title: Self-organized trunk-like-structures with somites and a neural tube

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

summary: The post-implantation embryo is subject to extensive growth, morphogenetic changes and lineage decisions that take place in utero and are therefore difficult to deconstruct in vivo. A robust in vitro culture system that mimics post-implantation mouse development would pave the path towards understanding the dynamics of these processes and how they are coupled. Small aggregates of mouse embryonic stem cells (mESCs) can undergo gastrulation-like events and elongation in vitro, resulting in aggregates with gene expression domains that reflect the post-occipital embryo (gastruloids1–3). However, these ordered patterns of gene expression do not correlate with embryo-like morphogenesis. Here we show that mechano-chemical manipulation of the aggregates results in Trunk-Like-Structures (TLS) with a high level of organization of the embryonic tissue layers, including the formation of a neural tube and somites. Comparative single-cell RNA-Seq (scRNA-Seq) of TLS and embryos demonstrated the molecular complexity of TLS, confirmed embryo-like gene-regulatory programs, and unveiled the presence of primordial germ cell like cells (PGCLCs). Finally, Tbx6-/- TLS formed ectopic neural tubes, recapitulating the in vivo phenotype. These results suggest that TLS are a powerful platform to study the morphogenetic changes and lineage decisions during post-implantation development in space and time.

overall_design: Single-cell RNAseq data were collected from TLSMG at 96h (6 pooled structures), 108h (5 pooled structures) and 120h (3 pooled structures) after aggregation. Libraries were sequenced with 10X Genomics single cell RNA sequencing system. Bulk RNAseq data were collected from 96h (10 pooled structures), Gastruloids (6 pooled structures), TLSMG (6 pooled structures), TLSMGC (6 pooled structures) and TLSMGCL (6 pooled structures) samples. Libraries and sequencing have been performed following the KAPA stranded RNA-Seq Kit instructions and reccomandation. NanoString profiling data were collected from mESC (20k cells), post-occipital E8.5 mouse embryo (3x pooled), post-occipital E9.5 mouse embryo (3x pooled) and 9 individual TLSMG.

first: Jesse

middle: V

last: Veenvliet

first: Adriano

last: Bolondi

first: Leah

last: Haut

first: Manuela

last: Scholze-Wittler

first: Dennis

last: Schiffler

first: Frederic

last: Koch

first: Milena

last: Pustet

first: Simon

last: Heimann

first: Rene

last: Buschow

first: Lars

last: Wittler

first: Bernd

last: Timmermann

first: Alexander

last: Meissner

first: Bernhard

last: Hermann


title: Whole blood microarray and bioinformatics analysis of young South China tigers differences in gene expression levels between natural breastfeeding and artificial feeding management

status: Public on Dec 11 2020

city: Longyan

first: xin

last: wang

state: Fujian

address: No.1 North Dongxiao Rd.

country: China

institute: Longyan University

summary: This study was designed to identify differentially expressed (DE) genes between natural breastfeeding young South China tiger whole blood and artificial feeding young South China tiger whole blood through  microarray and bioinformatics analysis, thus trying to identify modified metabolic pathways as a consequence of milk replacer during the suckling period.

overall_design: 4 samples from 1 natural breastfeeding young South China tiger in experiment NB, 4 samples from 4 artificial feeding young South China tigers in experiment AF.

first: Xin

last: Wang

first: Weihua

last: Xu

first: Kaixiong

last: Lin


title: Longitudinal multi-omics identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

type: Expression profiling by high throughput sequencing

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: SLUG is enhanced by chemotherapeutics and functions to promote invasion and metastasis by directly targeting MMP3 in Cervical Cancer

city: GUANGZHOU

first: Senwei

last: Jiang

state: GUANGDONG

address: 651 dongfengdong road

institute: Sun Yat-sen University Cancer Center

summary: Neoadjuvant chemotherapy (NACT) followed by radical surgery for patients in FIGO stages IB2-IIB has proven to reduce tumor volume and numbers. However, NACT followed by radical surgery has not been found to improve overall survival. In this study, 35 paired pre/post-NACT cervical cancer tissues and 167 cervical cancer samples were examined by immunohistochemical analysis, SLUG expression was potentially increased in cervical cancer tissues after neoadjuvant chemotherapy, which in turn positively correlated with pelvic lymph node metastasis. The expression of SLUG following neoadjuvant chemotherapy was identified as a poor survival indicator. Functional assays, Agilent microarray hybridization and CHIP assay were performed to determine SLUG’s downstream genes and pathways. SLUG overexpression promoted metastasis in cervical cancer in both in vitro and in vivo models, whereas SLUG silencing had the opposite effect. Mechanically, SLUG is not a prerequisite for EMT activation in cervical cancer models, but contributes to the invasiveness and metastasis of cervical cancer cells by directly tethering to the recognition sequence GCCAGGTGC in the MMP3 promoter region. Our results provide mechanistic insight into the potential pro-cancer effect of neoadjuvant chemotherapy, and demonstrates that the SLUG-MMP3 axis could serve as a target for improving the efficacy of chemotherapy.

overall_design: Using a Aligent SurePrint G3 Human Gene Expression v3 8×60K Microarray, to found  genes changed significantly in SLUG overexpressing Siha cells compared with control Siha cells

first: Lan

last: Zhang


title: Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells

status: Public on Dec 14 2020

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

country: USA

institute: national Institute of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Single cell chromatin accessibility assays reveal epigenomic variability at cis-regulatory elements among individual cells. We previously developed a single-cell DNase-seq assay (scDNase-seq) to profile accessible chromatin in a limited number of single cells. Here, we report a novel indexing strategy to resolve single-cell DNase hypersensitivity profiles based on bulk cell analysis. This new technique, termed indexing single-cell DNase sequencing (iscDNase-seq), employs the activities of terminal DNA transferase (TdT) and T4 DNA ligase to add unique cell barcodes to DNase-digested chromatin ends. By a three-layer indexing strategy, it allows profiling genome-wide DHSs for more than 15,000 single-cells in a single experiment. Application of iscDNase-seq to human white blood cells accurately revealed specific cell types and inferred regulatory transcription factors (TF) specific to each cell type. We found that iscDNase-seq detected DHSs with specific properties related to gene expression and conservation missed by scATAC-seq for the same cell type. Also, we found that the cell-to-cell variation in accessibility computed using iscDNase-seq data is significantly correlated with the cell-to-cell variation in gene expression. Importantly, this correlation is significantly higher than that between scATAC-seq and scRNA-seq, suggesting that iscDNase-seq data can better predict the cellular heterogeneity in gene expression compared to scATAC-seq. Thus, iscDNase-seq is an attractive alternative method for single-cell epigenomics studies.

