title: Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets

status: Public on Jul 09 2021

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Human pancreatic islets, including insulin secreting beta-cells are a major focus of transplantation strategies aimed at identifying new therapeutic approaches to counteract hyperglycemia in patients with diabetes. Identifying the transcriptomic signature of human islet cells provides insights into regulatory pathways that can be harnessed for planning therapeutic strategies. In this context, single-cell RNA-sequencing (scRNA-seq) has been used mostly in vitro. However, in experimental human islet transplantation models the small amount of tissue is principally used for immunostaining and poses a challenge in performing ‘omics’ studies that provide unbiased information. To circumvent this limitation, we report the use of single nucleus RNA-sequencing (snRNA-seq) on frozen/archived human islet grafts, to define the transcriptomic signature of islet cells preserved after in vivo studies. Interrogating nuclear RNA, we were able to successfully identify all islet endocrine cells, obtain adequate coverage of genes and define molecular pathways that are important for studying human islet cell biology (e.g. cell cycle, apoptosis, insulin secretion). Intersecting our nuclear transcriptomic output with publicly available single-cell RNA-seq datasets, revealed ~90% overlap of the detected genes. In conclusion, we propose that snRNA-seq represents a reliable strategy to probe transcriptomic profiles of fresh or archived transplanted human islets.

overall_design:
A total of 1000 hand-picked human islets equivalents (IEQs) from each of the 4 donors were transplanted under the kidney capsule of 8-to-12-week-old male Non-obese diabetic (NOD)/SCID-gamma  (NSG) mice and animals were followed for 4 weeks. At the end of the follow-up period, mice were sacrificed by cervical dislocation. Human islet grafts were rapidly dissected under the microscope, snap-frozen and stored at -80C. Frozen grafts were transferred to dounce tissue grinder tubes (D8938; Sigma) containing 0.5 ml ice-cold Nuclei EZ lysis buffer (NUC-101; Sigma) and homogenized with pestles A and B on ice each for one minute. Samples were transferred to clean 15 ml tubes and homogenizers were rinsed with 1.5 ml buffer followed by 2 ml buffer and transferred to the same 15 ml tubes to obtain a final volume of 4 ml. The tubes were vortexed briefly at moderate speed and set on ice for 5 minutes for cell lysis. To separate nucleus and cytoplasm, the tubes were centrifuged at 500x g for 5 minutes at 4C. The pellet containing nuclei was resuspended in 0.5 ml cold buffer by vortexing briefly at moderate speed and 3.5 ml cold buffer was added. The nuclear suspension was mixed by vortexing briefly and set on ice for 5 minutes. The tubes were centrifuged at 500x g for 5 minutes and the pellet was resuspended in suspension buffer (0.5 ml PBS containing 0.01% non-acetylated BSA; Sigma and 0.1% RNase inhibitor; 2313A from Clontech). The nuclear suspension was pipetted ten times with a 1 ml tip, filtered through a 30 um pre-separation filter (130-041-407; Miltenyi Biotech); cell number and cell viability were determined by cell counter using 0.4% trypan blue stain. The average number of total nuclei obtained from one-half graft was approximately 8.5x10e5 nuclei (1.7x10e6 cells/ml) with 5-10 um size and 93.3 +/-1.1% dead cell rate (n=32 samples across three independent experiments). The number of isolated nuclei was adjusted to 1000 nuclei/ul with suspension buffer and 10,000 nuclei were immediately used for generation of Gel Beads In-Emulsion (GEMs) and barcoding. Transcriptomic analysis was performed using the 10x Genomics Chromium Single Cell Gene Expression Assay.
Islets from an additional donor were collected and used for single-cell and single-nucleus RNA-sequencing. The data was deposited under the GEO accession number GSE207632.

first: Giorgio

last: Basile

first: Sevim

last: KahramanDirice

first: Rohit

last: Kulkarni


title: Next generation sequencing facilitates quantitative analysis of transcriptional profiling of Candida albicans treated with thiosemicarbazone derivative 19ak.

status: Public on Jul 08 2021

city: Jinan

first: Wenqiang

last: Chang

state: Shandong

address: No. 44 West Wenhua Road

country: China

institute: Shandong University

type: Expression profiling by high throughput sequencing

summary: Candida albicans SC5314 cells were treated with 19ak for mRNA profiling analysis through deep sequencing, in triplicate, using Illumina HiSeq X Ten. The sequence reads that passed quality filters were analyzed at the transcript isoform level. qRT–PCR validation was performed using SYBR Green assay. We find that genes invovled in mitochondrial respiration such as NUO1, NUO2 and MCI4 and ribosomal biogenesis such as RPL5,RPS43,RPS12 were downregulated. Genes invovled in reduction-oxidation progress and iron and zinc ions uptake were also regulated in 19ak-treated C. albicans cells.

overall_design: mRNA profiles of 19ak-treated Candida albicans SC5314 cells and untreated ones were generated by deep sequencing, in triplicate, using Illumina HiSeq X Ten.

first: Hongxiang

last: Lou


title: Expression data from ad libitum or restricted fed 16-week old broiler breeder hens

status: Public on Sep 15 2021

city: University Park

first: Francisco

middle: Javier

last: Diaz

state: PA

address: 313 Forest Resources Lab

department: Animal Science

country: USA

institute: Penn State University

summary:
Ovarian dysfunction is observed in broiler breeder hens fed ad libitum that is most apparent by a reduction in fertility success. Restricting caloric intake in these hens is currently the only effective treatment to improve reproductive efficiency. This analysis sought to determine the transcriptional changes in the ovarian cortex of prepubertal hens given full access to feed (FF) or were placed on a restricted feed (RF) diet.
Microarrays were employed to detail the differences in global gene expression that underlie the ovarian dysfunction observed in ad libitum fed hens.

overall_design: Broiler breeder hens at 2 weeks were either given full access to feed (FF) or were placed on restricted feeding (RF). At 16 weeks of age animals were euthanized by cervical dislocation and ovaries extracted for RNA expression analysis.

middle: J

first: Kate

last: Anthony


title: Gene expression profiles of radiation-induced hepatocellular carcinoma (HCC) in C3H mice

status: Public on Jul 14 2021

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Analysis of whole transcriptome gene expression in 6 groups of liver samples in mice: HCC induced by high-LET radiation, HCC induced by low-LET radiation, spontaneous HCC, non-tumor liver irradiated with high-LET radiation, non-tumor liver irradiated with low-LET radiation, normal liver without radiation.

overall_design: 34 Samples

first: Liang-Hao


title: Upper airway transcriptional profiling reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared to adults

status: Public on Jul 19 2021

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

summary: Unlike other respiratory viruses, SARS-CoV-2 disproportionately causes severe disease in older adults and only rarely in children. To investigate whether differences in the upper airway immune response could contribute to this disparity, we compared nasopharyngeal gene expression in 83 children (<19-years-old; 38 with SARS-CoV-2, 11 with other respiratory viruses, 34 with no virus) and 154 adults (>40-years-old; 45 with SARS-CoV-2, 28 with other respiratory viruses, 81 with no virus). Expression of interferon-stimulated genes (ISGs) was robustly activated in both children and adults with SARS-CoV-2 compared to the respective non-viral groups, with only relatively subtle distinctions. Children, however, demonstrated markedly greater upregulation of pathways related to B cell and T cell activation and proinflammatory cytokine signaling, including TNF, IFNγ, IL-2 and IL-4 production. Cell type deconvolution confirmed greater recruitment of B cells, and to a lesser degree macrophages, to the upper airway of children. Only children exhibited a decrease in proportions of ciliated cells, the primary target for SARS-CoV-2, upon infection with the virus. These findings demonstrate that children elicit a more robust innate and adaptive immune response to SARS-CoV-2 infection in the upper airway that likely contributes to their protection from severe disease in the lower airway.

overall_design:
Comparing host transcriptional response to SARS-CoV-2 infection versus response to other respiratory viral infection or non-viral acute respiratory infection.
>>> Submitter declares that the IRB protocol does not allow for upload of raw sequencing data due to patient privacy concerns. <<<

first: Eran

last: Mick

first: Alexandra

last: Tsitsiklis


title: Unraveling mitochondrial piRNAs in mouse embryonic gonadal cells

status: Public on Jul 01 2021

city: Madrid

first: Odei

last: Barreñada

address: C/ Ramiro de Maeztu 9

country: Spain

institute: CIB Margarita Salas - CSIC

type: Non-coding RNA profiling by high throughput sequencing

summary: Although mitochondria are widely studied organelles, the recent interest in the role of mitochondrial small non-coding RNAs (sncRNA) is providing new functional perspectives in germ cell development and differentiation. PIWI-interacting RNAs (piRNAs) are single-stranded sncRNAs of 20-35 nt generated from the processing of pre-piRNAs longer molecules to be functionally bound to PIWI proteins. Initially ascribed to germ cells, as protectors against transposons, we now know that they are also expressed in somatic cells. In mammals, germ cells differentiate at early stages of embryonic development in the primitive gonads as primordial germ cells (PGCs), initiating divergent pathways in both sexes, accompanied by somatic cells (SCs) of the ovary or testis. Previously, we identified mitochondrial piRNAs (mito-piRNAs) in mouse germ and somatic cells. However, a comparative analysis of mito-piRNAs between PGCs and SCs, between sexes and during early gonadal development has not been performed. We leverage NGS data obtained from PGCs and SCs purified from early differentiating embryonic ovaries and testis from E11.5 to E13.5. Using bioinformatic tools, here we unravel: the origin (from nuclear or mitochondrial genome), the levels of expression, the potential role of mito-piRNAs, as well as their association with genomic regions encoding other sncRNAs (such as tRNAs and rRNAs) and the mitochondrial regulatory region (D-loop). Finally, our results indicate nucleo-mitochondrial communication at both anterograde and retrograde signaling, mediated by mito-piRNAs.

overall_design: Mitochondrial piRNA of 12 different mouse samples, corresponding to PGCs and gonadal somatic cells from E11.5, E12.5 and E13.5 male and female gonads, generated by RNA-seq.

