks. MicroRNA expression in peripheral blood neutrophils and lymphocytes, and in situ hybridization of the sputum were used to identify the cellular sources of microRNAs. MicroRNA expression obtained before and after ozone exposure was also used to identify changes associated with neutrophil counts in the airway.

Results: Six microRNA modules were associated with clinical features of asthma. A single module (nely) was associated with a history of hospitalizations, lung function impairment, and numbers of neutrophils and lymphocytes in the sputum. Of the 12 microRNAs in the nely module, hsa-miR-223-3p was the highest expressed microRNA in neutrophils and was associated with increased neutrophil counts in the sputum in response to ozone exposure. Multiple microRNAs in the nely module correlated with two mRNA modules enriched for toll-like receptor (TLR) and Th17 signaling, and endoplasmic reticulum stress. Hsa-miR-223-3p was a key regulator of the TLR and Th17 pathways in the sputum of subjects with asthma.

Conclusions: This study of sputum microRNA and mRNA expression from patients with asthma demonstrates the existence of microRNA networks and genes that are associated with features of asthma severity. Among these, hsa-miR-223-3p, a neutrophil-derived microRNA, regulates TLR/Th17 signaling and endoplasmic reticulum stress.

overall_design: Cohort, Cases and controls. Sputum induction.

last: Gomez-Villalobos


title: RNA sequencing of trastuzumab plus pertuzumab-refractory tumor in a mouse xenograft model

city: Tsukuba

first: Hiroki

last: Irie

state: Ibaraki

address: Okubo 3

country: Japan

institute: Taiho Pharmaceutical Co., Ltd.

summary: We report RNA sequencing data of trastuzumab plus pertuzumab-refractory  tumor in a mouse xenograft model.

overall_design: mRNA profiles of trastuzumab plus pertuzumab-refractory NCI-N87 tumor in a mouse xenograft model and the non-treated NCI-N87 tumor in a mouse xenograft tumor

first: Hiraku

last: Itadani

first: Rumi

last: Kawabata


title: RNA sequencing of T-DM1-refractory tumor in a mouse xenograft model

summary: We report RNA sequencing data of T-DM1-refractory  tumor in a mouse xenograft model.

overall_design: mRNA profiles of T-DM1-refractory NCI-N87 tumor in a mouse xenograft model and the non-treated NCI-N87 tumor in a mouse xenograft tumor

first: Yayoi

last: Fujioka


title: Reduced Type I Interferon response signature detected in dendritic cells from prediabetic NOD mice compared to C57BL/6.g7 and Rag KO

city: Bethesda

first: Kristin

middle: V

last: Tarbell

state: MD

address: 10 Center Dr, Bldg 10 5-5832

department: Diabetes, Endocrinology, and Obesity Branch

institute: NIH/NIDDK


title: Genome-wide analysis of gene expression response to type II ribosome inactivating protein stenodactylin

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

summary: Time-series analysis of response to ribosome 28s damage at gene expression level

overall_design: Total RNA obtained from MOLM-13 cells treated with stenodactylin for 2,4, and 6 hours compared to untreated control

first: Massimo

last: Bortolotti

first: Vibeke

last: Andresen

first: André

last: Sulen

first: Letizia

last: Polito

first: Bjørn Tore

last: Gjertsen

first: Andrea

last: Bolognesi


title: Single-cell transcriptomes reveal a complex cellular landscape in the middle ear and differential capacities for acute response to infection gene expression by cell types in the middle ear

city: La Jolla

first: Chanond

last: Nasamran

state: CA

department: Center for Computational Biology and Bioinformatics

institute: University of California San Diego

summary: Single-cell transcriptomics were used to identify cells in the normal middle ear mucosa, to identify their differentially expressed genes, and to determine cell-type-specific expression of genes related to innate immunity .

overall_design: Three independent samples of pooled murine middle ear mucosa were used to generate 6370 cell transcriptomes, which were analyzed for cell marker, differential and innate immune gene expression.

first: Allen

last: Ryan


title: Enhancing WNT-Signaling Restores Cortical Neuronal Spine Maturation and Synaptogenesis in Tbr1 Mutants

city: San Francisco

first: Siavash

last: Fazel Darbandi

address: 1550 4th Street

department: Psychiatry

institute: University of California San Francisco

summary:
Tbr1 is a high confidence autism spectrum disorder (ASD) gene encoding a
transcription factor with distinct pre- and postnatal functions.
Postnatally, Tbr1 conditional mutants (CKOs) and constitutive heterozygotes have
immature dendritic spines and reduced synaptic density. Tbr1 regulates expression of
several genes that underlie synaptic defects, including a kinesin (Kif1a) and a WNT
signaling ligand (Wnt7b). Furthermore, Tbr1 mutant corticothalamic neurons have
reduced thalamic axonal arborization. LiCl and a GSK3b-inhibitor, two WNT-signaling
agonists, robustly rescue the dendritic spines, synaptic and axonal defects, suggesting
that this could have relevance for therapeutic approaches in some forms of ASD.

overall_design: Examination of TBR1 regulated genes in layer 5 FACS purified neurons from P5 mouse medial prefrontal cortex.

last: Darbandi

first: John

last: Rubenstein


title: Vaccine-induced tissue resident memory T cells and antibodies synergize to prevent mucosal HIV infection [CITE-seq]

city: Stanford

first: Madeleine

last: Scott

address: 729 Lagunita Dr

institute: Stanford

summary: This study measures single cell RNA and protein expression in Gag stimulated and non-stimulated vaginal tissue from four SIV-protected rhesus macaques.

overall_design: Vaginal tissue from four SIV-protected macaques was profiled by CITE-seq.

middle: K

first: Prabhu

last: Arunachalam


title: TAp63-regulated microRNAs suppress cutaneous squamous cell carcinoma

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

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

overall_design: Refer to individual Series


title: TAp63-regulated microRNAs suppress cutaneous squamous cell carcinoma [RNA-seq]

summary:
The goal of this study is to compare the differences in the global mRNA expression of WT and TAp63-/- skin and SCC
TAp63 is a p53 family member and potent tumor and metastasis suppressor. Here, we show that TAp63-/- mice exhibit an increased susceptibility to UVR- induced cutaneous squamous cell carcinoma (cuSCC). A human-to-mouse comparison of cuSCC tumors identified miR-30c-2* and miR-497 as underexpressed in TAp63-deficient cuSCC. Reintroduction of these microRNAs significantly inhibited the growth of cuSCC cell lines and tumors. Proteomic profiling of cells expressing either microRNA showed downregulation of cell cycle progression and mitosis associated proteins. A mouse to human and cross- platform comparison of RNA-Seq and proteomics data identified a 7-gene signature, including AURKA, KIF18B, PKMYT1, and ORC1, which were overexpressed in cuSCC. Knockdown of these factors in cuSCC cell lines suppressed tumor cell proliferation and induced apoptosis. Additionally, selective inhibition of AURKA suppressed cuSCC cell proliferation, induced apoptosis, and showed anti-tumor effects in vivo. Finally, treatment with miR-30c-2* or miR-497 microRNA mimics was highly effective in suppressing cuSCC growth in vivo. Our data establishes TAp63 as an essential regulator of novel microRNAs that can be therapeutically targeted for potent suppression of cuSCC.

overall_design: We performed a RNA-Seq analysis comparing the transcriptomes of WT skin (n=3), TAp63-/- skin (n=3), WT SCC (n=2), and TAp63-/- cSCC (n=4)

first: Andrew

last: Davis


title: Linking Phospho-Gonadotropin Regulated Testicular RNA Helicase (GRTH/DDX25) to Histone Ubiquitination and Acetylation Essential for Spermatid Development During Spermiogenesis

first: Raghuveer

last: Kavarthapu

address: 10 Center Dr, Bldg 10, Room 1E3340

department: NICHD

institute: National Institutes of Health (NIH)

summary: In this study, we examined genome-wide transcriptome profiles of germ cells isolated from GRTH Knock-In and WT mice testis using RNA-Seq. We used homozygous KI mice with R242H mutation in GRTH gene resulting loss of phospho-GRTH to further understand its role in spermatid development during spermiogenesis by analyzing the DEGs from RNA-Seq. The analysis of RNA-Seq data allowed us to find the relevant DEGs related to ubiquitination pathway that are essential for spermatid development. This study using KI mice model demonstrated that loss of phospho-GRTH impairs UBE2J1 and RNF8 dependent histone modifications hampering initial stages of spermatid elongation process.