overall_design: Profiling DNA accessibility with multiplex indexing tecnique at the single cell level

first: Weiwu

last: Gao

first: Wai

middle: L

last: Ku

first: Lixia

last: Pan

first: Jonathan

last: Perrie


title: Longitudinal multi-omics identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories [methylation]

summary: To help characterise the temporal dynamics of host response during COVID-19, we performed a longitudinal DNA methylation analysis in a cohort of 12 patients. DNA was extracted from peripheral blood sampled at up to 5 time points per patient. At each sample point, a patient’s disease trajectory, “pseudotime”, was categorised according to clinical parameters.  DNA methylation profiling by Illumina Bead Arrays was performed on each sample. We found CpG sites hypomethylated during COVID-19 were highly enriched in cis of transcripts related to positive regulation of TNF secretion and innate immune signalling, indicating potential long-term regulation of immunological misfiring by epigenetic processes.

overall_design: 6 patients were sampled at days 0, 2, 7, 10, 13 and/or at discharge. 6 healthy donors were sampled at a single time point.

first: Florian

last: Tran

first: Johanna

middle: I

last: Blase

first: Philip

last: Rosentiel


title: Longitudinal multi-omics identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories [sequencing]

summary: In order to characterise the temporal dynamics of host response during COVID-19, we performed a longitudinal multi-omics study using a two centre German cohort of 13 patients. Bulk RNA was extracted from peripheral blood sampled at up to 5 time points per patient. At each sample point, a patient’s disease trajectory, “pseudotime”, was categorised according to clinical parameters.  Both, whole transcriptome and B cell receptor sequence analysis was used to determine signatures specific to different disease trajectories. We identified coexpression modules that were associated with specific patterns across different COVID-19 disease trajectories. One module identified was related to failing interferon I response at the peak of disease severity.  A second module showed biphasic upregulation of transcripts associated with erythropoiesis.   Bulk BCR identified expansion of IgA+ and IgG+ cells. In sum, this study demonstrated distinct gene expression dynamics upon SARS-CoV-2 infection.

overall_design: 13 patients were sampled at days 0, 2, 7, 10, 13 and/or at discharge. 1 patient with mild disease was enrolled after recovery as a recovery control. 14 Healthy donors sampled at single time point were included as controls.

first: Elisa

last: Rosati


title: I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells

city: Bloomington

first: Nicholas

middle: S

last: Sokol

state: IN

department: Biology

institute: Indiana University


title: I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells I

summary: The adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. We describe a new proximity-based profiling method that relies upon a GAL4 driver, termed intestinal-kickout-GAL4 (I-KCKT-GAL4), exclusively expressed in intestinal progenitor cells. This method used UV cross-linked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven by I-KCKT-GAL4. Using I-KCKT-GAL4 based enhanced CLIP datasets provided here we mapped the RNA targets of a selective RNA binding protein, Fragile Mental Retardation Protein (FMRP).

overall_design: Identification of RNA targets of FMRP using enhanced CLIP.

first: Buddika

last: Kasun

first: Xu

last: Jingjing

first: Ariyapala

last: Ishara Surangi

first: Sokol

last: Nicholas Samuel


title: I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells II

summary: The adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. Here, we describe a new proximity-based profiling method that relies upon a GAL4 driver, termed intestinal-kickout-GAL4 (I-KCKT-GAL4), exclusively expressed in intestinal progenitor cells. This method used UV cross-linked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven by I-KCKT-GAL4. When applied to the general mRNA-binder, poly(A)-binding protein, the RNA profile obtained by this method identified 98.8% of transcripts found after progenitor cell sorting, and had low background noise despite being derived from whole animal lysate.

overall_design: Examination of the intestinal progenitor transcriptome using PABP CLIP.


title: Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

city: Worcester

first: Houda

last: Belaghzal

state: MA

address: 55 N Lake Ave

department: Program in Systems Biology

institute: University of Massachusetts Medical School

summary: Chromosomes are folded so that active and inactive chromatin domains are spatially segregated to form a variety of sub-nuclear neighborhoods. Compartmentalization is thought to occur through polymer phase/microphase separation mediated by interactions between loci of similar type. The nature and dynamics of these interactions are not known. We developed liquid chromatin Hi-C to map the stability of associations between loci genome-wide. Before fixation and Hi-C, chromosomes are fragmented removing the strong polymeric constraint to enable detection of intrinsic locus-locus interaction stabilities. We find that chromosome compartmentalization is dependent on the length of chromatin fragments. Compartmentalization is stable when fragments are over 10-25 kb. Fragmenting chromatin into pieces smaller than 6 kb leads to gradual loss of spatial genome organization. In addition to fragmentation level dissolution kinetics of chromatin interactions vary for different chromatin domains. Lamin associated domains are most stable, and speckle-associated loci are more dynamic. The polycomb-enriched B1 sub-compartment also displays highly unstable interactions. Cohesin-mediated loops dissolve after fragmentation, possibly because cohesin rings slide off nearby DNA ends. Liquid chromatin Hi-C provides a genome-wide view of chromosome interaction dynamics, revealing a range of conformational stabilities at different sub-nuclear structures.

overall_design: Two replicate timecourses of liquid chromatin Hi-C, Hi-C 2.0 and 5C in cells and mock nuclei, DpnII-seq timecourse

first: Tyler

last: Borrman

first: Andrew

middle: D

last: Stephens

first: Denis

last: Lafontaine

first: Sergey

last: Venev

first: Zhiping

last: Weng

first: John

middle: F

last: Marko

first: Job

last: Dekker


title: LINC00174 is a novel prognostic factor in Thymic Epithelial Tumors involved in cell migration and lipid metabolism

status: Public on Dec 10 2020

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

summary:
Thymoma and thymic carcinoma represent the two most characterized types of Thymic epithelial tumors (TET) which arise from epithelial cell of thymus. According to the different morphological features, lymphocytes and epithelial cells ratio and grade of malignancy, TET are divided in  thymoma A, AB, B1, B2, and B3 and thymic carcinoma.
We used microarrays to detail the global programme of gene expression distinguishing tumoral and normal thymic tissue, thus identifying networks of correlated mRNAs-lncRNAs.

overall_design: Fresh frozen thymic tumors and normal tissues from a small cohort (including 6 TET specimens and 3 normal counterparts), were profiled for gene expression using Affymetrix platform.

first: F

last: Fazi

first: A

last: Sacconi


title: O-GlcNAc regulates MTA1 transcriptional activity during breast cancer cells genotoxic adaptation

city: panjin

first: bo

middle: yu

last: liu

state: liaoning

address: Dagong Road 2

institute: Dalian University of Technology

summary:
Chromatin modifier metastatic tumor protein 1 (MTA1), closely correlated with the development and progression in breast cancer, has a fantastic role in multiple cellular processes, including gene expression and cell homeostasis. Although MTA1 is a stress-responsive gene, its role in genotoxic adaptation remains unexplored. Here, we demonstrate that O-GlcNAc modification promotes MTA1 to interact with chromatin and regulates target gene expression, contributing to breast cancer cell genotoxic adaptation. MTA1 is modified with O-GlcNAc residues at serine 237/241/246 in adriamycin adaptive breast cancer cells and that modification improves the genome-wide interactions of MTA1 with gene promotor regions by enhancing its association with nucleosome remodeling and histone deacetylation (NuRD) complex. Further, O-GlcNAc-modulated MTA1 chromatin-binding influences the specific transcriptional regulation of genes involved in the adaptation of breast cancer cells to genotoxic stress.
We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using anti-HA magnetic beads in HA-MTA1-WT or HA-MTA1-3A stably expressed MCF-7 cells. Next-generation sequencing libraries were generated and amplified for 15 cycles with BGISEQ kit. 100-300 bp DNA fragments were gel-purified and sequenced with BGISEQ-500 (BGI). Two biological replicates of the ChIP-seq were performed. We also analyzed gene expression in MTA1-WT and MTA1-3A expressed cells by RNA-seq.