first: Eduardo

last: Larriba

first: Daniel

last: Fernández-Pérez

first: Miguel

last: Brieño-Enriquez

first: Jesús

last: del Mazo


title: PKCl/i inhibition activates an ULK2-mediated interferon response to repress tumorigenesis [RNA-Seq]

status: Public on Sep 23 2021

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: The interferon (IFN) pathway is critical for cytotoxic T cell activation, which is central to tumor immunosurveillance and successful immunotherapy. We demonstrate here that PKCl/i inactivation results in the hyper-stimulation of the IFN cascade and the enhanced recruitment of CD8+ T cells that impaired the growth of intestinal tumors. PKCl/i directly phosphorylates and represses the activity of ULK2, promoting its degradation through an endosomal microautophagy-driven ubiquitin-dependent mechanism. Loss of PKCl/i results in increased levels of enzymatically active ULK2 that by direct phosphorylation activates TBK1 to foster the activation of the STING-mediated IFN response. PKCl/i inactivation also triggers autophagy that prevents STING degradation by chaperone-mediated autophagy. Thus, PKCl/i is a hub regulating the IFN pathway and three autophagic mechanisms that serve to maintain its homeostatic control. Importantly, single cell multiplex imaging and bioinformatics analysis demonstrated that low PKCl/i levels correlate with enhanced IFN signaling and good prognosis in colorectal cancer patients.

overall_design: Mouse tumor organoids (MTO) sgScr and sgPrkci were profiled in three biological replicates under normal conditions.

first: Juan

middle: F

last: Linares

first: Xiao

last: Zhang

first: Anxo

last: Martinez-Ordoñez

first: Angeles

last: Duran

first: Hiroto

last: Kinoshita

first: Hiroaki

last: Kasashima

first: Naoko

last: Nakanishi

first: Yuki

first: Ryan

last: Carelli

first: Luca

last: Cappelli

first: Esperanza

last: Arias

first: Masakazu

last: Yahiro

first: Masaichi

last: Ohira

first: Sanjay

last: Patel

first: Giorgio

last: Inghirami

first: Massimo

last: Loda

first: Ana

middle: M

last: Cuervo

first: Maria

middle: T

last: Diaz-Meco


title: IL15 in treatment of rhesus macaques

status: Public on Jun 28 2021

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Rhesus macaques vaccinated by rhesus cytomegalovirus vectors expressing simian immunodeficiency virus proteins (RhCMV/SIV) activate gene expression signature associated with IL15. To examine the gene expression signature activated by IL15, we performed longitudinal examinations of rhesus macaques during IL15 treament.

overall_design: Longitudinal profiling of rhesus macaques undergoing in vivo IL15 treatment.


title: Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration

status: Public on Jul 21 2021

city: Berlin

middle: S

last: Balzer

address: Charitéplatz 1

department: Dpt. of Nephrology and Medical Intensive Care

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: The kidney tubules have tremendous capacity to repair after acute injury, however, pathways guiding adaptive and maladaptive (fibrotic) repair are poorly understood.     We developed a model of adaptive and maladaptive kidney regeneration by titrating ischemic injury dose. We performed detailed biochemical and histological analysis and profiled transcriptomic changes at bulk and single-cell level in >110,000 cells over time. Our analysis highlighted kidney proximal tubule (PT) cells as key susceptible cells to injury. Adaptive PT repair correlated with fatty acid oxidation and oxidative phosphorylation. We identified a specific maladaptive/profibrotic PT cluster after long ischemia. These cells expressed proinflammatory and profibrotic cytokines and myeloid cell chemotactic factor. Druggability analysis highlighted pyroptosis and ferroptosis as vulnerable pathways in these profibrotic cells. Pharmacological targeting of pyroptosis/ferroptosis in animal model, pushed cells towards adaptive repair and successfully reduced fibrosis.    In summary, our single-cell analysis defined key differences in adaptive and maladaptive repair and identified druggable pathways for pharmacological intervention to prevent kidney fibrosis.

overall_design: n=20 mouse kidney scRNA-seq samples; n=6 control, n=2 IRI short 1d, n=2 IRI short 3d, n=2 IRI short 14d, n=2 IRI long 1d, n=2 IRI long 3d, n=2 IRI long 14d, n=1 IRI long 14d+VX765, n=1 IRI long 14d+Liproxstatin

first: Tomohito

last: Doke

first: Ya-Wen

last: Yang

first: Hailong

last: Hu

first: Hung

last: Mai

first: Ziyuan

last: Ma

first: Rojesh

last: Shrestha

first: Matthew

middle: B

last: Palmer

first: Katalin

last: Susztak


title: Expression data from  Minoxidil- and TCQA-3D treated HFDPCs

status: Public on Jun 24 2021

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential higher effect of minoxdil and TCQA in stimulating hair growth in 3D cultered dermal papilla cells.
HFDPCs were human primary cells line, treated with 0,1 µM minoxidil and 10 µM TCQA for 48 h. Microarray gene expression profiling was conducted for three biological replicates

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Expression data from  Minoxidil- and TCQA-2D treated HFDPCs

summary:
Gene expression profiling reveals a potential  effect of minoxdil and TCQA in stimulating hair growth in 2D cultered dermal papilla cells.
HFDPCs were human primary cells line, treated with 0,1 µM minoxidil and 10 µM TCQA for 48 h. Microarray gene expression profiling was conducted for three biological replicates


title: Targeting thymidine phosphorylase as a potential therapy for bone loss associated periprosthetic osteolysis

status: Public on Jun 10 2021

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

summary: The aim of this study was to identify macrophage-derived factors that promote osteoclast differentiation and periprosthetic bone destruction. To achieve this, we examined the effects of 12 macrophage-derived factors that were identified by RNA-seq analysis of stimulated macrophages on osteoclast differentiation. TYMP was found to trigger significant number of osteoclasts that exhibited resorbing activities on dentine slices. TYMP were detected in serum and synovial tissues of patients that had been diagnosed with aseptic loosening. RNA-seq for TYMP-induced-osteoclasts was then performed in an effort to understand action mode of TYMP. TYMP stimulation appeared to activate the tyrosine kinase FYN signaling associated with osteoclast formation. Oral administration of saracatinib, a FYN kinase inhibitor, significantly suppressed formation of bone osteolytic lesions in a polyethylene debris-induced osteolysis model. Our findings highlight a novel molecular target for therapeutic intervention in periprosthetic osteolysis.

overall_design: RNA-seq for macrophages stimulated by macrophage colony-stimulating factor, receptor activator of nuclear factor kappa-b ligand and thymidine phosphorylase

first: Matsumae

last: Gen

first: Terkawi

last: Alaa

first: Iwasaki

last: Norimasa


title: Patch-Seq Analysis of Respiratory Neurons of the preBötzinger Complex in Neonatal Mice

status: Public on May 28 2021

city: Williamsburg

first: Prajkta

last: Kallurkar

state: VA

address: 540 Landrum Dr, Integrated Science Center 3

institute: William & Mary

summary: Inspiratory breathing movements depend on neurons in the preBötzinger complex (preBötC). We use the Patch-Seq technique and next-generation sequencing to measure the transcriptomes of preBötC insporatory neurons. The preBötC inspiratory neurons can generate both, the rhythm and the rudimentary motor output pattern for inspiratory breathing. We used electrophysiological properties of  preBötC inspiratory neurons to categorize them as putative rhythm- and pattern-generators and then aspirated their cellular contents for scRNa sequencing.

overall_design: Patch-Seq on putative rhythm- and pattern-generating inspiratory neurons of the preBötzinger Complex in neonatal mice (P0-P3)

first: Yae

middle: K

last: Sugimura

middle: D

last: Picardo

first: Gregory

last: Smith

first: Margaret

last: Saha

first: Christopher

middle: A

last: Del Negro


title: The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution

status: Public on May 05 2021

city: Seattle

first: Michael

last: Dorrity

state: Washington

address: 3720 15th Ave NE, Foege Building, Room S313

institute: University of Washington

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Root cells from Arabidopsis seedlings profiled with single-cell ATAC-seq.

overall_design: single-cell ATAC-seq experiments were performed on the 10X Genomics platform

first: M

middle: W

first: C

last: Queitsch

first: J

last: Cuperus


title: Influence of the aminoglycoside antibiotic apramycin on host and phage DNA transcription during infection of S. venezuelae ATCC 10712 with phage Alderaan

status: Public on Apr 30 2021

city: Jülich

first: Max

last: Hünnefeld

address: Wilhelm-Johnen-Straße

department: Institute for Bio- and Geosciences 1: Biotechnology

institute: Forschungszentrum Jülich

summary: Bacterial populations face the constant threat of viral predation exerted by bacteriophages (or phages). In response, bacteria have evolved a wide range of defense mechanisms against phage challenges. Here, we show that aminoglycosides, a well-known class of antibiotics produced by Streptomyces, are potent inhibitors of phage infection. We observed a broad phage inhibition by aminoglycosides. We demonstrate that aminoglycosides do not prevent the injection of phage DNA into bacterial cells but instead block an early step of the viral life cycle. In this context, we used RNA sequencing of S. venezuelae cells infected with phage Alderaan to comparatively investigate the influence of apramycin on phage DNA tanscription at two different time points after inital infection.

overall_design: Infection of S. venezuelae ATCC 10712 carrying the empty plasmid pIJLK04 (AprR) with phage Alderaan was comparatively performed in presence and absence of 10 µg/ml apramycin as biological duplicates. From all 4 cultivations, samples were taken 90 min and 180 min after infection ( = 8 samples) by harvesting cells on ice.

first: Larissa

last: Kever

first: Julia

last: Frunzke


title: Identification of the stress granule transcriptome via RNA-editing in bulk S2 cells, single S2 cells and in Drosophila neurons

status: Public on May 30 2021

city: Utrecht

first: Wessel

middle: van

last: Leeuwen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Stress granules are phase separated assemblies formed around mRNAs that have now been identified after stress granule purification from cell culture. Here, we present a purification free method to detect stress granules RNAs in single cells and in tissues, including those displaying cell heterogeneity. We adapted TRIBE (Target of RNA-binding proteins Identified by Editing) to detect stress-granule RNAs by fusing a stress-granule RNA-binding protein (FMR1) to the catalytic domain of an RNA-editing enzyme (ADAR). RNAs colocalized with this fusion are edited, producing mutations that are detectable by sequencing. We then show that this “in situ" method can reliably identify stress granule RNAs in single S2 cells and in Drosophila neurons, and that they encode cell cycle, transcription and splicing factors. The identification of stress granule RNAs without perturbation opens the possibility to examine cell-to-cell variability and identify the RNA content not only in stress granules, but also in other RNA based assemblies in single cells derived from tissues.