overall_design: Transcriptome profiles of germ cells isolated from 5 WT and 5 GRTH-Knock-In mice were obtained using Illumina RNA-Seq for differential gene expression analysis.

first: Rajakumar

last: Anbazhagan

first: Ashish

last: Sharma

first: Joseph

last: Shiloach

first: Maria

last: Dufau


title: An Ancient COI1-independent Function for Reactive Electrophilic Oxylipins in Thermotolerance [array]

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: Seeds of the double mutant opr3-3 coi1-1 were germinated in Johnson media supplemented with 0.5 µM coronatine, to select homozygous coi1-1 plants, at 21°C under long-day conditions (16-h light/8-h dark)

overall_design: Transcriptomic profile of opr3-3 coi1-1 double mutant in response to OPDA

first: Isabel

last: Monte

first: Sophie

last: Kneeshaw

first: Jose

middle: M

last: Chini

first: Angel

last: Zamarreño

last: García-Mina

first: Roberto

last: Solano


title: An Ancient COI1-independent Function for Reactive Electrophilic Oxylipins in Thermotolerance [seq]

summary: Algal discs were  transferred to a 12-well plate containing 2 ml liquid 0.5 Gamborg’s B5 mock or OPDA 25 µM, incubated for 2 hours on a shaker (120 rpm) and then the algae were frozen in liquid nitrogen and ground to a fine powder.

overall_design: 3 replicates for mock and OPDA-treated samples

first: Andrea


title: An Ancient COI1-independent Function for Reactive Electrophilic Oxylipins in Thermotolerance

sample_organism:
Arabidopsis thaliana
Klebsormidium nitens


title: Transcriptome profiling of purified red blood cells from Nxf1 mutant and control mice [Erythrocytes]

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

summary:
Purpose: Nxf1 is thought to be an essential nuclear exporter of messenger RNA (mRNA) in eukaryotic cells. Whether perturbations in the Nxf1 pathway affect mammalian physiology is not known. The aim of this study is to determine the impact of a Nxf1 mutation in the representation of mRNA transcripts in erythrocytes.
Methods: Red blood cells were obtained from cardiac puncture, mixed with 100µl Aster Jandl citrate-based anticoagulant and subsequently diluted in 2 ml of phosphate buffer saline (PBS) with 2mM EDTA. This suspension was layered with 1.5 ml Ficoll-paque PLUS (GE Healthcare) and centrifuged at 400g for 30 minutes at room temperature with minimal acceleration and brake. The red blood cell containing pellet was washed twice with PBS 2mM EDTA and lysed for RNA extraction. The purity of each sample was checked by flow cytometry to assess the relative contamination of Ter199+ red blood cells  with CD41+ platelets, CD45+ lymphocytes and DRAQ5+ (Thermo Fisher Scientific) nucleated cells. Red blood cell suspensions used for RNAseq were > 99.8% pure. RNA was extracted with Qiagen RNA extraction kit.

overall_design: Erythrocytes were purified from individual Nxf1 mutant males (n=3) and three individual littermate wild-type controls (n=3).

middle: E

first: Stephane

last: Chappaz

first: Benjamin

middle: T

last: Kile


title: Transcriptome profiling of blood cells from Nxf1 mutant and control mice


title: Transcriptome profiling of purified mouse platelets from Nxf1 mutant and control mice [Platelet]

summary:
Purpose: Nxf1 is thought to be an essential nuclear exporter of messenger RNA (mRNA) in eukaryotic cells. Whether perturbations in the Nxf1 pathway affect mammalian physiology is not known. The aim of this study is to determine the impact of a Nxf1 mutation in the representation of mRNA transcripts in platelets.
Methods: Platelets were purified from individual males. Blood was obtained by cardiac puncture into 0.1 volume of Aster Jandl citrate-based anticoagulant. Mouse platelet rich fraction was obtained by centrifugation of the murine blood at 125 g for 8 min at room temperature, followed by centrifugation of the supernatant buffy coat at 125 g for 8 min. Mouse platelets were washed by two sequential centrifugations at 860 g for 5 min in 140 mM NaCl, 5 mM KCl, 12 mM trisodium citrate, 10 mM glucose, and 12.5 mM sucrose, pH 6.0.The platelet pellet was resuspended in 10 mM Hepes, 140 Mm NaCl, 3 mM KCl, 0.5 mM MgCl2, 10 mM glucose, and 0.5 mM NaHCO3, pH 7.4.  The purity of each platelet suspension was assessed by flow cytometry and suspensions for which more than 98% of total events were CD41+ platelets were pooled together.  RNA was purified with Norgen cytoplasmic and nuclear fractionation RNA purification kit.

overall_design:
Platelets were purified from individual Nxf1 mutant males (littermate controls are available from GEO accession GSE75896). The purity of each suspension was assessed by flow cytometry.  Suspensions of identical genotype for which more than 98% of total events were CD41+ platelets were pooled together. Pooled platelet preparations from mutant (this study) and wild-type littermate controls (GSE75896) were prepared on 3 distinct days.

The GSM4196370-GSM4196372 sample records are duplicated sample records of GSM1969530-GSM1969532 (in GSE75896) for the convenient retrieval of the complete raw data from SRA.


title: miR-206 knockout shows it is critical for myogenesis and directly regulates newly identified target mRNAs

city: Boulder

first: Jennifer

last: Kugel

address: 3415 Colorado Ave

institute: University of Colorado Boulder

summary: The goal of this study was to identify miR-206 regulated mRNA targets in differentiating C2C12 cells

overall_design: RNA-Seq after pull-down with a miR-206 antisese oligo from C2C12 cells under two conditions: undifferentiated (Day 0) and day 4 differentiatied (Day 4)

first: Georgiana

last: Salant

first: Kimngan

last: Tat

first: James

last: Goodrich

middle: F


title: Expression data from Sprague Dawley rat lenses cultured for 4 days - addition of various inhibitors

city: Fukui-shi

first: Fumito

last: Kanada

address: 3-9-1 Bunkyo

institute: Fukui univercity

summary: We created a rat sugar cataract model and examined the effects of various inhibitors on lens clouding. Lenses were removed from 6-week-old SD rats and cultured in M199 medium containing 30 mM galactose.

overall_design: All lens samples were compared to galactose. First, we extracted a group of genes significantly reduced in the Ctrl and C646, and a group of genes significantly.  increased in the TSA. Next we compared genes that had more than doubled variation in any of the non-TSA samples

first: Yoshihiro

last: Takamura

first: Seiji

last: Miyake

first: Kazuma

last: Kamata

first: Mayumi

last: Inammi

first: Masaru

last: Inatani

first: Masaya

last: Oki


title: Naloxone influences NSCs proliferation and differentiation

city: Guangzhou

first: Lining

last: Liang

address: 190,Kaiyuan Ave.