overall_design: MTA1 ChIP-seq was performed in HA-MTA1-WT and HA-MTA1-3A expressed MCF-7  cells using anti-HA magnetic beads. Gene expression profiling of HA-MTA1-WT and HA-MTA1-3A expressed MCF-7  cells were performed by RNA-seq.

first: Xueqin

last: Xie

first: Qiutong

last: Wu

first: Keren

last: Zhang

first: Yimin

last: Liu

first: Nana

first: Qiushi

last: Chen

first: Lingyan

last: Wang

first: Wenli

last: Li

first: Jianing

first: Yubo


title: Mettl14 is required for mouse postimplantation development by facilitating epiblast maturation

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: N6-methyladenosine (m6A) is the most prevalent and reversible internal modification of mammalian messenger and noncoding RNAs mediated by specificm6A writer, reader, and eraser proteins. As an m6A writer, the methyltransferase-like 3-methyltransferase–like 14 (METTL14)–Wilms tumor 1–associated protein complex dynamically regulates m6A modification and plays important roles in diverse biologic processes. However, our knowledge about the complete functions of this RNA methyltransferase complex, the contributions of each componenttothemethylation, andtheir effects on different biologicpathways are still limited. By using both in vivo and in vitro models, we here report that METTL14 is indispensable for postimplantation embryonic development by facilitating the conversion from naive to primed state of the epiblast. Depletion of Mettl14 leads to conspicuous embryonic growth retardation from embryonic d 6.5, mainly as a result of resistanceto differentiation, which further leads to embryonic lethality early in gestation. Our data highlight the critical function of METTL14 as an m6A modification regulator in orchestrating early mouse embryogenesis.

overall_design: To investigate the molecular consequences of Mettl14 depletion in mouse early embryogenesis, we isolated mRNA from control and Mettl142/2 embryos at E5.5 and performed RNA sequencing. We chose E5.5 mouse embryos because the mutant embryos at this stage were not distinguishable in morphology from normal littermates, thus minimizing molecular changes ascribed to secondary developmental defects in the absence ofMETTL14.

first: Tie-Gang

last: Meng

first: Zheng-Hui

last: Zhao


title: Co-Morbid Multiple Sclerosis and Psoriasis: Clinical Outcomes and Gene Expression

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

summary:
Psoriasis was found to ameliorate multiple sclerosis (MS) outcomes when it MS onset. However, the molecular basis for this observation remains unclear.
Herein, we compared the blood mononuclear cell transcriptome of psoriasis and MS comorbide (P/MS) patients with that of patients with either psoriasis or MS to understand the clinical observation.

overall_design: A total of 45 patients (16 P/MS, 17 multiple sclerosis only (MSO), and 12 psoriasis only (PSO) patients) that met the inclusion criteria and 10 healthy control (HC) participants were analyzed.

first: Gadi

last: Miron

first: Anat

last: Achiron

first: Aviv

last: Barzilai


title: Temporal study of the effect of acute systemic inflammation on the cerebral endothelial cells (CECs) and microglia in mice

city: Charlestown

first: Mahesh Chandra

last: Kodali

department: Neurology

institute: Massachusetts General Hospital / Harvard Medical School

summary: To capture the global gene expression patterns in the CECs and microglia following acute systemic inflammation, we injected the mice with LPS and sacrificed them after 30 min, 1 hr and 2 hrs, immediately followed by the isolation of the brains and dissociation to yield single cell suspension, immunolabelling and finally flow assisted cell sorting of CECs (CD45- CD13- CD31+) and microglia (CD45 low-mid CD11b+). RNA was then isolated from the cells followed by RNA-seq.

overall_design: mRNA profiles of CECs and microglia isolated from the brains of mice (C57BL6, Wild type, 2-3 months old)  injected (intra peritoneal) with 10mg/kg LPS for 30 min, 1 hr and 2 hrs or PBS n= 3 (males) each group.

first: Mahesh

middle: C

first: Hao

first: Francesca-Fang

last: Liao


title: Heterotrimeric G-protein interactions are conserved despite regulatory element loss in some plants

status: Public on Dec 15 2020

city: Saint Louis

first: Sona

last: Pandey

state: MO

address: 975 north warson road

institute: Donald Danforth Plant Science Center

summary:
Purpose: To study the shared transcriptional network between suppression transgenic plants of BdG and overexpresssion plants of SiRGS in B. distachyon.
Method: Total RNA was isolated from 2 independent transgenic lines of amiR-BdG and Bd-SiRGS-OE. RNA-seq library preparation, sequencing and initial quality control analysis were performed by Novogene Inc. The sequences were analyzed for quality using FastQC. Transcripts per million (TPM) abundance was estimated by pseudo-aligning the reads with that of the k-mer index available from the reference genome of B. distachyon from Phytozome using Kallisto. Differentially expressed genes were sorted using Sleuth program with likelihod ration cutoff of false discovery rate (FDR) < 0.05. The log2 fold change was calculated from the TPM values derived for the wild-type and transgenic plants.
Result: The transcriptome data showed more that 60% of overlap between amiR-BdG and Bd-SiRGS-OE. Among common genes more than 90% showed similar expression pattern when screened for several developmental and hormonal signaling pathways.

overall_design: B. distachyon was used as wild-type control. 2 independent transgenic lines of amiR-BdG and Bd-SiRGS-OE were used. The tissue were collected as whole seedlings at 2-week-old stage.

first: Nikita

last: Bhatnagar


title: m6A independent genome-wide METTL3 and METTL14 redistribution drives senescence-associated secretory phenotype [rna.M3]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Methyltransferase-like 3 (METTL3) and 14 (METTL14) are core subunits of the methyltransferase complex (MTC) that catalyzes mRNA N6-methyladenosine (m6A) modification.  Despite the expanding list of m6A-dependent function of the MTC, m6A independent function of the METTL3 and METTL14 complex remains poorly understood.  Here we show that genome-wide redistribution of METTL3 and METTL14 drives senescence-associated secretory phenotype (SASP) in a m6A-independent manner.  METTL3 and METTL14 are necessary for SASP.  However, SASP is not regulated by m6A mRNA modification.  METTL14 is redistributed to the enhancers, while METTL3 is localized to the pre-existing NF-B sites within the promoters of the SASP genes during senescence.  METTL3 interacts with NF-B and they are mutually dependent on their associations with the promoters of SASP genes.  METTL14 but not METTL3 is necessary for function of SASP gene enhancers.  METTL3 and METTL14 are required for both the tumor-promoting and immune surveillance functions of senescent cells mediated by SASP in vivo in mouse models.  In summary, our results report a m6A independent function of the METTL3 and METTL14 complex in promoting SASP through regulating transcription by genome-wide redistribution of METTL14 to enhancers and METTL3 to promoters of SASP genes during senescence.