overall_design: 7 samples of bulk S2 cells are analyzed, which include a non-induced sample (no expression of ADAR), 3 replicates of induced + Schneider's (basal condition) and 3 replicates of induced + arsenite (stress condition).  7 samples of Drosophila brain cells are analyzed, which include a non-induced sample (no expression of ADAR), 3 replicates of induced + Schneider's (basal condition) and 3 replicates of induced + arsenite (stress condition).  2 384-well plates are analyzed, which contain single S2 cells in each well treated with either induced + Schneider's (basal condition) or induced + arsenite (stress condition)

first: W

last: van Leeuwen

last: VanInsberghe

first: N

last: Battich

first: F

last: Salmén

first: A

last: van Oudenaarden

last: Rabouille


title: Expression profiling of Peritoneal Macrophages from lupus-diseased-BWF1 mice and NZW/balbc control mice

city: Santiago

first: Gabriela

last: Tejon

state: Ñuñoa

address: Las Palmeras 3425

department: Sciences

country: Chile

institute: Universidad de Chile

summary: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the production of autoantibodies, immune complex deposition, and tissue damage. Several studies have demonstrated the contribution of innate immune cells, including macrophages, in promoting SLE. Macrophages, one of the most abundant cell populations in the peritoneal cavity, are considered multifunctional and phenotypically diverse. Moreover, they can change their phenotype and function in response to environmental signals. However, macrophages' tissue-specific properties in the peritoneal cavity in steady-state and during the progression of SLE remain poorly defined. Using the BWF1 murine model of SLE, we analyzed the phenotype and function of peritoneal macrophages during the disease’s onset. We found a higher frequency of peritoneal macrophages in diseased mice than age-matched controls. Additionally, macrophages from diseased animals expressed lower levels of CD206, MHC-II, and Sirpa. RNAseq analysis identified 286 differentially expressed genes in peritoneal macrophages from diseased-BWF1 mice compared to control mice. Functional experiments demonstrate that peritoneal macrophages from diseased-BWF1 mice secrete higher levels of cytokines when activated with R848 or CpG compared to control cells. Additionally, we observed that peritoneal macrophages from both diseased and control mice could inhibit the activation and proliferation of peritoneal LPS-activated B cells.  Advancing awareness of the role and phenotype of peritoneal macrophages in SLE may contribute to a better understanding of these types of diseases and the development of novel therapies.

overall_design: Peritoneal macrophages mRNA profiles of lupus-diseased-BWF1 mice (BWF1 mice) and non-lupus-susceptible mice (control mice) were generated by deep sequencing, in triplicate, using MiSeq Reagent Kit v3 150-cycle PE

first: Nicolás

last: Valdivieso

first: Felipe

last: Flores-Santibañez

first: Veronica

last: Barra-Valdebenito

first: Victor

last: Martinez


title: Comprehensive profiling of the secretome formulations of fetal and perinatal human amniotic fluid stem cells

status: Public on Apr 26 2021

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

summary: We previously reported that c-KIT+ human amniotic-fluid derived stem cells obtained from leftover samples of routine II trimester prenatal diagnosis (fetal hAFS) are endowed with regenerative paracrine potential driving pro-survival, pro-angiogenic, anti-fibrotic and proliferative effects on target cells. hAFS can be also isolated from III trimester clinical waste samples during C-section scheduled procedures (perinatal hAFS), thus offering an easily accessible alternative source. Nonetheless, little is known about their paracrine profile. Here we provide a detailed characterization of the hAFS total secretome (i.e. whole of the soluble paracrine factors released by the cells in their conditioned medium, hAFS-CM) and the extracellular vesicles (hAFS-EVs) within it as from II trimester fetal- versus III trimester perinatal cells. Fetal- and perinatal hAFS were characterized and subject to hypoxic preconditioning to enhance their paracrine potential. Their secretome formulations were analyzed in terms of protein and chemokine/cytokine content, with the EV cargo further investigated by RNA sequencing. While the appearance of fetal and perinatal hAFS, along with their corresponding secretome formulations was overlapping, the profiling of their paracrine cargo revealed some differences according to gestational stage and hypoxic preconditioning. While both cell sources provided paracrine formulations enriched with neurotrophic, immunomodulatory and endothelial stimulating factors, the more immature fetal hAFS secretome was defined by a more pronounced pro-angiogenic, pro-resolving and anti-aging profile over the perinatal one, while the corresponfing EV…. Moreover, small RNA profiling showed a relevant enrichment of microRNA in both the fetal and perinatal hAFS-EV cargo, with a steadily expressed pro-resolving miRNA core as reference molecular signature. Here we confirm that hAFS represents an appealing source of regenerative paracrine factors; the selection of either fetal or perinatal hAFS secretome formulations for future paracrine therapy should be evaluated considering the specific clinical scenario.

overall_design: miRNAseq of EVs obtained from c-KIT+ human amniotic-fluid derived stem cells from 2 different gestational stages and 2 different conditions. Amniotic fluids derived from 6 different donors.

first: Davide

last: Ceresa

first: Ambra

last: Costa

first: Federico

last: Villa

first: Sveva

last: Bollini


title: Circulating MicroRNA Profiles as Potential Biomarkers for differentiated thyroid cancer recurrence

status: Public on Apr 25 2021

city: Móstoles

first: Garcilaso

last: Riesco-Eizaguirre

state: Madrid

address: Calle Río Júcar, s/n

department: Endocrinology

institute: Hospital Universitario de Móstoles, Universidad Francisco de Vitoria

summary: This study sought to identify the profile of circulating miRNAs and its response to human recombinant TSH in thyroid cancer patients with recurrent disease

overall_design: We obtained serum samples from 37 patients, 18 with recurrent/persistent disease and 19 with complete remission. We used next generation sequencing to define the miRnomes. We made a transversal study by comparing serum miR profiles of patients with or without recurrent/persistent disease and a longitudinal study looking at differences in serum miR content after rhTSH stimulation.

first: Jelena

last: Miljuš

first: María

last: Guillén-Sacoto

first: León

last: Wert-Lamas

last: Ramirez-Moya

first: Mercedes

last: Robledo

first: Pilar

last: Santisteban


title: Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging

status: Public on May 10 2021

city: Boston

first: Vadim

middle: N.

last: Gladyshev

state: MA

address: 77 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital and Harvard Medical School

type: Methylation profiling by high throughput sequencing

summary: The notion that germline does not age goes back to the 19th century ideas of August Weismann. However, being in a metabolically active state, germline accumulates damage and other age-related changes over time, i.e., they age. For new life to begin in the same young state, they must be rejuvenated in the offspring. Here, we developed a new multi-tissue epigenetic clock and applied it, together with other aging clocks, to track changes in biological age during mouse and human prenatal development. This analysis revealed a significant decrease in biological age, i.e.  rejuvenation, during early stages of embryogenesis, followed by an increase in later stages. We further found that pluripotent stem cells do not age even after extensive passaging and that the examined epigenetic age dynamics is conserved across species. Overall, this study uncovers a natural rejuvenation event during embryogenesis and suggests that the minimal biological age (the ground zero) marks the beginning of organismal aging.

relation:
Reanalysis of: GSE120132
Reanalysis of: GSE121690
Reanalysis of: GSE130735
Reanalysis of: GSE34864
Reanalysis of: GSE51239
Reanalysis of: GSE56697
Reanalysis of: GSE60334
Reanalysis of: GSE76261
Reanalysis of: GSE80672
Reanalysis of: GSE98151

overall_design: We remapped the raw reads of several available mouse datasets (ENCSR486XIX, GSE120132, GSE56697, GSE121690, GSE60334, GSE130735, GSE76261, GSE34864, GSE80672, GSE51239, GSE98151) to the mouse rDNA sequence, as follows. Raw sequences were downloaded and extracted using SRA Toolkit. Reads were trimmed and quality filtered by TrimGalore! v0.6.4 using the --rrbs option for RRBS. Methylation levels were extracted using Bismark v0.22.2. Reads were mapped to the mouse rDNA sequence (BK000964.3).

first: C

last: Kerepesi


title: Gene regulation in human lymphoma tissue

status: Public on May 25 2021

city: Uppsala

first: Lena

last: Claesson-Welsh

address: Dag Hammarskjölds väg 20

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary: Among the different human lymphoma types, some express the soluble protein Histidine-rich glycorprotein (HRG)  in CD20+ tumor cells. Normally HRG is expressed by hepatocytes. We were interested in comparing the gene expression patterns in lymphoma expressing HRG or not in marginal zone lymphomas, which was the lymphoma type with the highest prevalence f HRG (37%).

overall_design: Frozen marginal zone lymphoma and MALT lymphoma tissue samples were collected.

first: Tor

last: Persson Skare


title: NusG is an intrinsic transcription termination factor that stimulates motility and cooperatively coordinates global gene expression with NusA

status: Public on Apr 19 2021

city: State College

first: Paul

last: Babitzke

address: 203 Althouse Laboratory

institute: Pennsylvania State University

summary: In this work we conducted Term-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis. Using this approach, we found that NusG is an intrinsic termination factor that works single and cooperatively with NusA.

overall_design: Term-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis followed by in vitro and physiological follow-up

first: Zachary

last: Mandell

first: Reid

last: Oshiro

first: Alexander

middle: V

last: Yakhnin

first: Mikhail

last: Kashlev

first: Daniel

last: Kearns


title: Transcriptome changes specifically associated with apple (Malus domestica) root defense response during Fusarium proliferatum MR5 infection

status: Public on Apr 09 2021

city: taian

first: yanan

last: duan

address: 61 Daizong Street

institute: Shandong Agricultural University

summary: Purpose: The aim of this study was to identify the specific transcriptomic  changes in apple root tissue in response to infection by F. Proliferatum.The characterized transcriptome changes during apple root defense responses to F. Proliferatum inoculation should facilitate the identification of the key molecular components, which may differentiate the resistance and susceptibility among apple rootstock germplasm.

overall_design: The inoculation of seedlings with F. Proliferatum was performed by dipping the root system into the inoculum forc 2h and then planting treated seedlings into aseptic soil. Control plants were mock inoculated with 0.5% PCB and then transplanted and maintained the same manner as pathogen infected plants.