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences

summary: Naloxone is an opioid-receptor antagonist used to reverse the effects of opioid.In our study, we treated NSCs (neural stem cells) with naloxone and damgo (a selective μopioid receptor agonist), and examined their effects on NSCs proliferation and differentiation.Naloxone was found to promote NSCs  proliferation and  neural differentiation, while the effects of damgo was very week. The results suggested that naloxone may work indepedent of opioid receptors. To investigate the underlying mechanisms, RNA-seq was conducted. For proliferation analysis,p8 NSCs were cultured with or without naloxone or damgo for 3 days. For differentiation analysis,p8 NSCs was induced to differentiate with or without naloxone or damgo, samples on D2,4,8 were collected and analyzed.

overall_design: p8 and p13 NSC were set as negative control.Samples cultured +/- naloxone and damgo, and samples differentiated +/- naloxone and damgo on D2,4,8 were collected.

first: Jinlong

last: Chen

first: Hao

last: Sun

first: Hui

last: Zheng


title: DNA methylation maps of mouse NSCs treated with naloxone

type: Methylation profiling by high throughput sequencing

summary: In our study,we examined the effects of naloxone (an opioid receptor antagonist) on NSCs (neural stem cells) proliferation and differenntiation. Briefly, we treated NSCs with naloxone in the proliferation and differentiation system. Naloxone was shown to acclerate NSCs proliferation and increase neural differentiation.To investigate how DNA methylation is affected upon naloxone treatment, cells cultured 3 days with naloxone and cells differentiated  with naloxone at D2 were collected, genomic DNA was extracted and subjected to RRBS analysis.

overall_design: Reduced representation bisulphate sequencing of p8 NSCs cultured with naloxone and NSCs differentiated with naloxone.

first: Songwei

last: He


title: Transcriptional profiling of mammalian habenula using scRNAseq

city: Seattle

first: Koichi

last: Hashikawa

state: WA

address: 1959 NE Pacific St. HSB J135

institute: University of Washington

summary:
The habenula complex is appreciated as a critical regulator of motivated and pathological behavioral states via its output to midbrain nuclei.  Despite this, transcriptional definition of cell populations that comprise both the medial (MHb) and lateral habenular (LHb) subregions in mammals remain undefined. To resolve this, we performed single-cell transcriptional profiling and highly multiplexed in situ hybridization experiments of the mouse habenula complex in naïve mice and those exposed to an acute aversive stimulus. Transcriptionally distinct neuronal cell types identified within the MHb and LHb, were spatially defined, and differentially engaged by aversive stimuli. Cell types identified in mice, also displayed a high degree of transcriptional similarity to those previously described in zebrafish, highlighting the well conserved nature of habenular cell types across the phylum.  These data identify key molecular targets within habenula cell types, and provide a critical resource for future studies.

We applied scRNAseq to unbiasedly characterize mammalian habenula transcriptome. We obtained transcriptional dataset of 11,878 cells including 5,558 neuronal cells.

overall_design: To characterize transcriptional identities of single cells in the mammalian habenula, we utilized droplet based chromium technology developed by 10x Genomics. We microdissected the habenula from brain live slices of adult male mice (P50-55), enzymatically digested the tissue to obtain well dissociated highly viable single cells (viability >80 %), captured single cell transcriptomes, and generated cDNA libraries for subsequent sequencing.

first: Yoshiko

first: Garret

last: Stuber


title: Transcriptome profiling of cytoplasmic fraction of naïve CD8 T cells from Nxf1 mutant and control mice [Lymphocytes]

first: Matthew

last: Ritchie

summary:
Purpose: Nxf1 is thought to be an essential nuclear exporter of messenger RNA (mRNA) in eukaryotic cells. Whether perturbations in the Nxf1 pathway affect mammalian physiology is not known. The aim of this study is to determine the impact of a Nxf1 mutation in the representation of mRNA transcripts in the cytoplasm of naïve CD8 T cells.
Methods: For Naïve CD8 T cell isolation, splenocyte suspensions were submitted to red blood cell lysis, stained first with biotinylated CD8 antibodies and then labelled with anti-Biotin microbeads. CD8+ T cells were magnetically enriched by positive selection on MACS separation columns, stained with fluorescently-labelled antibodies before being FACS-sorted as CD8+ CD44low CD62L+. Sorted Naïve T cells were fractionated with Norgen cytoplasmic and nuclear fractionation RNA purification kit. Only cytoplasmic fractions were used for subsequent RNAseq.

overall_design: CD8 Naïve T cells were FACS-sorted from individual Nxf1 mutant males (n=3) and littermate wild-type controls (n=3) .

first: Gordon

last: Smyth

first: Stephane

last: Chappaz

first: Benjamin

last: Kile


title: Different Campylobacter species show variances in their heat stress response [Campylobacter coli]

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Background: The food-borne pathogen Campylobacter is one of the most important zoonotic pathogens. Compared to other zoonotic bacteria, Campylobacter species are quite susceptible to environmental or technological stressors. This might be due to the lack of many stress response mechanisms described in other bacteria. Nevertheless, Campylobacter is able to survive in the environment and food products. Although some aspects of the heat stress response in Campylobacter (C.) jejuni are already known, information about the heat stress response in the related species C. coli and C. lari are still unknown. Results: The stress response to elevated temperatures (46°C) was investigated by survival assays and whole transcriptome analyses for the strain C. jejuni NCTC11168, C. coli RM2228 and C. lari RM2100. While C. jejuni showed highest thermotolerance followed by C. lari and C. coli, none of the strains survived at this temperature for more than 24 hours. Transcriptomic analyses revealed that only 3 % of the genes in C. jejuni and approx. 20 % of the genes of C. coli and C. lari were differentially expressed after heat stress, respectively. The transcriptomic profiles showed enhanced gene expression of several chaperones like dnaK, groES, groEL and clpB in all strains, but differences in the gene expression of transcriptional regulators like hspR, perR as well as for genes involved in metabolic pathways, translation processes and membrane components. However, the function of many of the differentially expressed gene is unknown so far. Conclusion: We could demonstrate differences in the ability to survive at elevated temperatures for C. jejuni, C. coli and C. lari and showed for the first time transcriptomic analyses of the heat stress response of C. coli and C. lari. Our data suggest that the heat stress response of C. coli and C. lari are more similar to each other compared to C. jejuni, even though on genetic level a higher homology exists between C. jejuni and C. coli. This indicates that stress response mechanisms described for C. jejuni might be unique for this species and not necessarily transferable to other Campylobacter species.

overall_design: mRNA profiles of heat stressed (46°C) vs non-stressed (37°C) Campylobacter coli cultures were investigated in duplicate

first: Carolin

last: Riedel

middle: U

first: Thomas

last: Alter

first: Cynthia

last: Sharma

first: Greta

last: Gölz


title: Different Campylobacter species show variances in their heat stress response [Campylobacter lari]

overall_design: mRNA profiles of heat stressed (46°C) vs non-stressed (37°C) Campylobacter lari cultures were investigated in duplicate


title: Different Campylobacter species show variances in their heat stress response

sample_organism:
Campylobacter coli
Campylobacter lari

platform_organism:
Campylobacter coli
Campylobacter lari


title: IMPDH1/YB-1 Positive Feedback Loop Assembles Cytoophidia and Represents a Therapeutic Target in Metastatic Tumors

status: Public on Mar 03 2020

city: wuhan

first: Hailong

last: Ruan

state: hubei

address: 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, China

institute: wuhan union hospital

summary: Recently, cytoophidium, a non-membrane-bound intracellular polymeric structure, has been shown to exist in various organisms, including tumor tissues, but its function and mechanism have not yet been examined. Examination of cytoophidia-assembled gene IMPDH and CTPS mRNA levels showed that only IMPDH1 levels were significantly higher in the clear cell renal cell carcinoma (ccRCC). IMPDH1 was positively correlated with the metastasis-related gene YB-1, and served as an independent prognostic factor in ccRCC. Kaplan–Meier analysis indicated that patients with tumors that expressed high IMPDH1 levels had a shorter overall survival (OS) and disease-free survival (DFS). Furthermore, detection of cytoophidia by immunofluorescence staining in ccRCC tissues showed that IMPDH1-assembled cytoophidia are positively associated with tumor metastasis. Mechanistically, IMPDH1 and YB-1 formed an autoregulatory positive feedback loop: IMPDH1 maintained YB-1 protein stabilization; YB-1 induced IMPDH1 expression by binding to the IMPDH1 promoter motif. Functionally, IMPDH1-assembled cytoophidia physically interacted with YB-1 and translocated YB-1 into the cell nucleus, thus correlating with ccRCC metastasis. Our findings provide the first solid theoretical rationale for targeting the IMPDH1/YB-1 axis to improve metastatic renal cancer treatment.