overall_design: RNA-seq in control and senescent IMR90 cell lines with different METTL3 status

first: Rugang

first: Pingyu


title: Effect of acute systemic inflammation on the Cerebral Vasculature in mice

summary: To capture the global gene expression patterns in the cerebral vasculature following acute systemic inflammation, we injected the mice with LPS and sacrificed them after 15 min, 30 min, and 4 hrs, followed by the isolation of the cerebral vessels. RNA was isolated from the vessel lysates, followed by library preparation and RNA sequencing.

overall_design: mRNA profiles of cerebral vessels isolated from the brains of mice (C57BL6, Wild type, 2-3 months old)  injected (intra peritoneal) with 10mg/kg LPS for 15 min, 30 min and 4 hrs or PBS. (n=3 in each group, every sample in each group includes the cerebral vessels from one male and one female mice pooled together)


title: m6A independent genome-wide METTL3 and METTL14 redistribution drives senescence-associated secretory phenotype [MeRIP-seq]

overall_design: MeRIP-seq in control and senescent IMR90 cell lines

last: Zhang


title: m6A independent genome-wide METTL3 and METTL14 redistribution drives senescence-associated secretory phenotype [RNA-seq]

overall_design: RNA-seq in control and senescent IMR90 cell lines with different METTL14 status

last: Liu


title: Viral-Induced Alternative Splicing of Host Genes Promotes Influenza Replication

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

summary: Competition and interplay between host and viral gene expression programs is a critical determinant of infection susceptibility and a potential target for anti-viral therapies. Viral infection is well documented to induce the expression of numerous host genes that are part of the innate immune response. Here we show that infection of human lung epithelial cells with Influenza A virus (IAV) also induces a broad program of alternative splicing of host genes. While these splicing-regulated genes are not enriched for known regulators of viral infection, we find that many of these genes do modulate the infection and/or replication of IAV in an siRNA screen. Moreover, inhibition of the IAV-induced splicing pattern in several genes tested also reduces viral infection. We further show that approximately a quarter of the IAV-induced splicing events are regulated by hnRNP K, a host protein we have previously implicated in the nuclear speckle-dependent splicing of the IAV M transcript.  Notably, hnRNP K abundance at nuclear speckles is increased upon IAV infection. We propose that this change in subnuclear localization may alter the accessibility of hnRNP K for host transcripts, thereby leading to a program of host splicing changes that promote IAV replication.

overall_design: Human lung adenocarcinoma epithelial cells were infected with flu virus  or knocked  down (via lentivirus-expressed shRNA) for hnRNP K or NS1-BP. Three bioligical replicates per condition with mock controls were used.

first: Matthew

middle: G

last: Thompson

first: Mark

last: Dittmar

last: Mallory

first: Prasanna

last: Bhat

first: Beatriz

middle: M

last: Fontoura

first: Sara

last: Cherry

middle: W


title: Skeletal muscle aging and pathways regulated by 15-PGDH inhibition

city: Stanford

last: Blau

state: CA

address: Stanford University School of Medicine, 269 Campus Drive, CCSR 3210

institute: Baxter Laboratory for Stem Cell Biology,

summary: To identify signalling pathways and genes regulated by 15-PGDH inhibition by SW033291

overall_design: RNA-seq of young and aged quadriceps muscle treated either with vehicle or 15-PGDH inhibitor SW033291

first: Adelaida

last: Palla

first: Meenakshi

last: Ravichandran

first: Helen


title: m6A independent genome-wide METTL3 and METTL14 redistribution drives senescence-associated secretory phenotype

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

overall_design: Refer to individual Series


title: Transforming growth factor beta signaling and decidual development in mice

status: Public on Dec 09 2020

city: COLLEGE STATION

first: Qinglei

last: Li

state: TX

address: 4458 TAMU

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

summary: Transforming growth factor β (TGFβ) signaling regulates multifaceted reproductive processes via its transmembrane receptor complex-associated machinery. It has been shown that the type 1 receptor of TGFβ (TGFBR1) is indispensable for female reproductive tract development, pregnancy success, and fertility. However, the role of TGFβ signaling in decidual development and function remains poorly defined. Our objective is to determine the impact of uterine-specific deletion of Tgfbr1 on the differentiation of endometrial stromal cells in pregnant mice, with a focus on the cellular and molecular properties of the decidua. An approach combining histological and immunohistochemical analyses, quantitative PCR, western blot, and RNA-sequencing was utilized. Our results show that decidual development is altered in TGFBR1 conditionally depleted uteri, substantiated by downregulation of genes associated with inflammatory response and uterine natural killer cell abundance, reduced presence of non-decidualized fibroblasts in the antimesometrial region, and impaired decidual cell differentiation. Notably, conditional ablation of TGFBR1 results in the formation of decidua containing more abundant alpha smooth muscle actin (ACTA2)-positive cells at the peripheral region of the antimesometrial side versus controls. This finding is corroborated by upregulation of a subset of smooth muscle marker genes in Tgfbr1 conditionally-deleted decidua. The abnormal cell differentiation is accompanied with increased cell proliferation and enhanced decidual ERK1/2 signaling upon decidual regression. In summary, this study has identified an important role of TGFBR1 in decidual cell differentiation by revealing that conditional ablation of TGFBR1 in the uterus profoundly impacts the cellular and molecular properties of the decidua. Our results suggest that TGFBR1 is required for the development of an integral decidua, a transient but crucial structure that supports embryo development.

overall_design: RNA sequencing of E6.5 wild type (WT) and Tgfbr1 Pgr-Cre knockout mouse decidual

first: Xin

last: Fang


title: m6A modification maps of mRNA in bone marrow-derived macrophages (BMDMs) from mouse

city: Chicago

first: Jie

last: Du

address: 900 E. 57th Street

institute: University of Chicago

summary: We report the application of sequencing technology for high-throughput profiling of mRNA m6A methylation in mice BMDMs with or without PBS treatment. By obtaining over thirty billion bases of sequence from m6A antibody immunoprecipitated mRNA, we generated m6A methylation maps of mouse BMDMs in the presence or absence of LPS. We find that SOCS1 mRNA methylation is robustly enhanced by LPS treatment in WT BMDMs, leading to the increase of SOCS1 expression. However, LPS challenge fails to increase SOCS1 expression in the M14-/- BMDMs, indicating m6A modification plays a cirital role in the SOCS1 expression. This study provides a framework for the application of comprehensive mRNA m6A profiling towards characterization of BMDMs.