first: Yanan

last: Duan


title: Single cell RNA-seq of spermatogenesis in WT and Zfp541-KO mice (10x Chromium)

status: Public on Apr 16 2021

city: Hangzhou

first: Li

last: Li

state: Zhejiang

address: Shilongshan ST #18, Xihu District

institute: Westlake University

summary: The DSB-machinery, which induces the programmed DNA double-strand breaks (DSBs) in leptotene and zygotene stages during meiosis, needs to be kept in silence after the initiation of pachytene stage to prevent the activation of DSB checkpoint that may lead to meiotic arrest or apoptosis of germ cells. However, the mechanisms underlying this repression remain largely unknown. Here, we report that ZFP541, a germ cell-specific zinc finger protein, is responsible for the suppression of DSBs formation at late pachytene. Lack of Zfp541 in mice leads to generation of DSBs in late pachytene spermatocytes by DSB formation related-proteins and causes male infertility due to meiotic failure. Plated-based scRNA-seq of Zfp541-/- spermatocytes revealed that ZFP541 negatively regulates many meiotic prophase genes, including genes for DSB formation and their upstream transcriptional regulators, in late pachytene spermatocytes. These results were confirmed by 10x single-cell RNA-seq data on spermatogenesis of Zfp541-/- testes, which suggested that Zfp541 is required for repressing the activation of pre-pachytene gene expression programs from early to late pachytene. ZFP541 ChIP-seq on pachytene and diplotene spermatocytes demonstrated that ZFP541 occupies the promoters of meiosis initiators (e.g., Meiosin and Rxra) and a subset of their downstream genes to repress their transcription, and thus prevent the reactivation of pre-pachytene gene expression programs in pachytene spermatocytes. Thus, our results not only revealed the role of ZFP541 in maintaining the repression of pre-pachytene transcriptional programs in pachytene spermatocytes but also provide new insight into the regulation of meiotic progression by timely turning off pre-pachytene genes.

overall_design: We performed 10x scRNA-seq using sorted tetraploid cells from WT and Zfp541-/- testes. The 10x scRNA-seq generated 17,253 high quality single-cell profiles covering 15 developmental stages associated with distinct expression signatures, from differentiated spermatogonia on to elongated spermatids.

first: Jianze

last: Xu

first: Jianing

last: Gao


title: Transcriptome analysis of early and late pachytene spermatocytes in WT and Zfp541-KO mice (Smart-Seq2)

overall_design: To identify differentially expressed genes (DEGs) in Zfp541-KO spematocytes, single-cell RNA-seq was performed on synchronized spermatocytes using a modified Smart-Seq2 method (Chen et al., 2018). Briefly, 2-dpp mice were pipette fed WIN 18,446 (MP) for 7 consecutive days. At Day 8 of WIN 18,446 treatments, these animals were received an injection of RA (Sigma), and then left to recover. We collected testes enriched for early (260 hours after retinoic acid treatment) and late pachytene (360 hours after retinoic acid treatment) cells from WT and Zfp541-KO mice.

first: Huan

last: Zhang


title: Universal prediction of cell cycle position using transfer learning

status: Public on Apr 07 2021

city: Baltimore

first: Jonathan

middle: Joseph

last: Augustin

state: MD

address: 733 N. Broadway Rm#332

institute: Johns Hopkins Medical Institute

summary: The cell cycle is a highly conserved, continuous process which controls faithful replication and division of cells. Single-cell technologies have enabled increasingly precise measurements of the cell cycle as both as a biological process of interest and as a possible confounding factor.  Despite its importance and conservation, there is no universally applicable approach to infer position in the cell cycle with high-resolution from single-cell RNA-seq data. Here, we present tricycle, an R/Bioconductor package,to address this challenge by leveraging key features of the biology of the cell cycle, the mathematical properties of principal component analysis of periodic functions, and the ubiquitous applicability of transfer learning.  We show that tricycle can predict any cell’s position in the cell cycle regardless of the cell type, species of origin, and even sequencing assay. The accuracy of tricycle compares favorably to gold-standard experimental assays which generally require specialized measurements in specifically constructed in vitro systems.  Unlike gold-standard assays, tricycle is applicable to any single-cell RNA-seq dataset. Tricycle is highly scalable, universally accurate, and eminently pertinent for atlas-level data.

overall_design: single cell RNA-seq in WT E14.5 cortical neurospheres

first: Briana

last: Winer

first: Loyal

last: Goff


title: Expression data from Human Fetal Astrocytes and Neurons transduced with WT and mutant HTT

city: Rochester

first: John

last: Mariani

address: 601 Elmwood Avenue

department: Neurology

institute: University of Rochester

summary: Glial pathology has been implicated as a causal contributor to the dysfunction and death of striatal neurons that characterizes Huntington disease. In this study, we investigated mutant HTT (mHTT)-associated changes in gene expression by both mouse and human striatal astrocytes. Mouse striatal astrocytes were FACS-sorted from two distinct models, R6/2 and zQ175 mice, which respectively express exon1-only truncated or full-length HTT, while human astrocytes were generated from either hESCs expressing full-length mHTT, or fetal striatal glia transduced with exon1-only mHTT. Comparison of differential gene expression between each of these conditions and their normal HTT controls, and to one another, revealed astrocyte-specific alterations in both truncated and full-length mHTT models that were shared by both species, yet with differences that clearly distinguished glia derived from each model. Overlap of these data sets revealed that the patterns of mHTT-associated transcriptional dysregulation depended not only upon species, but also upon whether the astroglia expressed truncated or full-length mHTT. These data revealed a common set of conserved, mHTT-associated dysregulated pathways that may present targets for the rescue of glial pathology in HD, while revealing that the gene expression of glia expressing truncated mHTT may differ substantially from that of glia expressing full-length mHTT.

overall_design: Cells from the lateral ganglionic eminence of 14-18 week gestational aged human brains were isolated, transduced with a reporter only, WT HTT, or a mutant HTT, and sorted via MACS on the absence or presence of PSA-NCAM for whole genome microarray expression analysis.

middle: N

first: Abdellatif

last: Benraiss

first: Steven

last: Goldman


title: Expression data from Huntington's disease mouse models of striatal astrocytes and microglia

overall_design: Two mouse models (R6/2 and zQ175) and their littermate controls were sacrificed at 6 or 12 weeks (R6/2) or 6 or 12 months (zQ175), their striata dissected, dissociated, and astrocytes (GLT1+/CD11b-), microglia (GLT1-/CD11b+), and negative cells (GLT1-/CD11b-) were FACS selected for whole genome microarray expression analysis


title: Gene expression data from memory Rictor-/- and WT Tfh and Th1 cells in LCMV acute infection

status: Public on Jun 06 2021

city: Chongqing

first: Yifei

last: Wang

address: Gaotanya Street

department: Institute of Immunology

institute: Third Military Medical University

summary:
Microarray experiments were performed to demonstrate the transcriptome changes due to Rictor deficiency in memory follicular T helper (Tfh) and Type 1 T helper (Th1) cells.
These data revealed that the immunological memory formation and persistance associated genes are changed in Rictor-null memory Tfh and Th1 cells, indicating that Rictor is essential for memory CD4 T cell pool.

overall_design: Polyclonal memory Rictor-null and WT Tfh and Th1 cells (2 samples per group, each sample was pooled from at least 10 mice) were sorted at day 60-post LCMV Armstrong infection, followed by total RNA extracted and sent to microarray analysis.

first: Lilin

last: Ye

first: Yaxing

last: Hao

first: Qin

last: Tian


title: Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships

status: Public on May 13 2021

city: Sherbrooke

first: Étienne

last: Fafard-Couture

state: Québec

address: 3201 Jean-Mignault

department: Biochemistry and functional genomics

country: Canada

institute: University of Sherbrooke

summary:
Background: Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions.

Results: We used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver and brain). We identify 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. 59% of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, compared to only 16% of the correlated non-coding host gene/snoRNA pairs.

Conclusions: Our results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.

overall_design: Ribodepleted and fragmented TGIRT-Seq librairies were generated from RNA samples originating from various healthy human tissues with three biological replicates each.

first: Michelle

last: Scott


title: Treatment of MCF-7 cells with TRAIL and Smac mimetic (LCL-161)

status: Public on Feb 24 2021

city: Lund

first: Christer

last: Larsson

address: Medicon Village, Bldg 404:C3

department: Laboratory Medicine

institute: Lund university

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

overall_design: Refer to individual Series


title: Ob/ob and WT mice transcriptome sequencing

status: Public on Feb 23 2021

city: Jinju

first: Gu

middle: Seob

last: Roh

address: Jinju, Gyeongnam, Republic of Korea

department: Department of Anatomy and Convergence Medical Science, College of Medicine

country: South Korea

institute: Gyeongsang National University

summary: Leptin deficient mice is an appealing model for studying of metabolic syndromes. In this data, we provide 7 different tissues’ RNA-seq reads for each leptin-deficient mice (ob/ob) and wild type mice.

overall_design: Ob/ob and WT mice have been raised on two different diets; Normal diet and high fat diet. Each mouse has been dissected after 20 weeks and 7 tissues, which are hypothalamus, hippocampus, epididymal fat, liver, aorta, skeletal muscles,  and heart, have been sequenced for transcripts.


title: Single nucleus multi-omics regulatory atlas of the murine pituitary [single nuclei ATAC-Seq]

city: Los Angeles

first: Michel

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: The pituitary regulates growth, reproduction and other endocrine systems. To investigate transcriptional network epigenetic mechanisms in this gland, we generated paired single nucleus (sn) transcriptome and chromatin accessibility profiles in single mouse pituitaries, and genome-wide sn methylation datasets. Our analysis provided insight into cell type epigenetics, regulatory circuit and gene control mechanisms. Latent variable transcriptome and accessibility data representation resolved both inter-sexual and inter-individual variation in gene control programs. Multi-omics analysis of cell type-specific gene regulatory networks distinguished distinct mechanisms. Particularly, the FoxL2 gonadotrope network is controlled both by FoxL2 expression and by target gene epigenetic status. Co-accessibility analysis comprehensively identified putative regulatory regions, including a region that overlapped the fertility-linked rs11031006 human polymorphism. In vitro CRISPR-deletion at this locus increased Fshb levels, supporting this domain’s predicted regulatory role. The public pituitary atlas [link] is a resource for elucidating cell-type specific gene regulatory mechanisms and principles of transcription circuit control.