overall_design: RNA-seq for IMPDH1 and input control. RNA-seq for three independent shRNA against IMPDH1, as well as scrambled control, each performed in triplicate

first: Ke


title: RNA-Seq for a differential gene expression bewteen KLHL14 wild-type(+/+) and KLHL14 knockout(-/-) TMD8 ABC-DLBCL cell line upon treatment with a BTK inhibitor, ibrutinib

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

summary: The goal of this study is to examine gene expression changes in TMD8  KLHL14(+/+) or TMD8 KLHL14(-/-) cells during ibrutinib treatment. The samples have 35 to 63 million pass filter reads with more than 92% of bases above the quality score of Q30.The average mapping rate of all samples is 95%. Unique alignment is above 86%. There are 3.65 to 6.25% unmapped reads.The mapping statistics are calculated using Picard software. The samples have between 0.86-1.29% ribosomal bases. Percent coding bases are between 58-62%. Percent UTR bases are 27-31%, and mRNA bases are between 87-90% for all the samples. We show that TMD8 KLHL14(-/-) cells have less down-regulation of  NF-kB signatures and IL10/JAK1/STAT3 signatures upon ibrutinib treatment when compared to TMD8 KLHL14(+/+) cells.

overall_design: mRNA profilies of TMD8 KLHL14(+/+) and KLHL14(-/-) cells treated with either DMSO or Ibrutinib (2nM) for 24h were generated by paired-end sequencing on HiSeq4000

first: Jaewoo

last: Choi

first: Louis

last: Staudt


title: Severe hydroxymethylbilane synthase deficiency causes depression-like behavior and mitochondrial dysfunction in a mouse model of homozygous dominant acute intermittent porphyria

city: Vienna

first: Stefanie

last: Berger

address: Schwarzspanierstraße 17

country: Austria

institute: Medical University Vienna

summary: Acute intermittent porphyria (AIP) is an autosomal dominant inborn error of heme biosynthesis due to a pathogenic mutation in the Hmbs gene, resulting in half-normal activity of hydroxymethylbilane synthase. Factors that induce hepatic heme biosynthesis induce episodic attacks in heterozygous patients. The clinical presentation of acute attacks involves the signature neurovisceral pain and may include psychiatric symptoms. Here we used a knock-in mouse line that is biallelic for the Hmbs c.500G>A (p.R167Q) mutation with ~5% of normal hydroxymethylbilane synthase activity to unravel the consequences of severe HMBS deficiency on affective behavior and brain physiology. Hmbs knock-in mice (KI mice) model the rare homozygous dominant form of AIP and were used as tool to elucidate the hitherto unknown pathophysiology of the behavioral manifestations of the disease and its neural underpinnings. Extensive behavioral analyses revealed a selective depression-like phenotype in Hmbs KI mice; transcriptomic and immunohistochemical analyses demonstrated aberrant myelination. The uncovered compromised mitochondrial function in the hippocampus of knock-in mice and its ensuing neurogenic and neuroplastic deficits lead us to propose a mechanistic role for disrupted mitochondrial energy production in the pathogenesis of the behavioral consequences of severe HMBS deficiency and its neuropathological sequelae in the brain.

overall_design: The aim of this study was to examine the consequences of severe HMBS deficiency on affective behavior and to examine the underlying pathophysiological principles in a mouse model of homozygous AIP. KI mice harboring a point mutation in the HMBS gene were compared to WT littermate controls in behavioral, molecular and biochemical studies. In-vivo and ex-vivo experiments were further investigated using primary neuronal cultures of KI and WT mice.

first: Miranda

last: Stattmann

first: Ana

last: Cicvaric

first: Francisco

last: Monje

first: Pierluca

last: Coiro

first: Matej

last: Hotka

first: Gerda

last: Ricken

first: Johannes

last: Hainfellner

first: Susanne

last: Greber-Platzer

first: Makiko

last: Yasuda

first: Robert

last: Desnick

first: Daniela

last: Pollak


city: ST CATHARINES

first: Shasha

last: Hu

address: 1812 Sir Isaac Brock Way

department: Biological department

institute: Brock University

summary: A spontaneously phenotypically degenerated strain of M. robertsii strain ARSEF 2575 (M. robertsii lc2575; lc = low conidiation) showed a reduction in conidiation and fungal virulence after successive subculturing on artificial medium. However, the conidial production and fungal virulence of a phenotypically degenerated M. robertsii were recovered by serially passaging through a plant host. The DNA methylation level of phenotypically degenerated Metarhizium robertsii M. robertsii lc2575 and this fungi after solider bean passages were tested through the whole genome bisulfite sequencing. The results showed that approximately 0.379 % of cytosines are methylated in the fungi after bean passages, almost the same as the DNA methylation level in M. robertsii lc2575 (0.375%). The distribution of different methylated regions located more on intergenic regions of  fungi after bean passages than M. robertsii lc2575. Gene Ontology (GO) analysis and KEGG analysis of DMR-associated genes revealed that amino acid, carbohydrate and fatty acid metabolism.

overall_design: Genome-wide analysis of DNA methylation in phenotypically degenerated Metarhizium robertsii and fungi after solider bean passages

first: Michael

last: Bidochka


title: Lung Tissue Gene Expression Profiles in Mice Exposed to Multi-walled Carbon Nanotubes.

city: morgantown

first: Anna

last: Shvedova

state: WV

address: 1095 willowdale Rd

department: HELD

institute: CDC/NIOSH

summary: Pulmonary exposure to multi-walled carbon nanotubes (MWCNT) is established to cause local acute and chronic inflammation, fibroproliferative responses, immunotoxicity, and systemic responses in rodent studies. However, the search for representative biomarkers of exposure is an ongoing endeavor. Whole blood gene expression profiling is a promising new approach for the identification of novel disease biomarkers over more invasive methods. We asked if the whole blood transcriptome reflects pathology-specific changes in lung gene expression caused by aspiration of MWCNT. To answer this question, we performed mRNA sequencing analysis of the whole blood and lung tissue in a murine model of MWCNT bolus pharyngeal aspiration.

overall_design: Global gene expression profiles in the lungs of mice 56 days after administration of 40 µg of multi-walled carbon nanotubes via pharyngeal aspiration, were compared with expression profiles of mice administered vehicle solution.

first: Timur

middle: O

last: Khaliullin

first: Naveena

last: Yanamala


title: Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg enfection in C57BL/6 mice

city: bern

first: Ghalia

last: Boubaker

state: Bern

address: Länggassstrasse, 122

department: INSTITUT OF PARASITOLOGY

country: Switzerland

institute: UNIVERSITY OF BERN

summary: We report a comprehensive analysis of the hepatic miRNA transcriptome at one-month post-infection of experimental primary alveolar echinococcosis (AE), a parasitic infection a parasitic infection caused upon ingestion of E. multilocularis eggs. In infected mice, the expression levels of 28 miRNAs were significantly altered. Of these, 9 were up-regulated and 19 were down-regulated as compared to the non-infected controls. We also studied the issue related to functionally mature arm selection preference (5p and/or 3p) from the miRNA precursor and showed that 9 pre-miRNAs exhibited different arm selection preferences in normal versus infected liver tissues. In conclusion, this study provides first evidence that miRNAs are regulated early in primary murine AE. Thus, further research on the regulation of miRNAs during AE is needed, since miRNAs constitute an attractive potential option for development of novel therapeutic approaches against AE.

overall_design: Hepatic miRNA profiles of 1-month E. multilocularis- infected mice (3 mice) and non-infected mice (2 mice) were produced by next-generation sequencing,  using Illumina NextSeq 500 instrument.