overall_design: Examination of mRNA m6A modifications in mice BMDMs with or without LPS treatment.

first: Yanchun

first: Wang

last: Liao


title: Regulation of cigarette smoke-induced airway inflammation by JunD

city: Chengdu

first: Yongchun

last: Shen

address: Medical clinic 37 Guoxue Alley

institute: West China Hospital of Sichuan University

summary: Cigarette smoke (CS)-induced airway inflammation is an important pathologic feature of chronic obstructive pulmonary disease (COPD). Recent studies suggest a potential role of JunD in the regulation of inflammation, but its role in CS-induced airway inflammation has not been reported. This study aimed to determine its role in CS-induced airway inflammation through bioinformatics analysis and in vitro and in vivo experiments. Data from the Gene Expression Omnibus (GEO) database (GSE37147) were analyzed using weighted gene co-expression network analysis (WGCNA) and key driver analysis (KDA), and these analyses were validated using the GSE47460 dataset. The effect of CS on JunD expression was examined in lung tissues of COPD patients and CS-exposed mice and in CS extract (CSE)-exposed BEAS-2B cells. The effects of CSE on airway epithelial inflammatory injury after JunD knockdown or overexpression were also investigated. mRNA-seq and chromatin immunoprecipitation (ChIP)-seq were used to explore the mechanism of JunD-mediated CS-induced airway inflammation. Mice were injected with adeno-associated virus serotype 9 (AAV9)-JunD vector or control vector and then exposed to CS for 4 weeks, and lung tissue morphology and airway inflammation were evaluated. KDA of the lung function-related gene modules in GSE37147 revealed a potential role of JunD in COPD, which was validated in GSE47460. JunD was downregulated in lung tissues of COPD patients and CS-exposed mice and in BEAS-2B cells. JunD knockdown aggravated CSE-induced tumor necrosis factor (TNF)-α and interleukin (IL)-1β release by BEAS-2B cells, while JunD overexpression attenuated these effects. mRNA-seq and ChIP-seq identified several JunD-regulated genes, which are involved in the immune response and TNF signaling pathway and are commonly dysregulated in cell models of airway inflammation. In vivo, JunD overexpression attenuated the CS-induced inflammatory cell infiltration and inflammatory cytokine release in mouse lungs. Thus, JunD is involved in CS-induced airway inflammation and JunD-based therapy may be useful in CS-induced airway disorders.

overall_design: RNA-seq of JunD + CSE vs. EV + CSE in BEAS-2B cells, and ChIP-seq in CSE-induced BEAS-2B cells.

first: Deqing

last: Yang

first: Dan

last: Xu

first: Lian

first: Tao

last: Wang

first: Chun

last: Wan

first: Bai

last: Zhuo

first: Qiunan

last: Zuo

first: Lei

last: Chen

first: Fuqiang

last: Wen


title: Single cell RNA sequencing of advanced gastric cancer

city: Seoul

first: Hye Hyeon

last: Eum

address: 222, Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of Korea

summary: To define the cellular characteristics of malignant ascites of advanced gastric cancer patients and search for therapeutic strategies, we applied single cell RNA sequencing to cancer cells and tumor associated macrophages (TAM), present in large numbers in malignant ascites. We analyzed 180 cells from 4 malignant ascites and 1 cerebrospinal fluid metastasis. The results indicate that the anti-inflammatory characteristics of the tumor associated macrophages are concocted by the tumor cells. By constructing reference transcriptomes for M1 and M2 type macrophages, we found a strong non-inflammatory property of macrophages recovered from the malignant ascites of gastric cancer.

overall_design: Total five samples were collected from four patients diagnosed as advanced gastric cancer. We obtained four peritoneal ascites and one cerebrospinal fluid (AGC04CSF). To construct reference M1 or M2 type macrophages, PBMC-derived CD14+ cells were collected from two healty donors. Isolated CD14+ cells were cultured 7 days with M-CSF. At day 7, M-CSF containing media were removed then LPS and IFN-γ (for M1) or IL-4 and IL-10 (for M2) were supplied. After additional 48 hour of culture, cells were collected by smooth scrapping then applied to single-cell RNA sequencing. By removing low quality cells, total 162 cells from AGC patients, 97 cells from M1, and 45 cells from M2 were analyzed.

first: Hae-Ock

last: Lee

first: Woong-Yang

last: Park

first: Jeeyun


title: Effect of Ad5-porcine interferon-α  pre-treatment in Ebola virus induced gene expression in pigs

city: toronto

first: Chandrika

last: Senthilkumaran

state: ON

address: 8, Wisteria RD

country: Canada

institute: Canadian food inspection agency

summary:
Microarray analysis was done to compare the response of EBOV-infected pigs that were pre-treated with Ad5-porIFNα or PBS. At 3 days post EBOV infection, pigs that had been pre-treated with Ad5-porIFNα displayed upregulation of many genes related to the immune response in contrast to pigs treated with PBS.
The largest category of induced genes included cytokines and chemokines that affect T-cell differentiation (IL27) and T-cell recruitment (CCL5, CCL23, CCL24, CXCL9, CXCL11)

overall_design: To investigate any modulatory effects of the Ad5-porIFNα pre-treatment on the course of EBOV-induced pathogenesis, we harvested PBMCs from each pig at 3 and 5 or 6 DPI, and the BALF pellet of all animals at the time of necropsy. We then extracted RNA from these samples and performed microarray analysis

first: Andrea

last: Kroeker

first: Greg

last: Smith

first: Fayna

last: DiazSanSegundo

first: Bradely

last: Pickering

first: Hana

last: Weingartl

first: Teresa

last: De Los Santos


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and METTL14 KO bone marrow-derived macrophages(BMDM) Transcriptomes

first: Jie

last: Du

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived BMDM transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: BMDM mRNA profiles of 6-week-old wild-type (WT) and METTL14 knockout (M14−/−) mice with or without LPS treatment were generated by deep sequencing, in triplicate, using Illumina Hi-Seq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build mm9) and identified 11,902 transcripts in WT and M14−/− BMDMs with BWA workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 20% of the transcripts showed differential expression between the WT and M14−/− BMDMs, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to BMDM function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of BMDM transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: BMDM mRNA profiles of 6-week old wild type (WT) and M14-/- mice with or without LPS treatment

first: Yanchun

last: Li

first: Wang

last: Liao


title: m6A independent genome-wide METTL3 and METTL14 redistribution drives senescence-associated secretory phenotype [carRNA-m6A-seq]

first: Priyankara

last: Wickramasinghe

overall_design: carRNA-m6A-seq in control and senescent IMR90 cell lines with and without siMETTL3 and siMETTL14 knockout

first: Rugang

last: Zhang

first: Pingyu

last: Liu


title: Characterization and generation of human definitive multipotent hematopoietic stem/progenitor cells

city: Guangzhou

first: Tianyu

last: WANG

address: 190 Kai Yuan Avenue, Science Park

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

summary: Definitive hematopoiesis generates hematopoietic stem/progenitor cells (HSPCs) that give rise to all mature blood and immune cells, but remains poorly defined in human. Here, we resolve human hematopoietic populations at the earliest hematopoiesis stage by single-cell RNA-seq. We characterize the distinct molecular profiling between early primitive and definitive hematopoiesis in both human embryonic stem cell (hESC) differentiation and early embryonic development. We generate definitive HSPCs from hESCs that hold the multipotency to differentiate various blood and immune cells, as validated by single-cell clonal assay. Strikingly, the generated HSPCs from hESCs give rise to various blood and lymphoid lineages in vivo. Lastly, we characterize gene-expression dynamics in definitive and primitive hematopoiesis and reveal an unreported role of ROCK-inhibition in enhancing human definitive hematopoiesis. Our study provides a prospect for understanding human early hematopoiesis and a firm basis to generate blood and immune cells for clinical purposes.