overall_design: Single nucleus chromatin accessibility profiling of adult mouse pituitaries by single nuclei ATAC-seq, using Illumina

first: Frederique

last: Ruf-Zamojski

first: Zidong

first: Gregory

last: Smith

first: Natalia

last: Mendelev

first: Hanqing

last: Liu

first: German

last: Nudelman

first: Mika

last: Moriwaki

first: Hanna

last: Pincas

first: Rosa

middle: G

last: Castanon

first: Yongchao

last: Ge

first: Venugopalan

last: Nair

first: Nitish

last: Seenarine

first: Mary-Anne

last: Amper

first: Xiang

last: Zhou

first: Luisina

last: Ongaro

first: Chirine

last: Toufaily

first: Gauthier

last: Schang

first: Joseph

middle: R

last: Nery

first: Anna

last: Bartlett

first: Andrew

last: Aldridge

first: Nimisha

last: Jain

first: Gwen

last: Childs

first: Olga

last: Troyanskaya

last: Ecker

first: Judith

middle: L

last: Turgeon

first: Corrine

last: Welt

first: Daniel

last: Bernard

first: Stuart

middle: C

last: Sealfon


title: An amygdala circuit that supresses social engagement

status: Public on Feb 22 2021

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 43 Vassar St

institute: Massachusetts Institute of Technology

summary: Innate social behaviors, such as mating and fighting, are fundamental to animal reproduction and survival. However, social engagements are associated with risks for the individual, such as pathogenic infection and physical injury. Little is known about the neural mechanism that allows for appropriate risk assessment and the suppression of hazardous social interactions. We have identified the posteromedial nucleus of the cortical amygdala (COApm) as a locus required for the suppression of mating with an unhealthy female and aggressive behaviors towards a dominant male intruder. Using anatomical tracing, functional imaging, and circuit-level epistatic analyses, we show that suppression of social engagements is mediated by the COApm projections onto the glutamatergic population of the medial amygdalar nucleus (MEA). We further show that this projection that governs social engagements is demarcated by expression of both the neuromodulator thyrotropin-releasing hormone (TRH) in the COApm and the TRH-receptor (TRHR) in the postsynaptic MEA glutamatergic neurons. Modulating TRH-expressing neurons as well as infusing TRHR ligand into the MEA phenocopy functional manipulation of the COApm-MEA circuit. We have, therefore, uncovered a novel neural mechanism that endows animals with the ability to modulate innate reproductive and aggressive social interactions according to the health and threat status of reciprocating individuals. Deficits in such a mechanism may lead to the spread of disease, while uncontrolled engagement may lead to pathological conditions, such as social withdrawal and depression.

overall_design: To conduct circuit-based interrogation of COApm neurons projecting to MEAvGlut2+ neurons, we performed Translating Ribosome Affinity Purification (TRAP) using rabies viral tracing in the vGlut2-Cre mice.

first: Hyeseung

last: Lee

first: Jeong-Tae

last: Kwon

first: Gloria

last: Choi


title: Expression studies familial bilateral macronodular adrenal hyperplasia

city: ADELAIDE

first: Lucia

last: Gagliardi

state: SA

address: Wayfinding 8G480, 1 Port Road

department: Endocrine and Metabolic Unit

country: Australia

institute: Royal Adelaide Hospital

summary: The objectives were to determine the molecular mechanisms involved in the development and progression of familial BMAH tumours, and the mechanisms of their inefficient steroidogenesis.

overall_design: Two normal adrenal glands (controls - no replicates), two nodules (no replicates) from each of three affected siblings were studied

first: Hamish

last: Scott

first: David

middle: J

last: Torpy


title: Preeclampsia is associated with reduced ISG15 levels impairing extravillous trophoblast invasion.

status: Public on Apr 04 2021

city: Tampa

first: Asli

last: Ozmen

state: Florida

address: 560 Channelside Drive

department: ObGyn

institute: University of South Florida

summary: Preeclampsia (PE), a major cause of excess maternal and perinatal morbidity and mortality, has a worldwide prevalence of 2-8%. Excess inflammation with immune maladaptation in the maternal decidua causes shallow trophoblast invasion, resulting in incomplete spiral artery transformation that are characteristic of PE. To mimic the separate and combined paracrine effects of IL-11 and IL-6 on trophoblasts in normal versus preeclamptic pregnancies, primary cytotrophoblast (CTB) cultures treated with IL-11 or IL-6 or IL-11+IL-6 were analyzed by whole genome microarray. These microarray analyses revealed that IL-11 treated CTBs displayed a total of 283 differentially expressed genes (159 of which are up-regulated and 124 are down-regulated), whereas IL-6 treated CTBs displayed a total of 243 differentially expressed genes (120 are up-regulated and 123 are down-regulated) compared control group. However, IL-11+IL-6 co-treated CTBs exhibited 276 differentially expressed genes (146 of which are up-regulated and 130 are down-regulated) compared to control group.   Since IL-11 and IL-6 can compete to activate target cells through binding their shared receptor, the global transcription repertoire of CTB cultures treated with IL-11+IL-6 was compared to those treated with either IL-11 or IL-6. A total of seven genes are differentially regulated by IL-11+IL-6 co-treatment vs. treatment with IL-11 alone (four of which are up-regulated and three down-regulated), whereas compared to IL-6 alone, a total of six genes are differentially regulated by IL-6+IL-11 (all of which are down-regulated). Microarray results of this study support that co-existence of IL-6 and IL-11 impairs the global transcription repertoire of trophoblasts compared to the presence of IL-11 alone, most probably through a mechanism that partial or complete IL-6 binding to gp130 blocks IL-11 action. Importantly, ISG15 is the only commonly affected gene and is downregulated by IL-6 and IL-11 co-treatment compared to control or treatment with either IL-11 or IL-6 alone, suggesting its involvement in PE.

overall_design: Primary cultured cytotrophoblasts (CTBs) obtained from term placental samples were subjected to RNA extraction, quantification, and evulation, followed by  hybridization on Illumina beadchip. Three biological replicates were used (N=12 total samples).

first: A

first: O

last: Guzeloglu-Kayisli

first: S

last: Tabak

first: X

last: Guo

first: N

last: Semerci

first: C

last: Nwabuobi

first: K

last: Larsen

last: Wells

last: Uyar

last: Arlier

first: I

last: Wickramage

first: H

last: Totary-Jain

first: F

last: Schatz

middle: O

last: Odibo

last: Lockwood

first: U

last: Kayisli


title: Single nucleus multi-omics regulatory atlas of the murine pituitary

first: Michel

last: Zamojski


title: Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage

status: Public on Feb 19 2021

city: New Haven

first: Lauren

last: Sansing

state: CT

address: 300 George Street, suite 353

institute: Yale School of Medicine

summary: Longitudinal transcriptomic profiling of myeloid cells from cerebral hemorrhage patients reveals conserved features of the inflammatory response and highlights the potential importance of cellular metabolism in guiding macrophage functions and improved patient outcomes.

overall_design: 399 longitudinal transcriptional profiles of CD14+ monocytes/macrohages and neutrophils isolated from peripheral blood and hematoma effluent of 21 patients, as well as from the peripheral blood of 5 healthy controls.Includes technical replicates of some, but not all samples.

middle: H

first: Alex

last: Shalek

first: J

last: Love

first: Michael

last: Askenase

first: Britany

last: Goods


title: Transcriptome analysis reveals the response mechanism of Frl-mediated resistance to Fusarium oxysporum f. sp. radicis-lycopersici (FORL) infection in tomato

status: Public on Apr 01 2021

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

overall_design: Tomato Fusarium crown and root rot (FCRR) is caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL), we performed a transcriptome analysis of FORL for the first time. Our results are not only useful for understanding the mechanism of Frl-mediated resistance to FORL infection but also provide a basis for cloning the Frl gene.

first: Yuqing

last: Sun


title: Transcriptome analysis of MDBK cells infected with cytopathic bovine viral diarrhea virus (BVDV)

status: Public on Feb 07 2021

city: Puławy

first: Paweł

last: Mirosław

address: 57, Partyzantow Avenue

department: Department of Virology

country: Poland

institute: NATIONAL VETERINARY RESEARCH INSTITUTE

summary: Transcriptional profiling by array was performed to investigate differentially expressed genes (DEGs) in BVDV-infected MDBK cells and to further explore the molecular mechanism of underlying functional changes caused by infection.

overall_design: The material for transcriptomic studies was total RNA obtained from MDBK cells 24 and 72 hours after infection with a cytopathic strain of bovine diarrhea virus and from uninfected cells.

first: Marzena

last: Rola

first: Mirosław

last: Polak


title: Gene expression analysis suggests immunological changes of peripheral blood monocytes in the progression of patients with coronary artery disease

status: Public on Feb 16 2021

city: Beijing

first: Chenxi

last: Song

address: No 167 Beilishi Road

institute: Fuwai Hospital Chinese Academy of Medical Sciences

summary:
Objectives: To analyze the gene expression profile of peripheral blood monocytes in different stages of coronary artery disease (CAD) by transcriptome sequencing, and to explore potential genes and pathway involved in CAD pathogenesis.
Methods: According to the screening of coronary angiography and quality control of blood samples, 8 intermediate coronary lesion patients were selected, then 8 patients with acute myocardial infarction and 8 patients with normal coronary angiography were matched by age and gender. Transcriptomics sequencing was conducted for the peripheral blood monocytes of these 24 samples by using Illumina HiSeq high-throughput platform. Then differentially expressed genes (DEGs) were analyzed. Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation and protein-protein interaction (PPI) network were applied to annotate the potential functions of DEGs.
Results: Compared with the normal coronary angiography group, we identified a total of 169 DEGs in the intermediate coronary lesion group, which were significantly enriched in 59 GO terms and 17 KEGG pathways. Compared with the normal coronary angiography group, we found a total of 2028 DEGs, which were significantly enriched in 311 GO terms and 20 KEGG pathways in the acute myocardial infarction group. The cross-comparison between normal versus intermediate coronary lesion group, and normal versus acute myocardial infarction group included 98 differential genes with 65 up regulated and 33 down regulated genes, which were significantly enriched in 46 GO terms and 10 KEGG pathways. During the progression of CAD, there was a significant up-regulated expression of CSF3、IL-1A、CCR7 and IL-18, and down-regulated expression of  MAPK14. Besides GO items such as inflammatory response was significantly enriched, KEGG analysis showed the most remarkable enrichments in IL-17 signaling pathway and cytokine-cytokine receptor interactions.
Conclusions: Transcriptomics profiles vary in patients with different severity of CAD. CSF3、IL-1A、CCR7、IL-18 and MAPK14, as well as IL-17 signaling pathway and cytokines and cytokine receptor interaction signaling pathway related with inflammatory response might be the potential biomarker and targets for the treatment of coronary artery disease.