first: Sebastian

last: Strempel

first: Bruno

last: Gottstein


title: Cohesin causes replicative DNA damage by trapping DNA topological stress

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

institute: University of Sussex

summary: DNA topological stress inhibits DNA replication fork (RF) progression and contributes to DNA replication stress. In Saccharomyces cerevisiae we demonstrate that centromeric DNA and the rDNA array are especially vulnerable to DNA topological stress during replication. The activity of the SMC complexes cohesin and condensin are linked to both the generation and repair of DNA topological stress linked damage in these regions. At cohesin enriched centromeres cohesin activity causes the accumulation of DNA damage, RF rotation and precatenation, confirming that cohesin dependent DNA topological stress impacts on normal replication progression. In contrast, at the rDNA cohesin and condensin activity inhibit the repair of damage caused by DNA topological stress. We propose that as well as generally acting to ensure faithful genetic inheritance, SMCs can disrupt genome stability by trapping DNA topological stress.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: To identify the chromosomal contexts where DNA topological stress leads to DNA damage during DNA replication, we examined cells where endogenous DNA topological stress was elevated by the depletion of Top2 in wt and various mutants. Specifically, we identified regions where DNA replication was disrupted by chromatin immunoprecipitation of H2AS129P or RPA1, followed by next generation sequencing (ChIP-SEQ). For RPA1 we used strand specific sequencing. Each experiment was repeated at least two times.

first: Nicola

last: Minchell

first: Jonathan

last: Baxter


title: Lung and Whole Blood Gene Expression Profiles in Mice Exposed to Multi-walled Carbon Nanotubes

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

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

overall_design: Refer to individual Series


title: Molecular and Cellular Responses to the TYK2/JAK1 Inhibitor, PF 06700841, Reveal Reduction of Skin Inflammation in Plaque Psoriasis

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: One Gustave L. Levy Place, Box 1077

department: Population Health Science and Policy

institute: Icahn School of Medicine at Mount Sinai

summary: The interleukin (IL)-23/T-helper type 17 cell axis is a target for psoriasis. The tyrosine kinase 2 (TYK2)/Janus kinase 1 (JAK1) inhibitor, PF 06700841, will directly suppress TYK2-dependent IL-12 and IL-23 signaling and JAK1-dependent signaling in cells expressing these signaling molecules, including T cells and keratinocytes. This clinical study sought to define the inflammatory gene and cellular pathways through which PF 06700841 improves the clinical manifestations of psoriasis. Patients (n=30) with moderate-to-severe psoriasis were randomized to once-daily 30 mg (n=14) or 100 mg (n=7) PF 06700841, or placebo (n=9) for 28 days. Biopsies were taken from non-lesional and lesional skin at baseline, weeks 2 and 4. Changes in the psoriasis transcriptome and genes induced by IL-17 in keratinocytes were evaluated with microarray profiling and RT-PCR. Reductions in IL-17A, IL-17F, and IL-12B mRNA were observed as early as 2 weeks and ~70% normalization of lesional gene expression after 4 weeks. Immunohistochemistry showed significant decreases in markers of keratinocyte activation, epidermal thickness, KRT16 and Ki-67 expression, and immune cell infiltrates CD3+/CD8+ (T cells) and CD11c (dendritic cells) after 2 weeks of treatment, corresponding with improvement in histologic score. PF 06700841 improves clinical symptoms of chronic plaque psoriasis by inhibition of pro-inflammatory cytokines that require TYK2 and JAK1 for signal transduction.

overall_design: Skin biopsies of lesional and non-lesional skin were collected at Baseline (week0), only lesional biopsies were collected at weeks 2 and 4.

first: Karen

last: Page

first: Maria

last: Suprun

first: Elena

last: Peeva


title: Whole Blood long non-coding RNA and mRNA abundance  in Mice Exposed to Multi-walled Carbon Nanotubes.

overall_design: Global mRNA and lncRNA abundance in the whole blood of mice 56 days after administration of 40 µg of multi-walled carbon nanotubes via pharyngeal aspiration (n=5), were compared with expression profiles of mice administered vehicle solution (n=5).


title: Norrie Disease Protein (NDP) gene knockdown patient-derived glioblastoma stem cell lines

city: Montreal

first: Francois

last: Lefebvre

state: QC

address: 845 Sherbrooke St W

department: Human Genetics

institute: McGill University

summary: RNA-Seq to test differential gene expression in response to Norrie Disease Protein (NDP) gene knockdown glioblastoma stem cells.

overall_design: Two sets of NDP (Norrie Disease Protein) gene knockdown experiment samples (Representing two cell lines; one ASCL1-low "G411" and one ASCL1-high "G523" patient-derived GBM stem cell lines): Each set is composed of 9 samples, 3 for the scrambled control (labeled R then a digit representing the replicate number), 3 for the first knockdown construct (shNDp-A; labeled A then a digit representing the replicate number), and 3 for the second knockdown construct (shNDP-C; labeled C then a digit representing the replicate number) (Targeting same gene). Total sample number=18 (9 for each cell line).

first: Ahmed

last: El-Sehemy

first: Valerie

last: Wallace

first: François


title: Epigenomic Profiling and Single_Nucleus_RNA_Seq of Adult Human Retina, Macula, and RPE/Choroid

first: Timothy

last: Cherry

department: Developmental Biology and Regenerative Medicine

institute: Seattle Children's Research Institute

summary: Cis_regulatory elements (CREs) orchestrate the dynamic and diverse transcriptional programs that assemble the human central nervous system (CNS) during development and maintain its function throughout life. Genetic variation within CREs plays a central role in phenotypic variation in complex traits including the risk of developing disease. However, the cellular complexity of the human brain has largely precluded the identification of functional regulatory variation within the human CNS. We took advantage of the retina, a well_characterized region of the CNS with reduced cellular heterogeneity, to establish a roadmap for characterizing regulatory variation in the human CNS. This comprehensive resource of tissue_specific regulatory elements, transcription factor binding, and gene expression programs in three regions of the human visual system (retina, macula, retinal pigment epithelium/choroid) reveals features of regulatory element evolution that shape tissue_specific gene expression programs and defines the regulatory elements with the potential to contribute to mendelian and complex disorders of human vision.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ATAC_Seq was performed on 8 adult human retina and 3 macula samples; ChIP_Seq for histone modifications on 3 adult human retina, 3 macula, and 2 retina pigment epithelium/choroid samples; ChIP_Seq for 5 different transcription factors on adult human retina samples; RNA_Seq from cellular nuclei from 7 adult human retina, 3 macula, and 3 retinal pigment epithelium/choroid samples; single nucleus RNA_seq from 3 adult human retina samples.


title: Coordination of germ-layer lineage choice by TET1 during primed pluripotency

status: Public on Mar 02 2020

city: Leuven

first: Kian

last: Koh

address: Herestraat 49, O&N IV - box 804

department: KU Leuven Department of Development and Regeneration

country: Belgium

institute: KULeuven


title: Fetal cortical transcriptomic changes after oxytocin induced aberrant uterine contractility

city: St. Louis

first: Arvind

last: Palanisamy

state: MO

address: 660 S Euclid Ave

department: Anesthesiology

institute: Washington University School of Medicine

summary: We report changes in the fetal brain cortical transcriptome after oxytocin-induced aberrant uterine contractility using unbiased RNA-seq analysis.

overall_design: We performed RNA-seq analysis to examine differential gene expression in the E21 fetal cortex 24 h after maternal administration of either oxytocin (100 mcg/kg i.v; n = 5 pups from 5 independent dams) or same volume of saline (5 pups from 5 independent mothers). With an FDR adjusted p < 0.05, only mt-nd2 was determined to be significantly differentially expressed in the fetal brain after maternal oxytocin.


title: Coordination of germ-layer lineage choice by TET1 during primed pluripotency (ATAC-seq)

summary: Gastrulation in the early post-implantation stage mammalian embryo begins when epiblast cells ingress to form the primitive streak or develop as the embryonic ectoderm. The DNA dioxygenase Tet1 is highly expressed in the epiblast and yet continues to regulate lineage specification during gastrulation when its expression is diminished. Here, we show how Tet1 plays a pivotal role upstream of germ layer lineage bifurcation. During the transition from naive pluripotency to lineage priming, a global reconfiguration re-distributes Tet1 from Oct4 co-bound promoters to distal regulatory elements at lineage differentiation genes which are distinct from high-affinity sites engaged by Oct4. An altered chromatin landscape in Tet1-deficient primed epiblast-like cells is associated with enhanced Oct4 expression and binding to Nodal and Wnt target genes, resulting in collaborative signals that enhance mesendodermal and inhibit neuroectodermal gene expression during lineage segregation. A permissive role for Tet1 in neural fate induction involves Zic2-dependent engagement at neural target genes at lineage priming, is dependent on the signaling environment during gastrulation and impacts neural tube closure at post-gastrulation. Our findings provide mechanistic information for epigenetic integration of pluripotency and signal-induced differentiation cues.