overall_design: 10X Single-cell RNASeq of FACS-sorted CD43+ hematopoietic cells differentiated from H1 hESCs at day 8 (hESCs-HPCs), as well as FACS-sorted Lin-CD34+CD38- HSPCs mobilized in human peripheral blood (PB-HSPCs).

first: Yanling

last: Zhu

last: Wang

first: Jiaming

last: Gu

first: Guangjin

last: Pan


title: m6A independent genome-wide METTL3 and METTL14 redistribution drives senescence-associated secretory phenotype [ChIP-seq]

overall_design: CHIP-seq and cut-and-run in control and senescent IMR90 cell lines


title: Gene expression data from whole lung homogenates

city: Ann Arbor

first: Vibha

middle: N.

last: Lama

state: Michigan

address: 1150 W. Medical Center Drive

department: Internal Medicine

institute: University of Michigan

summary: Understanding the distinct pathogenic mechanisms which culminate in allograft fibrosis and chronic graft failure

overall_design: Lung explants were harvested at various timepoints post-transplant

middle: N


title: Early zebrafish development time course transcriptome

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

department: Computational Biology

institute: Stowers Institute for Medical Research

overall_design: Three RNA-seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly (A) capture and ribosomal depletion. Also, we sequenced embryos, using poly (A) capture, that were treated with alpha-amanitin (200ng/ul) to inhibit zygotic transcription.

first: Ariel

middle: A

last: Bazzini

first: Santiago

last: Medina


title: To study the function of KLF5 in squamous cancers and gastrointestinal cancers [HiChIP]

city: Salt Lake City

first: Xiaoyang

address: 1950 CIrcle of Hope

institute: University of Utah

summary: To identify KLF5 target genes by integrating ChIP-seq, HiChIP and RNA-seq assays

overall_design: HiChIP of H3K27ac to map enhancer-promoter loops in HARA squamous cancer and HT55 colorectal cancer cell lines

first: Yanli


title: To study the function of KLF5 in squamous cancers and gastrointestinal cancers [RNA-seq]

summary: To identify KLF5 target genes and study the gene regulation function of KLF5 by integrating ChIP-seq, HiChIP and RNA-seq assays

overall_design: RNA-seq in HARA squamous cancer and HT55 colorectal cancer cell lines with and with KLF5 knockout


title: Evaluation of mutation rate in plasmid and virus

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

institute: Icahn school of medicine at Mount Sinai

summary: We report the mutation profile of measles F gene by saturating mutagenesis.

overall_design: We evaluate the mutation rate of measles F gene in pCDNA3 backbone (shuttle plasmid), pEMC backbone (genome plasmid), and RT-PCR amplicon from virus after screening.

first: Satoshi

last: Ikegame

first: Benhur

last: Lee


title: To study the function of KLF5 in squamous cancers and gastrointestinal cancers


title: MACE RNA Sequencing Analysis of Conjunctival Squamous Cell Carcinoma and Papilloma Using Formalin-Fixed Paraffin-Embedded Tumor Tissue

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: The aim of this study was to elucidate the molecular mediators of conjunctival squamous cell carcinoma (SCC) and Papilloma (Pap) and to define their expression signature as an aid to the histologic classification. The transcriptional signatures of both conjunctival SCC and Pap presented in this study may improve our understanding of the diseases and their diagnosis and eventually contribute to successful personalized therapeutic approaches.

overall_design: MACE RNA sequencing of seven human conjunctival SCC, seven conjunctival Pap and ten healthy conjunctival samples as controls.

first: Stefaniya

last: Boneva

first: Anja

last: Schlecht

first: Peipei

first: Daniel

last: Boehringer

first: Hans

last: Mittelviefhaus

first: Thomas

last: Reinhard

first: Claudia

last: Auw-Haedrich

first: Guenther

last: Schlunck

first: Julian

last: Wolf


title: SIRT3, a therapeutic target in DLBCL

city: Baltimore

first: Heather

middle: Huot

last: Creasy

state: Maryland

address: 801 West Baltimore St

institute: Institute for Genome Sciences

summary: We report that in absence of ATM signaling SIRT3 stimluated pathways are critical for development of DLBCL

overall_design: RNA sequencing in DLBCL cell line HLY with wild type ATM (NT-HLY) and HLY cell line expressing shATM lentivirus for genetic inhibition of ATM

first: Kavita

last: Bhalla


title: Metabolism in synovial macrophages are reprogrammed by synovial fibroblasts under inflammatory condition

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

summary: Macrophages have plasticity to adapt microenvironment. In joint tissue, synovial macrophages (SM) and synovial fibroblasts (SF) are maintained in the homeostasis. In Rheumatoid arthritis, crosstalk between SM and SF via inflammatory response induce abnormal activation in respective cells and contribute to disease progression. However, the activation mechanisms in SM which are encouraged by SF are largely unclear. Here, we demonstrated metabolic reprogramming and immunological activation in SM by secretary stimulations from SF using primary culture synovial cell derived from arthritis model mice. To analyze interaction between SM and SF, primary culture of murine synovial cells was performed, respectively. RNA-seq analysis showed SF express abundant secretion-related gene. Thus, we investigated whether conditioned medium from SF (SF-CM) affects biological activity in SM. As the results, SF-CM condition induced both glycolysis and mitochondrial respiration to SM with increased uptake of glucose and glutamine at least, accompanied with cell survival. In addition, several inflammation markers were also upregulated in SM by SF-CM condition. Taken together, these results suggest that metabolic reprogramming were induced in SM by secretory stimulations from SF, followed by activated inflammatory response and long-live. These indicate that such phenotypes of SM may contribute to chronic inflammation in Rheumatoid arthritis

overall_design: mRNA profiles of primary synovial macrophages and synovial fibroblasts obtained from swollen ankle in CAIA mice were generated by deep sequencing, in triplicate, using Illumina Miseq.