overall_design: mRNA expression profile of peripheral blood monocytes in different stages of coronary artery disease (CAD) from 24 cases by transcriptome sequencing

first: Chunyue

first: Haitao

last: Zhang

first: Kefei

last: Dou


title: Transcriptome analysis of MDBK cells infected with non-cytopathic field strains of bovine viral diarrhea virus (BVDV)

status: Public on Feb 11 2021

summary: Transcriptional profiling by array was performed to investigate differentially expressed genes (DEGs) in MDBK cells infected with field strains of BVDV and to further explore the molecular mechanism of underlying functional changes caused by infection.

overall_design: The material for transcriptomic studies was total RNA obtained from MDBK cells 24 and 72 hours after infection with non-cytopathic field strains of bovine diarrhea virus and from uninfected cells.


title: Deregulation of alternative splicing by toxic CUG repeats in astrocytes from a mouse model of myotonic dystrophy

status: Public on Apr 02 2021

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem

summary: Myotonic dystrophy type 1 (DM1) is a severe multisystemic disorder mediated by toxic RNA and abnormal RNA processing. Although splicing defects can explain some key disease symptoms, important gaps exist in our understanding of brain pathology, impeding the rational development of therapies. Here we investigated the different impact of DM1 on astrocytes, using a transgenic mouse model that expresses DM1-associated toxic CUG repeats-containing RNA. RNA sequencing revealed critical missplicing in transcripts that regulate cell adhesion, cytoskeleton and morphogenesis specific to astrocytes. These defects correlated with functional abnormalities in the assembly of focal adhesions and migration in culture, as well as defective astrocyte ramification and reorientation in vivo. Our results demonstrate that DM1 is critically deleterious for the adhesion and morphogenesis of astrocytes, possibly compromising the support and regulation of synaptic function .

overall_design: In order to better understand astrocyte contribution to DM1 brain disease, we used the DMSXL mouse model. Transgenic DMSXL mice carry more than 1,000 CTG repeats in the human DMPK locus (Gomes-Pereira et al., 2007). RNA samples were prepared from WT and DMSXL primary astrocytes, grown for 15 days in vitro.

first: Diana

middle: M

last: Dincã

first: Sandra

last: Braz

first: Anchel

last: Gonzalez-Barriga

last: Polveche

first: Didier

last: Auboeuf

first: Cyril

middle: F

last: Bourgeois

first: Geneviève

last: Gourdon

first: Mário

last: Gomes-Pereira


title: Ex utero Mouse Embryogenesis from Pre-Gastrulation to Late-Organogenesis

status: Public on Feb 15 2021

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Establishment of the mammalian body plan occurs shortly after the embryo implants into the maternal uterus, and our understanding of post-implantation developmental processes remains limited. While methods for in vitro culture of pre- and peri-implantation mouse embryos are routinely utilized, approaches for robust culture of post-implantation embryos from egg cylinder stages until advanced organogenesis remain to be established. We develop herein highly stable ex utero post-implantation mouse embryo culture platforms, that enable appropriate development of embryos before gastrulation (E5.5) until the hind limb formation stage (E11). Late gastrulating embryos (E7.5) are grown in 3D rotating bottles settings, while extended culture from pre-gastrulation stages (E5.5 or E6.5) requires a combination of novel static and rotating bottle culture protocols. Histological, molecular, and single cell RNA-seq analysis validate that the ex utero developed embryos recapitulate precisely in utero development. This culture system is amenable to introducing a variety of embryonic perturbations and micro-manipulations that can be followed ex utero for up to 6 days. Establishment of a system to robustly grow normal mouse embryos ex utero from pre-gastrulation to advanced organogenesis represents a valuable tool to investigate post-implantation embryogenesis, eliminating the uterine barrier to mechanistically interrogate morphogenesis and tissue specification in mammals.

overall_design:
Mouse embryos at E6.5 days post fertilization were cultured ex utero 2 days (equivalent to E8.5) and 4 days (equivalent to E10.5) and analyzed by single cell RNA seq. In utero developed embryos at matched stages were sequenced as control
RNA-seq was measured in vitro mouse ESCs and EpiSCs

first: Alejandro

last: Aguilera-Castrejon

first: Daoud

last: Sheban

first: Tom

last: Shani

first: Awni

last: Mousa

first: Jacob

last: Hanna


title: Effect of KHSRP KO in adult mouse neocortex (CTX)

status: Public on Feb 03 2021

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

institute: University of New Mexico

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

summary:
This study explores whether KHSRP deletion could affect the levels of mRNAs and lncRNAs in the mouse cortex
Total RNA from adult male mice (2-4 months old) was isolated using the Trizol method following by RNA precipitation with ethanol and quantitation of the resuspended RNA using Qubit and Nanodrop. RNA (1 microgram) was shipped to Arraystar to be analyzed using  GPL25015 Arraystar Mouse LncRNA microarray V3B (Agilent-055750 custom Probe Name version)

overall_design: RNA isolation were run in triplicates using 3 KHSRP KO and 3 wild type (WT) mice from the same litter that generated the KHSRP KO mice

first: Michela

last: Dell'Orco


title: RNA-seq datasets of OsRDR3 transgenic plants.

status: Public on Jan 31 2021

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

summary: Rice transgenic lines over-expressing RDR3 were showing vigrous growth phenotype. Height and tiller number of over-expression lines were increased comapred to wild-type controls. Homology dependent silenced line of RDR3 was extremley sick and did not survive beyond vegetative phase.

overall_design: We have performed RNA seq analysis using vegetative tissues of wild type, over-expression and knock-down tansgenic lines. Five weeks old seedlings were considered as vegetative tissues. Libraries were prepared from total RNA isolated from the tissues mentioned.

first: Padubidri

last: Shivaprasad

first: Anushree

last: Narjala

first: Jha

last: Vikram

first: Debjani

last: Basu


title: ChIP-seq of liver after SHAM or CLP with and without dexamethasone treatment

status: Public on Feb 01 2021

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Study of the occurrence of glucocorticoid resistance after CLP induced sepsis in mice

overall_design: Examination of changes in GR DNA binding in livers of C57BL/6J mice after CLP or SHAM operation followed after 6h with an injection of PBS or DEX, with organ isolation 2h post-injection. A total 4 groups with 3 biological replicates/group and 2 input DNA samples  were sequenced for a total of 14 samples

first: Jolien

last: Vandewalle

first: Ville

last: Paakinaho

first: Lies

last: Vancraeynest

first: Liza

last: Dewyse

first: Lise

last: Van Wyngene

first: Kelly

last: Van Looveren

first: Tineke

last: Vanderhaeghen

first: Charlotte

last: Wallaeys

first: Melanie

last: Eggermont

first: Sylviane

last: Dewaele

first: Leo

last: van Grunsven

first: Mieke

last: Dewerchin

first: Peter

last: Carmeliet

first: Karolien

last: De Bosscher

first: Johan

last: Van de Voorde

first: Jorma

last: Palvimo

first: Claude

last: Libert


title: sRNA-seq datasets of OsRDR3 transgenic plants.

first: Shivaprasad

last: Padubidri V.

summary: Rice transgenic lines over-expressing RDR3 were showing vigrous growth phenotype. Height and tiller number of over-expression lines were increased comapred to wild-type controls. Homology dependent silence line of RDR3 was extremley sick and did not survive beyond vegetative phase.

overall_design: We have performed small RNA-seq analysis using vegetative tissues  wild type, over-expression and knock-down tansgenic lines. Five weeks old seedlings were considered as vegetative tissues. Libraries were prepared from total RNA isolated from the tissues mentioned.

first: Padubidri

last: Shivaprasad

first: Anushree

last: Narjala

first: Jha

last: Vikram

first: Debjani

last: Basu


title: The sequence of immunotherapy->targeted therapy delivers long-term responses in melanoma through sustained anti-tumor immunity

status: Public on Jan 26 2021

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

summary: We report the effect of tumor microenvironments on response to therapy in a melanoma mouse model.

overall_design: AntiPD1 only vs AntiPD1 plus combo (ceritinib-trametinib)

first: Manali

last: Phadke

first: Zhihua

last: Chen


title: 3D Polypeptide Facilitates the Expansion of Rare, Circulating Peripheral Blood Hematopoietic Stem/Progenitor Cells with Repopulating Capabilities

status: Public on Jan 01 2021

city: hanghzou

first: xu

middle: yu

last: lin

state: zhejiang province

address: yuhangtang road 388

department: medicine school

country: China

institute: zhejiang university

summary: Hematopoietic stem/progenitor cells (HSPCs) have been successfully used in treating malignancies but with limited cell sources. Whether circulating HSPCs (cHSPCs) in nonmobilized peripheral blood (PB) with engraftment capability could be expanded remains elusive. Here, we developed a polypeptide three-dimensional culture system (3DCS) to expand cHSPCs in nonmobilized PB. We demonstrated that cHSPCs exhibited self-renewal and multilineage differentiation potential by in vitro and in vivo assays including serial transplantation assays. Moreover, we found that 3DCS-derived cHSPCs increased by ~10-fold in vitro and by more than 300-fold in vivo. Bulk RNA-Seq and high-throughput qRT-PCR revealed that cHSPCs showed expression patterns that were similar to those of bone marrow-derived CD34+ HSPCs. Single-cell RNA-Seq elucidated that the 3DCS produced a milieu of immunosuppression that included heterogenous HSPCs and Treg cells. Cytokine arrays illustrated that that 3DCS secreted cytokines, including TNF-α essential for HSPC survival. In conclusion, 3DCS facilitates the expansion of cHSPCs with repopulating capabilities, providing cells for personalized precision medicine.

overall_design: Single-cell RNA sequencing analysis was applied to detect the dynamic changes of cell types in 3DCS with normal PBMNCs derived from two donors. The samples at day0, day5, Day10 and day14 were collected and prepared for subsequent droplet-based scRNA-seq production according to the manufacturer’s protocol (10x Genomics, CA, USA). Libraries were sequenced on the Illumina Hiseq X10 platform according to the manufacturer’s instructions (Illumina).