overall_design: Examination of chromatain accessibility in wildtype and Tet1KO 2iL-cultured embryonic stem cells (ESCs) and epiblast-like cells (EpiLCs).

first: Xinlong

last: Luo


title: Coordination of germ-layer lineage choice by TET1 during primed pluripotency (ChIP-seq)

overall_design: Genome-wide binding profiles for Tet1 and Oct4 in 2iL-cultured embryonic stem cells (ESCs) and epiblast-like cells (EpiLCs).


title: Randomized PAM depletion of phylogenetically-diverse Cas12a nucleases

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: We report the PAMs of phylogenetically-diverse Cas12a nucleases using a cell-free TXTL-based PAM screen. By adding a 5N randomized PAM library and Cas12a-gRNA in vitro, recognized PAM sequences were cleaved, while non-recognized PAMs remained. By amplifying the non-cleaved DNA, we used next-generation sequencing to analyze the depletion of functional PAMs of these Cas12a nucleases.

overall_design: Uncleaved DNA from the randomized PAM library was amplified using Illumina Nextera Indices

first: Thomas

last: Jacobsen


title: iTag labelling of Liver, Plasma and VsWAT RNA

city: München

first: Raffaele

last: Teperino

address: Ingolstädter Landstraße 1

department: Institute of Experimental Genetics (IEG)

institute: Helmholtz Zentrum München

summary: Using a novel method for metabolic labelling of RNA called iTag RNA we  isolate hepatocytes' and kidney proximal epithelial cells' transcriptional response to a dietary challenge and identify multiple hepatocyte-secreted small ccfRNAs in plasma, and transfer of these hepatic derived ccfRNAs to VsWAT.

overall_design: mRNA /small RNA sequencing from liver plasma and kidney of male 12 week old mice following 2w 0f high fat diet feeding or low fat diet control


title: A toolset of constitutive promoters for engineering Rhodosporidium toruloides

city: Berkeley

first: Samuel

middle: Thomas

last: Coradetti

address: 1165 Glen Ave Apt B

department: Bioengineering

institute: UC Berkeley

summary:
Background: A key prerequisite for pathway engineering is the development of genetic tools and resources. Rhodosporidium toruloides is emerging as a promising host for the production of bioproducts from lignocellulosic biomass. However, there is a lack of characterized promoters to drive expression of heterologous genes for strain engineering in R. toruloides.

Results: The resulting data describes a set of native R. toruloides promoters, characterized over time in four media commonly used for this yeast. The promoter sequences were sorted using transcriptional analysis and several of them were found to drive expression bidirectionally. We measured promoter expression by flow cytometry using a dual fluorescent reporter system. From these analyses, we found a total of 20 constitutive promoters (12 monodirectional and 8 bidirectional), that are strong, stable, and can reliably be used for genetic manipulation of this emergent host.

Conclusions: We are presenting a list of robust constitutive promoters that are native to the emergent bioconversion host R. toruloides which helps to fulfill the lack of existing tools for this yeast and that can be applied in future metabolic engineering studies.

overall_design: RNAseq on a varety of media conditions to identify promoters driving robust expression

first: Luísa

last: Czamanski Nora

first: Maren

last: Wehrs

first: Joonhoon

last: Kim

first: Blake

last: Simmons

first: John

last: Gladden

first: Rafael

last: Silva-Rocha

first: Aindrila

last: Mukhopadhyay

first: Jeffrey

last: Skerker

first: James

last: Kirby


title: RNA-seq of human PBMC's and blood derived macrophages from healthy donors carrying the common (non permissive Treml4 expression) or minor (permissive Treml4 expression) allele for rs2803496 which controls Treml4 expression

status: Public on Mar 01 2020

city: Frederick

first: Marieli

last: Gonzalez-Cotto

department: Cancer & Inflammation Program

summary: Treml4 has been recently characterized as a protein-coding gene of the Trem family. It has been shown that its expression is controlled by two cis- eQTL's and that the minor allele a these locuses confers up to 6.5 fold increased relative risk of human coronary arterial calcification (CAC). Since Treml4 expression is confined to the myeloid compartment, we aimed to, first, determine if Treml4 expression correlates to inflammatory activation and, second, investigate how inflammatory gene expression is affected by Treml4 expression status in donors carrying the minor allele for a rs2803496.

overall_design: Peripheral blood monocytes cells or blood-derived macrophage  differentiated for 7 days and  treated with LPS or vehicle (PBS) for 8 or 12 hours were analized. Total RNA was extracted from 5 biological replicates for each group.

first: Shurjo

last: Sen

first: Daniel

last: McVicar


title: Treml4 promotes inflammatory programs in human and murine macrophages and alters atherosclerosis lesion composition in the Apolipoprotein E deficient mouse


title: RNA-seq on MHV68 infected GC B cells expressing distinct immunoglobulin light chains

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: We performed RNA-seq to examine the differences in GC B cells that were either infected with MHV68 or uninfected and between B cells that expressed IgL or IgK B cell receptor light chains.

overall_design: We used 3-4 replicates of GC B cells representing each experimental group.

first: C


title: Glioblastoma initiating cells are sensitive to histone demethylase inhibition due to loss of DNA repair capacity

city: Heidelberg

first: Jan-Philipp

last: Mallm

address: Im Neuenheimer Feld 267

institute: DKFZ

summary: Cancer stem cells are characterized by their self-renewal properties and their ability to regenerate a tumor. They have chromatin features that are reminiscent of embryonic stem cells. Here, we link these stem cell-like characteristics of human glioblastoma initiating cells (GICs) to a loss of heterochromatin features. Increased histone H3 lysine 9 trimethylation (H3K9me3) levels due to histone demethylase inhibition led to cell death in GICs but not in their differentiated counterparts. The induction of apoptosis was accompanied by the accumulation of DNA double-strand breaks. By ChIP-seq and RNA-seq analysis we found that DNA repair genes of the ATM and ATR pathway lost the active H3 lysine 9 acetylation (H3K9ac) and were downregulated upon knockdown of the histone demethylases KDM4C and KDM7A, while regulators of neuron differentiation were up-regulated. Thus, the H3K9me3-H3K9ac equilibrium is a crucial feature for maintaining the stemness in GICs and represents a chromatin feature that can be exploited to specifically target this tumor subpopulation.

overall_design:
ChIP-seq and RNA-seq of glioblastoma initiating cells and their differentiated counterparts with and without inhibition/knockdown of KDMs

**The submitter declares that the raw data were deposited to EGA (EGAS00001003750) due to data protection regulations.**

first: Sabrina

last: Schumacher

first: Karsten

last: Rippe


title: Total RNA sequencing data of murine bone marrow derived macrophages from  Apoe-/-  and Apoe-/-/Treml4-/- mice stimulated with oxLDL

summary: Treml4 has been recently caracterized as a protein-coding gene of the Trem family. It has been shown that its expression is controlled by two cis- eQTL's and that the minor allele a these locuses confers up to 6.5 fold increased relative risk of human coronary arterial calcification (CAC). Since Treml4 expression is confined to the myeloid compartment, we aimed to, first, determined if Treml4 expression correlates with lipid laden macrophages and, second, investigate how  gene expression is affected by Treml4 expression status utlizing a global knockdown mouse for Treml4 under the apolipoprotein deficient background.

overall_design: Apoe-/-  and Apoe-/-/Treml4-/- DKO BMDM were differentiated for 7 days and then treated with high (60ug/ml) or low (10ug/ml) oxLDL concentration or vehicle (PBS) for 16 hours. Total RNA was extracted from 3 biological replicates for each group.