first: Noritaka

last: Saeki


title: Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development

city: Amsterdam

first: Louis

last: Vermeulen

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine

country: Netherlands

institute: Academic Medical Center

summary: We use a 3D in vitro organoid model to study the early phase of colorectal cancer development. In reaction to Wnt activation we observe downregulation of location specific genes and differentiation markers. Furthermore, the signature of Wnt target genes differs between organoids representing three locations of the murine intestine. The location specific Wnt signatures are dominated by genes which have been lowly expressed in the tissue of origin, and are the targets of transcription factors that are activated following enhanced Wnt signalling. We concude that the cell of origin has a substantial effect on the reaction to Wnt activation in a simple intestinal adenoma model.

overall_design: From three different murine intestinal locations we grow organoids. These are transformed to resemble adenomas after Wnt activation through lentiviral transduction with a stable form of beta-Catenin. The gene expression before and after Wnt activation is compared within each intestinal origin and across the three locations using RNA sequencing.

first: Ronja

last: Adam

first: Cayetano

last: Pleguezuelos-Manzano

first: Salvatore

last: Simmini

first: Nicolas

last: Léveillé


title: High-throughput sequencing of zebrafish wild-type and duox mutant larvae

city: Hefei

first: bing

last: hu

address: School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China

summary: To determine the molecular basis for the dual oxidase in circulation in duox mutant zebrafish, we performed high-throughput sequencing at 4 dpf. Results revealed 375 up-regulated genes and 360 down-regulated genes in the duox mutant zebrafish compared with wild-type zebrafish. We found that some mitochondrial genes are down-regulated in duox mutant zebrafish, which was reconfirmed with qRT-PCR.

overall_design: mRNA profiles of 4 dpf wild-type and duox mutant zebrafish were generated by deep seqeuncing.

first: R

last: Dalong

first: Y

last: Leiqing


title: Translational profiling reveals that mRNAs encoding cuticle collagens are translationally repressed upon nsun-1 knockdown

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

summary: By comparing mRNAs contained in the polysome fraction to total mRNAs in Caenorhabditis elegans exposed to either RNAi control or nsun-1 RNAi, we found that loss of NSUN-1 translationally represses genes associated with collagens, cuticle integrity and development. These changes explain phenotypes of nsun-1 depletion, which include impaired fecundity, gonad extrusion and reduced barrier function.

overall_design: 12 samples in total, three independent biological replicates, RNAi control vs. nsun-1 RNAi, total mRNAs and polysomal mRNAs for all conditions

first: Clemens

last: Heissenberger


title: Single cell RNA-seq analysis of feeder-free iPSC-derived gliogenic NS/PCs and neurogenic NS/PCs

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

summary: We performed single cell RNA sequencing to analyze the transcriptional profile of gliogenic NS/PCs and neurogenic NS/PCs derived from the same parental feeder-free iPSCs.

overall_design: Sigle cell RNA-seq profiling of 91 neurogenic NS/PCs and 150 gliogenic NS/PCs.


title: Adult ventricular cardiomyocytes

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

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

overall_design: Refer to individual Series


title: Comprehensive transcriptome analysis in Babao Dan treated pancreatic cancer cell line derived xenograft mouse models

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Babao Dan has efficient therapeutic effects on patients with pancreatic cancer.However, little is known about how Babao Dan works on molecular levels.Here, we comprehensively investigate the transcriptome change after Baoba Dan treatment through a pancreatic cancer derived cell line xenografts mouse model.

overall_design: Illuminate the complexity of transcriptome change after Babao Dan treatment through high-throughput sequencing data.


title: Sequential expression profile of feeder-free iPSC-derived gliogenic NS/PCs by RNA-seq

summary: We performed RNA sequencing to profile the temporal dynamics of gene expression during gliogenic NS/PC differentiation from human iPSCs.

overall_design: RNA-seq profiles comparing feeder-free iPSC, feeder-free iPSC-derived embryoid body, and feeder-free iPSC-derived gliogenic NS/PCs.


title: Photoperiod-mediated Chromatin Accessibility in the Single Cell Types of Leaf Phloem and Epidermis in Arabidopsis

city: beijing

first: Liangyu

last: Liu

address: 105, North Road of Western 3rd Ring

institute: Capital Normal University

summary: Photoperiodic control of the phase transition from vegetative to reproductive growth plays a key role in high plants. Although leaves are considered to be the major organs to perceive the day-length signal, it is not clear what the specific responses happen in the vasculature and epidermis tissues. Here, we performed ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and RNA-seq with purified phloem and epidermis nuclei by applying INTACT (isolation of nuclei tagged in specific cell/tissue types) sorting method. We found that accessible chromatin regions (ACR) in phloem showed higher variations than epidermis during sensing the long-day signal. These cell/condition-type-specific ACR changes are basically related with gene expression. Taken together, our cell type specific studies sheds light on photoperiodic control of the flowering transition and also investigating of plant development mechanism.

overall_design: ATAC-seq and RNA-seq in 2 cell types.

first: Zefu

last: Lu


title: PRO-seq assay in adult ventricular cardiomyocytes

summary: PRO-seq assay was performed for the quantitative detection of nascent pre-mRNA transcripts induced by phenylephrine (PE) and adenoviral overexpression of SRF serine-103 mutants in adult ventricular cardiomyocytes

overall_design: Adult ventricular cardiomyocytes were stimulated with PE 24 hours after adenoviral infection with SRF WT, S103A and S103D mutants. Nuclei were collected 1 hour after PE treatment, then subjected to precision nuclear run-on sequencing (PRO-seq).

first: Jinliang


title: ChIP assay in adult ventricular cardiomyocytes

summary: ChIP assay was performed to study the genomic location of SRF myocytes cistrome in adult ventricular cardiomyocytes. The myocytes were stimulated by phenylephrine (PE) combined with adenoviral overexpression of SRF serine-103 mutants.

overall_design: Adult ventricular cardiomyocytes were stimulated with PE 24 hours after adenoviral infection with SRF WT, S103A and S103D mutants. Cells were fixed 1 hour after PE treatment, then subjected to Chromatin Immunoprecipitation (ChIP) by PolII, H3K27ac, Flag, SRF and p-SRF(s103) antibodies.


title: H3K79me2 dynamics in medium spiny neurons mediate long-term behavioral and cell type-specific molecular effects of early life stress

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Animals susceptible to chronic social defeat stress (CSDS) exhibit depression-related behaviors, and show aberrant transcription across several limbic brain regions. The nucleus accumbens (NAc) in particular shows unique susceptible versus resilient phenotypes at the transcriptional, neuroanatomical, and physiological levels. Early life stress (ELS) promotes susceptibility to CSDS in adulthood, but associated enduring changes in transcriptional control mechanisms in NAc have not yet been investigated. Here, we examined long-lasting changes in histone modifications induced in NAc by ELS and studied their underlying mechanisms in mediating heightened lifelong stress susceptibility in male and female mice. We identify methylation of lysine 79 of histone H3 (H3K79me) and the enzymes that control this modification, selectively in D2-type medium spiny neurons, as crucial for the expression of ELS-induced stress susceptibility, and reveal the transcriptional networks regulated by this mechanism. Finally, we demonstrate the potential clinical viability of this approach by showing that systemic delivery of a small molecule inhibitor of H3K79me reverses ELS-induced behavioral deficits.