first: Yulin

last: Xu

first: Xiangjun

last: Zeng

first: Xin

last: Guo

first: He

last: Huang


title: Three dimension polypeptide scaffolds facilitates to expand rare circulating hematopoietic stem/progenitor cells in normal peripheral blood

summary:
Purpose: Circulating hematopoietic stem/progenitor cells (cHSPCs) are rare in normal human peripheral blood (PB) without mobilization. We apply a novel three-dimension culture system (3DCS) seeded with no mobilized PB monocytes (PBMNCs), to expand cHSPCs. Two-dimension culture system (2DCS), primary PBMNCs and CD34+ HSPCs derived from bone marrow serves as system, negative and positive control groups respectively. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism for cHSPCs.
Methods: Four groups are designed in the study including the samples cultured in 2DCS, cultured in 3DCS, normal primary PBMNCs and CD34+ HSPCs derived from mobilized peripheral blood. Total RNA was extracted from the cells followed by mRNA enrichment with poly-T oligo-attached magnetic beads. Cells from 2DCS and normal primary PBMNCs served as controls (the number of repetitions for the groups, n = 3). Mobilized bone marrow-derived CD34+ HSPCs were purified with EasySep Human CD34 Positive Selection Kit (StemCell Technologies) serving as positive control (n = 4). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit (NEB, Illumina®, USA) following manufacturer’s recommendations. Index codes were added to attribute sequences to each sample. Preferential 150~200 bp in length of cDNA fragments were selected and purified with AMPure XP system (Beckman Coulter, Beverly, USA). PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and index (X) Primer after adaptor of cDNA being ligated with USER Enzyme (NEB, USA). At last, PCR products were purified with AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded products was carried out on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. Sequencing raw data were generated using the Illumina HiSeqTM platform, and 125 bp/150 bp paired-end reads were selected.
Results: Bulk RNA sequencing analysis reveals that the samples in 3DCS have more similarity expression pattern with CD34+ hematopoietic stem/progenitor cells (HSPCs) than ones in 2DCS and PBMNCs, for their expression higher level of the specific hematopoietic stem signatures including core stem transcription factors (TFs) as Runx1, HoxA9, HoxB4 and GATA2, self-renewal genes, surface epitopes, and some signaling pathways essential for HSPC fate determination. This study provides a novel culture system to expand rare cHSPC in normal PB, and the underlying molecular and functional signatures are dissected.
Conclusions: Our study demonstrates the first detailed analysis of normal peripheral blood-derived cHSPC transcriptomes based on RNA-seq technology. Our results show that 3DCS facilitates to expand the rare circulating HSPCs with repopulating capacity. The underlying molecular and functional signatures of cHSPCs are dissected. The study provides a platform for normal PB further clinical applications in cell transplantation and personalized precision medicine.

overall_design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism for 4 different groups including the samples from 2DCS, 3DCS, primary normal PBMNCs and CD34+ HSPCs purified from mobilized peripheral blood.


title: ChIP-seq of adenovirus core protein VII

status: Public on Jan 21 2021

city: Seattle

first: Daphne

last: Avgousti

state: WA

address: 1100 Fairview Avenue North C1-201

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

summary: To determine whether adenovirus core protein VII preferentially binds specific host chromatin regions, we performed native chromatin immunoprecipitation of protein VII-bound chromatin followed by next-generation sequencing (ChIP-seq).

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: Native ChIP-seq was performed from chromatin purified from the diploid human cell line IMR-90 infected with WT adenovirus type 5 at MOI = 10 at 20 hours post infection. Native chromatin purified from Saccharomyces cerevisiae (as in PMID: 23468649) 4 hours post-galactose induction to express adenovirus protein VII was spiked in at 5% of the reaction. Chromatin IPs were performed for total histone H3 and protein VII using an endogenous antibody against the viral protein (PMID: 23468649). 10% input control was sequenced as well as H3 and VII ChIP libraries. Sequences were aligned to the human genome (hg38), S. cerevisiae (sacCer3), and human adenovirus type 5 (NCBI Reference Sequence AC_000008.1) to assess protein VII localization.

first: Kelsey

last: Lynch


title: Blood DNA methylation profiles from schizophrenia cases and controls

status: Public on Dec 31 2020

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylation450 BeadChip (“450K array”) in DNA samples isolated from blood for schizophrenia cases and controls. This samples were profiled as part of a wider study where they were meta-analysed with other cohorts.

overall_design: This data includes 720 adult samples profiled as part of a schizophrenia case control study design. Specifically it includes data for 364 schizophrenia cases, 349 controls and 7 fully methylated controls.

first: E

last: Hannon

first: J


title: Genetic Dissection of the RNA Polymerase II Transcription Cycle with ChRO-seq from F1 hybrid mice

status: Public on May 31 2021

city: Ithaca

first: Charles

middle: G.

last: Danko

state: NY

address: Hungerford Hill Rd.

department: Baker Institute for Animal Health, College of Veterinary Medicine

institute: Cornell University

summary: How DNA sequence affects the dynamics and position of RNA Polymerase II during transcription remains poorly understood. Here we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, which was composed of both existing and novel DNA sequence motifs, allowing us to redefine molecular models of both core transcriptional processes. Our results implicate the strength of base pairing between A-T or G-C dinucleotides as key determinants to the position of Pol II initiation and pause. We reveal substantial and heritable differences in the position of transcription termination, which frequently do not affect the composition of the mature mRNA. Finally, we identified frequent, organ-specific changes in transcription that affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals.

overall_design:
We analyzed ChRO-seq data from eight organs from 7 independent reciprocal crosss of C57BL/6 (B6) and Castaneus F1 hybrid mices.
We analyzed RNA-seq data from brain and liver from C57BL/6 (B6) and Castaneus F1 hybrid mices.


title: Natural killer cell subsets characterisation in blood and peripheral lymph node in natural host during simian immunodeficiency virus infection

status: Public on Dec 21 2020

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: The goal of this project is todetermine if natural killer (NK) cells could be able to control HIV replication and reduce or eliminate viral reservoirs leading to HIV cure or a functional cure. Despite thirty years of work and significant progress, HIV infection continues to be an incurable disease. Antiretroviral therapy (ART) has significantly decreased the morbidity and mortality, but lifelong treatment is merely suppressive and does not cure HIV/AIDS. This is because of the existence of a reservoir of viral DNA+ (vDNA+) in cells of the lymphoid tissues with an intact provirus that is thought capable of initiating new rounds of HIV replication (i.e. latency). In addition to this inducible reservoir data suggest ongoing low-level virus replication and persistence in lymphatic tissues of some patients that is related to suboptimal drug levels in these tissues. Strategies are needed that can address both issues.   NK cells are innate immune effectors that recognize virally infected targets through a cadre of activating and inhibitory receptors but become dysfunctional in HIV infected people.  Strikingly, African green monkeys (AGM) and sooty mangabeys mount a strong control of viral replication in lymph node follicles shortly after the viremia peak that lasts throughout infection. Several mechanisms have been proposed to be implicated in the strong control of viral replication in natural host’s lymph nodes, such as NK cell-mediated control. Indeed, we have recently shown that NK cells could migrate into the b cells follicles in a CXCR5 dependent manner and thus participate to the elimination of viral replication.   Thus the purpose of this study is too compare at the transcriptomic level different subset of NK cell isolated from blood and peripheral lymph node of chronically infected AGM to identify a transcriptomic signature which could be linked to an efficient control of SIV replication. This results could then provide a new aproche which could be exploited to generate functional NK cells against HIV in infected patients.

overall_design: Transcriptome profiling of different NK cells subsets according to CD16 and NKG2a/c expression in blood and peripheral lymph node in SIV infection

first: Nicolas

last: Huot

first: Beatrice

last: Jacquelin

first: Philippe

last: Rascle

first: Hugo

last: Varet

first: Vanessa

last: Contreras

first: Michaela

last: Müller-Trutwin


title: Aflatoxin B1 attenuates endocrine function, protein synthesis and energy production of human primary trophoblast

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

summary: Aflatoxin B1 (AFB1) is a mycotoxin produced by Aspergillus flavus and A. parasiticus. AFB1 targeted gene expression profiles were determined in human primary trophoblast cells, isolated from full term placentae after delivery, and exposed to 1 µM AFB1 for 72 hours. Gene expression profiling conducted with human HT-12 expression beadchips

overall_design:
Total RNA obtained from trophoblast cultures 72 hours after AFB1 treatment compared to untreated controls, analyzed with Illumina HT-12 microarray.
Complete raw data were not available.

first: R

last: El-Dairi

first: M

last: Pasanen

last: Rysä

first: P

last: Huuskonen


title: Stromal upregulation of SOX2 promotes tumorigenesis through the generation of a SFRP1/2-expressing cancer-associated fibroblast population [ATAC-seq]

status: Public on Nov 17 2020

city: New York

first: Jorge

last: Moscat

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: Although how CAFs impact the tumor epithelium is being progressively unveiled,  transcriptional processes of lineage plasticity in fibroblasts govern the acquisition of the CAF phenotype are much less understood. Here we show that the upregulation of SOX2 is a critical step in this process, which is negatively regulated by the atypical protein kinase (aPKC) PKCz. We demonstrate that the loss of PKCz is essential for the acquisition of the CAF phenotype and for the induction of the desmoplastic and more aggressive phenotype of intestinal tumors in a SOX2-dependent manner. Furthermore, we show here that the loss of PKCz drives the reprogramming of colon stromal fibroblasts into two different subpopulations that express either the Wnt regulators Sfrp1/2 or osteopontin, both ligands positively impinging into the mesenchymal and stem cell activation programs.

overall_design: WT sgScr, Prkcz-/- sgScr and Prkcz-/- sgSox2 colon fibroblasts were profiled in four biological replicates under normal conditions.

first: Hiroaki

last: Kasashima

first: Angeles

last: Duran

first: Yuki

last: Nakanishi

first: Anxo

last: Martinez-Ordoñez

first: Hiroto

last: Kinoshita

first: Juan

last: Linares

first: Miguel

last: Reina-Campos

first: Yotaro

last: Kudo

first: Antoine

last: L'Hermitte

first: Masakazu

last: Yahiro

first: Masaichi

last: Ohira

first: Daniele

last: Tauriello

first: Eduard

last: Batlle

first: Maria

middle: T

last: Diaz-Meco


title: Systematic analysis of differential rhythmic gene expression mediated by the circadian clock and feeding rhythms in mouse liver

status: Public on Dec 03 2020

city: Lausanne

first: Benjamin

middle: D

last: Weger

state: VD

address: Station 15

department: SV

country: Germany

institute: EPFL

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

overall_design: Refer to individual Series


title: Single-cell gene expression of anti-viral  WT and Bcl3-deficient effector T cells

status: Public on Jan 02 2021

first: Thomas

last: Ciucci

summary: Single-cell gene expression of effector CD8+ T cells  WT or Bcl3-deficient was determined by sRNAseq after LCMV Armstrong infection

overall_design: Mixed bone marrow chimera made of WT and Bcl3-deficient cells were infected with LCMV Armstrong. 8 days post-infection GP33+ CD8+ T cells were sorted and gene expression was determined by scRNAseq

first: Hemant

last: Jaiswal

first: Ulrich

last: Siebenlist

first: Remy

last: Bosselut


title: Gene expression profile of mouse infected by Angiostrongylus cantonensis

status: Public on Oct 14 2020

city: Guang zhou

first: Hongli

last: Zhou

address: 74 2nd Zhongshan Road, Guangzhou, China

institute: Sun Yat-Sen University

summary: Infection by Angiostrongylus cantonensis accounted for the meningitis characterized by accumulation of eosinophils in non-permissive host like mouse and human. However, the underlying molecular basis is still obscure. To uncover the specific molecular mechanism responsible for the meningitis caused by Angiostrongylus cantonensis, we carried out gene expression array for mouse brain with infection by Angiostrongylus cantonensis.