first: Jennifer

last: Barb


city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

summary: RNA-seq analysis of human monocyte-derived dendritic cells generated in vitro with M-CSF, IL-4 and TNF-a, cultured at pH 7.3, or pH 6.5, or in the presence of mTORC1 inhibitor Temsirolimus.

overall_design: Human CD14+ monocytes were cultured with M-CSF, IL-4 and TNF-a for 5 days, at pH 7.3 or pH 6.5 or in the presence of mTORC1 inhibitor Temsirolimus.

first: Fernando

last: Erra Diaz

first: Antonela

last: Merlotti


title: microRNA profiling in renal carcinoma

city: Madrid

first: Lucia

last: Trilla-Fuertes

address: Paseo de la Castellana 261

institute: Hospital Universitario La Paz

summary: Renal cell carcinoma comprises a variety of entities, the most common being the clear-cell, papillary and chromophobe subtypes. These subtypes are related to different clinical evolution; however, most therapies have been developed for clear-cell carcinoma and there is not a specific treatment based on different subtypes. In this study, one hundred and sixty-four paraffin samples from primary nephrectomies for localized tumors were analyzed. MiRNAs were isolated and measured by microRNA arrays. Significance Analysis of Microarrays and Consensus Cluster algorithm were used to characterize different renal subtypes. The analyses showed that chromophobe renal tumors are a homogeneous group characterized by an overexpression of miR 1229, miR 10a, miR 182, miR 1208, miR 222, miR 221, miR 891b, miR 629-5p and miR 221-5p. On the other hand, clear cell renal carcinomas presented two different groups inside this histological subtype, with differences in miRNAs that regulate focal adhesion, transcription, apoptosis and angiogenesis processes. Specifically, one of the defined groups had an overexpression of proangiogenic microRNAs miR185, miR126 and miR130a.  In conclusion, differences in miRNA expression profiles between histological renal subtypes were established. In addition, clear cell renal carcinomas had different expression of proangiogenic miRNAs. With the emergence of antiangiogenic drugs, these differences could be used as therapeutic targets in the future or as a selection method for tailoring personalized treatments.

overall_design: 394 microRNAs from 164 paraffin samples from patients diagnosed with renal carcinoma were analyzed.

first: Lucía

first: Natalia

last: Miranda

last: Castellano

first: Rocío

last: López-Vacas

first: Carlos

last: Farfán Tello

first: Guillermo

last: de Velasco

first: Felipe

last: Villacampa

first: Elena

last: López-Camacho

last: Prado-Vázquez

first: Andrea

last: Zapater-Moros

first: Enrique

last: Espinosa

first: Juan

last: AFresno Vara

first: Alvaro

last: Pinto

first: Angelo

last: Gámez-Pozo


title: OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification

first: Miruna

middle: Georgiana

last: Ghinia Tegla

state: New York

address: 85 St. Nicholas Terrace

department: Biology

institute: CCNY CUNY

summary: Development of the vertebrate eye, like many developmental systems, depends on genes that are used iteratively in multiple distinct processes. The OTX2 transcription factor is one such gene, with a requirement for eye formation, photoreceptor and retinal pigment epithelium specification, among others. During the time period of retinal fate choice, OTX2 is expressed in subsets of retinal progenitor cells with restricted fate choices. However, given the multiple roles for OTX2 and limitations of conventional conditional knockout strategies, the functional significance of its expression is unknown. The present study reports the use of CRISPR/Cas9 gene editing to produce somatic mutations of OTX2 in the chick retina, and identifies similar phenotypes to those observed in human patients. In addition, single cell RNA sequencing was used to determine the functional consequences of OTX2 gene editing by CRISPR/Cas9 on the population of cells derived from OTX2-expressing retinal progenitor cells. This not only confirms that OTX2 is required for the generation of photoreceptors, but also for maintaining the proliferative potential of cells and suppressing the formation of specific retinal fates. These include specific subtypes of retinal ganglion and horizontal cells, suggesting that in this context OTX2 functions to repress sister cell fate choices. Upregulation of key transcription factors involved in the formation of these cells was observed suggesting that OTX2 is upstream of critical nodes of gene regulatory networks of these alternative fates.

overall_design: 10x-based single cell RNA sequencing from retinal cells electroporated at E5 and cultured in explant form for 48h.

middle: G

first: Mark

last: Emerson


title: Ensemble learning for classifying single-cell data and projection across reference atlases

city: San Francisco

first: Aaron

last: Diaz

department: Neurological Surgery

institute: University of California, San Francisco

summary: Single-cell data are being generated at an accelerating pace. How best to project data across single-cell atlases is an open problem. We developed a boosted learner that overcomes the greatest challenge with status quo classifiers: low sensitivity, especially when dealing with rare cell types. By comparing novel and published data from distinct scRNA-seq modalities that were acquired from the same tissues, we show that this approach preserves cell-type labels when mapping across diverse platforms.

overall_design:
We developed an ensemble classifier of scRNA-seq, single-nuclei RNA-sequencing (snRNA-seq), and bulk-extraction RNA-sequencing (RNA-seq) data: Ensemble Learning for classifying Single-cell data and projection across reference Atlases (ELSA; https://github.com/diazlab/ELSA). We trained ELSA on public atlases and tested it on published single-cell data, novel scRNA-seq and snRNA-seq of human glioma tissues (4 patients, >11K cells, Table S1 and S2).
Note: Submitter did not submit the raw data files due to privacy concerns for patients.

first: Lin

last: Wang

first: Francisca

middle: L

last: Catalan

first: Husam

last: Babikir

first: Karin

last: Shamardani


title: Total RNA sequencing data of murine bone marrow derived macrophages from  WT and Treml4 deficient mice

first: Marieli

last: Gonzalez-Cotto

institute: National Cancer Institute

summary: Treml4 has been recently characterized as a protein-coding gene of the Trem family. It has been shown that its expression is controlled by two cis- eQTL's and that the minor allele a these locuses confers up to 6.5 fold increased relative risk of human coronary arterial calcification (CAC). Since Treml4 expression is confined to the myeloid compartment, we aimed to, first, determined if Treml4 expression correlates to inflammatory activation and, second, investigate how inflammatory gene expression is affected by Treml4 expression status utlizing a global knockdown mouse for Treml4.

overall_design: WT and Treml4-/- BMDM were differentiated for 7 days and then treated with LPS or vehicle (PBS) for 8 or 12 hours. Total RNA was extracted from 2 biological replicates for each group and

first: Shurjo

last: Sen

first: Daniel

last: McVicar


title: Granulosa cell expression data from five different time points before and up to 36 hours after induction of ovulation in women receiving fertility treatment

city: Køge

first: Liv

middle: la Cour

last: Poulsen

address: Lykkebækvej 14

department: Gynaecology and Obstetrics

country: Denmark

institute: Zealand University Hospital

summary:
The process of ovulation includes oocyte meiotic maturation, follicle rupture and transformation of the follicle into a corpus luteum. These events are initiated by the midcycle surge of gonadotropins and require the coordinated regulation of thousands of genes. The aim of the study was to monitor the changes in granulosa cell gene expression across five different time points during the first 36 hours of ovulation until follicle rupture, in order to increase our understanding of the events of human ovulation.
We conducted a prospective cohort study including women undergoing ovarian stimulation for fertility treatment. Women were treated in a standard antagonist protocol with individually dosed human menopausal gonadotropin (hMG) or recombinant follicle stimulating hormone (rFSH). Ovulation was induced with either recombinant hCG (rhCG) or gonadotropin releasing hormone agonist (GNRHa). The granulosa cells were collected by transvaginal ultrasound-guided follicle puncture of one follicle at two specific time points during ovulation (repeated measurements), and the study covered a total of five time points: before ovulation induction (OI), 12, 17, 32 and 36 hours after OI.

overall_design: Fifty patients were included resulting in 100 samples of granulosa cells (two repeated samples per patient). 17 out of 100 samples were excluded from further analysis because of either insufficient RNA or bad quality of RNA resulting in outliers. The 83 remaining samples represented time points 0h (n=17), 12h (n=7), 17h (n=6), 32h (n=9) and 36h (n=44).

first: Olga

last: Østrup

first: Claus

last: Yding Andersen

first: Marie

last: Grøndahl

first: Anne

last: Englund


title: EBF-1 mutant bone marrow stroma confers long-term changes in hematopoietic stem cell potential

city: Freiburg im Breisgau

first: Josip

middle: Stefan

last: Herman

address: Stuebeweg 51

department: Quantitative Single Cell Biology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Here, we investigate the role of Early B-cell factor 1 (EBF1) in MSCs to support hematopoiesis. Ebf1 deletion in Cxcl12-abundant reticular (CAR) cells and PDGFRα+Sca1+CD45-CD31-Lin- (PαS) cells in the bone marrow decreases the numbers of HSCs and myeloid cells. Single cell and bulk transcriptome analysis, combined with analysis of chromatin accessibility in EBF1-deficient MSCs revealed decreased expression of adhesion molecules and altered niche composition. In consequence, HSCs exposed to the EBF1-deficient niche, exhibit altered chromatin accessibility and impaired occupancy by myeloid regulators like AP-1, ETS and IRF.

overall_design: Single cells from the bone marrow stroma as well as hematopoietic progenitors were sorted into 384-well plates and processed using a modified version of the CEL-Seq2 protocol (Hasimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8).

first: Marta

last: Derecka

middle: S

first: Senthilkumar

last: Ramamoorthy

first: Pierre

last: Cauchy

first: Ekaterina

last: Lupar

first: Dominic

last: Grϋn

first: Rudolf

last: Grosschedl


title: A Patient-specific screen identifies Medulloblastoma driver genes in-vivo and in human organoids

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

institute: Ospedale Pediatrico Bambino Gesù

type: Methylation profiling by genome tiling array

summary:
Group3 Medulloblastoma is a highly malignant pediatric brain tumor and despite patients harboring different genetic alterations they are treated with similar therapies. Here, we perform an in-vivo Patient-Specific screen and we identify Otx2 and c-Myc as strong inducers of Group3 Medulloblastoma. We demonstrate that the chromatin modifier Smarca4, also mutated in human patients, is able to reduce Otx2/c-Myc tumorigenic activity in-vivo.
Furthermore, Otx2/c-Myc co-overexpression in human cerebellar organoids generates Medulloblastoma-like organoids that induce brain cancer in mice with a DNA methylation signature similar to human Group3 MB. Finally, inhibition of histone methyltransferases reduces Otx2/c-Myc tumorigenesis in ex-vivo culture and in human cerebellar organoids. Therefore, understanding the role of different altered genes in Medulloblastoma patients will be of great importance to develop new personalized therapies.

overall_design: To classify new Group3 Medulloblastoma (MB) derived from human organoids, we analyzed the global DNA methylation profile of Otx2+c-Myc (OM) injected organoids and compared them with those derived from 36 MB patients, diagnosed and treated at the Ospedale Pediatrico Bambino Gesù (OPBG Rome).

first: Luca

last: Tiberi

first: Claudio

last: Ballabio

first: Marica

last: Anderle

first: Matteo

last: Gianesello

first: Chiara

last: Lago

first: Marina

last: Cardano

first: Giuseppe

last: Aiello

first: Silvano

last: Piazza

first: Davide

last: Caron

first: Francesca

last: Gianno

first: Andrea

last: Ciolfi

first: Lucia

last: Pedace

first: Angela

last: Matronuzzi

first: Marco

last: Tartaglia

first: Franco

last: Locatelli

first: Elisabetta

last: Ferretti

first: Felice

last: Giangaspero


title: ChIP-Seq of Smad4 in Th17 cells cultured at 37°C and 39.5°C and RNA-Seq of wild type and Smad4-deficient Th17 cells cultured at 37°C and 39.5°C

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

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

overall_design: Refer to individual Series


title: Global gene expression profile of wild type and Smad4-deficient Th17 cells cultured at 37°C and 39.5°C

summary: Febrile temperature enhanced Th17 differentiation in Smad4 SUMOylation-dependent manner. Smad4-deficiency impaired the febrile temperature-enhanced Th17 differentiation. In order to understand how febrile temperature and Smad4 contribute to Th17 pathogenicity, we conducted transcriptional analysis of wild type and Smad4-deficient Th17 cells cultured at 37°C and 39.5°C (Day 3).

overall_design: Naive CD4+ T cells were sorted from wild type and Smad4-deficient mice and differentiated into Th17 cells at 37°C and 39.5°C. The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions, and the RNA-seq library was constructed with NEXTflex RNA-seq kit (Bioo Scientific) and sequenced with BGI500 platform by BGI Genomics and successfully mapped to mouse genome. Reads counts were normalized based on RPKM/FPKM, fold changes were calculated for all possible comparisons.

first: Lu

last: Ni

first: Xiaohong

last: Zhao


title: CX3CR1+ mononuclear phagocytes gene-expression profile based on their location in the epididymis using RNA-sequencing

status: Public on Feb 29 2020

city: Boston

first: Maria

middle: Agustina

last: Battistone

state: Massachusetts

department: Program in Membrane Biology, Center for Systems Biology and Nephrology Division, Department of Medicine

institute: Massachusetts General Hospital. Harvard Medical Scholl

summary: In the epididymis, prevention of autoimmune responses against spermatozoa, while providing protection against pathogens, is important for male fertility. We previously showed that immune cells known as mononuclear phagocytes (MPs) are located either in the epididymal interstitium or in close proximity to the epithelium. In the initial segments (IS), these “intraepithelial” MPs extend slender luminal-reaching projections between epithelial cells. In this study, we performed an in-depth characterization of MPs isolated from IS, caput-corpus, and cauda epididymis of CX3CR1EGFP+/- mice that express EGFP in these cells. Flow cytometry analysis revealed region-specific subsets of MPs that express combinations of markers traditionally described in ‘dendritic cells’ or ‘macrophages’. RNA sequencing identified distinct transcriptomic signatures in MPs from each region, and revealed specific genes involved in inflammatory and anti-inflammatory responses, phagosomal activity, and antigen processing and presentation. Functional fluorescent in vivo labeling assays showed that higher percentages of CX3CR1+ MPs that captured and processed antigens were detected in the IS compared to other regions. Confocal microscopy showed that in the IS and corpus, circulatory antigens were internalized and processed by interstitial and intraepithelial MPs. However, in the cauda only interstitial MPs internalized and processed antigens, while intraepithelial MPs did not take up antigens, indicating that all antigens have been captured before they reached the epithelial lining. Cauda MPs may thus confer a stronger protection against blood-born pathogens compared to proximal regions. By identifying immunoregulatory mechanisms in the epididymis, our study may lead to new therapies for common disorders such as male infertility and epididymitis, and identify potential targets for immuno-contraception.

overall_design: EGFP+ CX3CR1+  cells were isolated by double cell sorting from the initial segments (IS), caput/corpus and cauda epididymal regions of CX3CR1 EGFP +/-  transgenic mice that specifically express EGFP in mononuclear phagocytes.

middle: A

first: Alexandra

middle: C

last: Mendelsohn

first: Raul

last: Spallanzani

first: Dennis

last: Brown

first: Anil

middle: V

last: Nair

first: Sylvie

last: Breton


title: ChIP-seq of old and new H3.3 in RPE1-hTERT cells

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: On of the H3.3 genes (H3F3B) was C-terminally tagged with a recombination-induced tag exchange (RITE) tag in human RPE1-hTERT cells  to follow old (V5 tag) and new (FLAG tag) H3.3 and measure the dynamics of H3.3. New H3.3 was induced by activating Cre recombinase with 4-hydrotamoxifen (4OHT). ChIP-seq was done on old H3.3 and new H3.3 8h and 24h after 4OHT treatment.

overall_design: ChIP-seq of old H3.3-V5 and new H3.3-FLAG in human RPE1-hTERT cells.