overall_design: Four female BALB/c mice were randomly diveded into two group (2 mice each group) named control group and Angiostrongylus cantonensis (AC) infection group. For AC infection group, mice were infected with 20 stage three larvae of AC intragastrically while the mice of control group were treated by saline with the same way. All mice were raised in the specic pathogen free (SPF) environment. At 21 days post-infection, all mice were sacrificed and the whole brain tissues were used for totoal RNA extraction prior to screening by gene expression profile array.

first: Zhiyue

last: Lv


title: CGH of natural Saccharomyces cerevisiae strains

city: Torino

first: Irene

last: Stefanini

address: via Accademia Albertina

institute: University of Turin

summary: Comparative Genomic Hybridization of natural Saccharomyces cerevisiae strains vs lab reference strains.

overall_design: 11 Saccharomyces cerevisiae strains were analysed. Each strain was analyzed in 2 biological replicates. The diploid laboratory strain BY4743 was used as the reference

first: Duccio

last: Cavalieri


title: Stromal upregulation of SOX2 promotes tumorigenesis through the generation of a SFRP1/2-expressing cancer-associated fibroblast population [RNA-seq]

first: Jorge

last: Moscat

first: Hiroaki

last: Kasashima

first: Angeles

last: Duran

first: Yuki

last: Nakanishi

first: Anxo

last: Martinez-Ordoñez

first: Hiroto

last: Kinoshita

first: Juan

last: Linares

first: Miguel

last: Reina-Campos

middle: V


title: Temporal profiles of hepatic gene expression in PAR bZip triple knockout mice

first: Benjamin

last: Weger

summary: The circadian clock and rhythmic food intake are both important regulators of rhythmic gene expression in the liver. It remains, however, elusive to which extent the circadian clock network and natural feeding rhythms contribute to rhythmic gene expression. To systematically address this question, we developed an algorithm to investigate differential rhythmicity between a varying number of conditions. Mouse knockout models of different parts of the circadian clock network (Bmal1, Cry1/2, and Hlf/Dbp/Tef) exposed to controlled feeding regimens (ad libitum, night restricted feeding) were generated and analyzed for their temporal hepatic transcriptome. A genetical ablation of core loop elements altered feeding patterns that were restored by night restricted feeding. Mainly genes with a high amplitude were driven by the circadian clock but natural feeding patterns equally contributed to rhythmic gene expression with lower amplitude. We observed that Bmal1 and Cry1/2 KOs differed in rhythmic gene expression and identified differences in mean expression levels as a predictor for rhythmic gene expression. In Hlf/Dbp/Tef KO, mRNA levels of Hlf/Dbp/Tef target genes were decreased, albeit rhythmicity was overall preserved potentially due to the activity of the D-Box binding repressor NFIL3. Genes that lost rhythmicity in Hlf/Dbp/Tef KOs were identified to be no direct targets of PARbZip factors and presumably lost rhythmicity due to indirect effects.   Collectively, our findings provide unprecedent insights into the diurnal transcriptome in mouse liver and defines the contribution of subloops of the circadian clock network and natural feeding cycles. The developed algorithm and a webapp to browse the outcomes of the study are publicly available to serve as a resource for the scientific community.

overall_design: RNA-Seq from mRNA of mouse liver across the course of a day. Time-series include mRNA profiles of PARbZip proficient (Hlf+/+/Dbp+/+/Tef+/+) and deficient (Hlf-/-/Dbp-/-/Tef-/-) mice under an ad libitum feeding regimen.

first: Cedric

last: Gobet

first: Eva

last: Martin

first: Frederic

last: Gachon

first: Felix

last: Naef


title: Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression

status: Public on Oct 31 2020

first: Ivana

last: Grbesa

address: 413 E 69th St

department: Urology

institute: Weill Cornell Medicine

summary: The rapid transcriptional response to the transcription factor, glucocorticoid receptor (GR), including gene activation or repression, is mediated by the spatial association of genes with multiple GR binding sites (GBSs) over large genomic distances. However, only a minority of the GBSs have independent GR-mediated activating capacity, and GBSs with independent repressive activity were rarely reported. To understand the positive and negative effects of GR we mapped the regulatory environment of its gene targets. We show that the chromatin interaction networks of GR-activated and repressed genes are spatially separated and vary in the features and configuration of their GBS and other non-GBS regulatory elements. The convergence of the KLF4 pathway in GR-activated domains and the STAT6 pathway in GR-repressed domains, impose opposite transcriptional effects to GR, independent of hormone application. Moreover, the ROR and Rev-erb transcription factors serve as positive and negative regulators, respectively, of GR-mediated gene activation. We found that the spatial crosstalk between GBSs and non-GBSs provides a physical platform for sequestering the Ep300 co-activator from non-GR regulatory loci in both GR-activated and -repressed gene compartments. While this allows rapid gene repression, Ep300 recruitment to GBSs is productive specifically in the activated compartments, thus providing the basis for gene induction.

overall_design: Examination of the effects of silencing of STAT6, Klf4, Rorβ+Rorγ and Rev-erb-β on transcriptional response to glucocorticoids

first: Ofir

last: Hakim


title: Mechanism of tolerance improvement of Escherichia coli W against 3-hydroxypropionic acid by deletion of a less characterized transcription factor yieP

status: Public on Nov 09 2020

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

sample_organism:
Escherichia coli K-12
Escherichia coli W


title: The versatility of Ascorbate Peroxidase-aided mapping uncovers insights of the nuclear lamina interactions and function

city: Baltimore

first: Joseph

last: Tran

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

summary: APEX2 based identification of RNA and DNA at the nuclear lamina

overall_design: Fractionation-seq, APEX2-seq (for RNA), APEX2-based proximity mapping of RNAs and APEX2-based proximity mapping of LADs, and H3K9me3 ChIPseq. All samples have two replicates, except the H3K9me3 CHIPseq, which was done across cell cycle stages once.

first: Yixian

last: Zheng


title: Single-cell sequencing of the Wistar and SHR stellate ganglia

status: Public on Oct 01 2020

city: Oxford

first: David

last: Paterson

address: Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

summary: We report 10x Genomics based single-cell sequencing of the dissociated Wistar and Spontaneously Hypertensive Rat (SHR) stellate ganglia at 5-6 weeks of age.

overall_design: Single-cell sequencing of dissociated stellate ganglia from two rat strains.

first: Harvey

last: Davis

first: Neil

last: Herring


title: Translational landscape of SARS-CoV-2 and infected cells

status: Public on Nov 23 2020

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

summary:
Purpose: Numerous viruses manipulate the host translation machinery and specifically block host mRNA translation. The goal of this study is to define the translational landscape of SARS-CoV-2 and SARS-CoV-2 infected cells using a combination of RNA-seq and ribo-seq approches, the latter being a powerful proxy for protein-level changes.
Methods: Vero E6 and primary human bronchial epithelial cells were infected with SARS-CoV-2 at varying multiplicities of infection and followed throughout early and late phases of infection.  Parallel samples were processed for RNA-seq and Ribo-seq. Sequencing reads were cleaned off of adapters and rRNAs. Reads were first mapped to the SARS-CoV-2 genome and then to the African green monkey and human genomes using STAR. Mapped reads were further annotated and processed using publicly available software and custom scripts deposited at Github. DE gene expression analysis was performed usign EdgeR. Gene set enrichment analysis was done using TcGSA.
Results: We provide the transcriptomic and translatomic landscape of SARS-CoV-2-infected cells from multiple RNA-seq and ribo-seq libraries. We found that the robust transcriptional upregulation of numerous chemokines and cytokines are translationally blocked in SARS-CoV-2-infected cells.
Conclusions: Our study represents the first detailed analysis of viral and host translational landscape in infected cells and demonstrate that translation of host mRNAs involved in innate immunity is specifically blocked. The optimized data analysis workflows reported here should provide a framework for translational profiling studies in other settings.

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

middle: B


title: microRNA 125a Regulates MHC-I Expression on Esophageal Adenocarcinoma Cells, Associated With Suppression of Anti-tumor Immune Response and Poor Outcomes of Patients

city: Amsterdam

first: Sanne

last: Hoefnagel

state: Noord-Holland

address: Meibergdreef 9

department: Gastroenterology

country: Netherlands

institute: Academic Medical Centre Amsterdam

summary:
BACKGROUND & AIMS: Immune checkpoint inhibition may affect outcomes of highly aggressive cancers, such as esophageal adenocarcinoma (EAC). In this regard, the MHC-I pathway and the tumor immune microenvironment are key factors that need to be explored.

METHODS: We investigated post-transcriptional mechanisms of MHC-I regulation through functional and molecular studies of EAC cell lines and of EAC biopsies. We performed RNA-sequencing of fifty-one treatment-naïve EAC biopsies to evaluate the status of the MHC-I pathway and the tumor immune microenvironment with respect to patient response and disease outcomes.

RESULTS: We found that in EAC miR-125a-5p and miR-148a-3p regulate TAP2 and MHC-I expression. Interestingly, MHC-I pathway expression correlated with poorer therapeutic response. Moreover, MHC-I status correlated with a tumor immune-inflamed microenvironment, in which upregulation of PD-L1, PD-L2 and IDO1 were associated to worse patient survival.

CONCLUSIONS: Our data indicate that EAC patients with a proficient MHC-I expression and a tumor immune-inflamed microenvironment have poorer outcomes after neo-adjuvant therapy and may benefit from immune checkpoint inhibition.

first: K

middle: K

last: Krishnadath