overall_design: Studying methylation of lysine 79 of histone H3 (H3K79me) in D2-type medium spiny neurons, studying transcriptional effects downstream of this epigenetic mechanism

first: Hope

last: Kronman

first: Catherine

last: Peña

first: Angélica

last: Torres-Berrío

first: Simone

last: Sidoli

first: Benjamin

last: Garcia

first: Li

last: Shen

first: Eric

last: Nestler


title: Human transcription factors responsive to initial reprogramming are predominantly legitimate during iPSC reprogramming

status: Public on Dec 08 2020

city: Birmingham

first: Kejin

last: Hu

state: AL

address: 1825 University Blvd.

department: Department of Biochemistry and Molecular Genetics

institute: UAB School of Medicine

summary: The four transcription factors OCT4, SOX2, KLF4 and MYC (OSKM) together can convert human fibroblasts to induced pluripotent stem cells (iPSCs). It is, however, perplexing that they can do so only for a rare population of the starting cells with a long latency. Transcription factors (TFs) define identities of both the starting fibroblasts and the end product, iPSCs, and are of paramount importance for the reprogramming process as well. It is critical to upregulate or activate iPSC-enriched TFs while downregulate or silence the fibroblast-enriched TFs. This report explores the initial TF responses to OSKM as the molecular underpinnings for both the potency aspect and limitation sides of the OSKM reprogramming. The author first defined the TF reprogramome, i.e., the full complement of TFs to be reprogrammed. Most TFs were resistant to OSKM reprogramming at the initial stages, which agrees with the inefficiency and long latency of iPSC reprogramming. Surprisingly, the current analyses revealed that the majority of the TFs (83 genes) that did respond to OSKM induction underwent legitimate reprogramming. The initial legitimate transcriptional responses of TFs to OSKM reprogramming were observed from fibroblasts from a different individual.  Such early biased legitimate reprogramming of the responsive TFs aligns well with the robustness aspect of the otherwise inefficient and stochastic OSKM reprogramming

overall_design: There are 19 RNA-seq in this deposit. We sequenced RNA from two human embryonic stem cell (ESC) lines, H1 and H9, each of which has two repeats. We have also sequenced two normal human fibroblast cell lines from different individuals  four technical repeasts for each cell line. We have also sequenced RNA from one fibroblasts transduced with the four reprogramming factors (OSKM), two of which were 48 hours post transduction and the other two were 72 hours post factor transduction. We additionally sequenced RNA from another fibroblast cell line transduced with OSKM, but the RNA samples were taken at 96 hours post transduction (three technical repeats).

first: Ricardo

last: Cevallos

first: Yvonne

last: Edwards


title: Effect of glutathione reductase (Gsr) deficiency on lung transcriptomics in embryonic mice and neonatal and adult mice exposed to hyperoxia.

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Gsr is an antioxidant enzyme responsible for maintaining the supply of reduced glutathiones which reduce reactive oxigen species and maintain cellular redox balance. However, the the role for Gsr in the developemnt of oxidative lung injury is not well characterized.
We used microarray analysis to identify Gsr-dependent genes and pathways in embyronic, neonate, and adult lungs. We also determined Gsr-dependent lung transcriptomics in mouse neonates and adults which were neonatally exposed to hyperoxia (O2) or air.

overall_design: Lungs from Gsr-wildtype (Gsr-WT, C3H/HeN) and Gsr-knockout (Gsr-KO) embryos were isolated at embryonic day 19 (E19). Lungs from Gsr-wildtype and Gsr-knockout mice exposed to room air or hyperoxia during postnatal days 0-5 (P0-P5) were collected at P5 and P56.  Lung total RNA was isolated and hybridization on Affymetrix Mouse 430_2 arrays.

first: Hye-Youn

last: Cho

first: Steven

last: Kleeberger

first: Trent

last: Tipple


title: Differential Gene Expression Analysis Reveals Pathways Important in Early Post-Traumatic Osteoarthritis in an Equine Model

city: Urbana

first: Ann

middle: Marie

last: Kemper

state: IL

address: 1008 W Hazelwood Dr

institute: University of Illinois

summary: Objective: To quantify gene expression changes in the synovium of osteoarthritis-affected joints in an equine metacarpophalangeal joint (MCPJ) chip model specifically designed to recapitulate early post-traumatic osteoarthritis (PTOA). Design: Synovial samples were collected arthroscopically from the MCPJ of 11 adult horses before (pre-OA) and after (OA) surgical induction of osteoarthritis and from sham-operated joints. Briefly, in this model, an osteochondral fragment is created in one randomly chosen MCPJ at the proximal dorsomedial aspect of the first phalanx. The fragment is replaced in the fragment bed after creation so that subchondral bone is not exposed to the opposing cartilage surface. The opposite MCPJ is sham-operated. After a two week recover period, the horses are treadmill-exercised for 14 weeks and then the osteochondral fragment is removed (16 weeks after creation). Synovial tissue samples were collected arthroscopically from the MCPJ of eleven adult horses before (pre-OA) and 16 weeks after (OA) experimental induction of OA as well as from the sham-operated joints (sham).  After sequencing of synovial RNA, Salmon was used to quasi-map reads to the reference genome and quantify transcript abundances. Differential expression analysis was performed with the limma-treat method using a fold-change cutoff of 1.1. Functional annotation was performed with PANTHER and Reactome at FDR < 0.05.  Results: RNA was successfully extracted from 28 samples (6 pre-OA, 11 OA, 11 sham). Sequencing yielded 15.7-29.4 million paired-end reads per sample. “Sham” and “pre-OA” were not different and were grouped. 321 genes were upregulated and 351 genes were downregulated in OA synovium compared to unaffected. Gene ontology (GO) terms related to extracellular matrix (ECM) organization and growth factor binding were overrepresented among differentially expressed genes. There were 20 significantly enriched pathways; these included pathways involved in ECM turnover, O-glycosylation of TSR domain-containing proteins, and growth factor signaling.  Conclusions:  Most enriched pathways and overrepresented GO terms reflect a state of high metabolic activity and tissue turnover in OA-affected tissue, suggesting efforts at healing and restoring homeostasis. Limitations of this study include a small sample size and capture of a single point post-injury. Differentially expressed genes falling within key pathways may represent potential diagnostic markers or therapeutic targets for PTOA.

overall_design: Synovial samples were collected arthroscopically from the MCPJ of 11 adult horses before (pre-OA) and after (OA) surgical induction of osteoarthritis and from sham-operated joints.  Briefly, in this model, an osteochondral fragment is created in one randomly chosen MCPJ at the proximal dorsomedial aspect of the first phalanx. The fragment is replaced in the fragment bed after creation so that subchondral bone is not exposed to the opposing cartilage surface. The opposite MCPJ is sham-operated. After a two week recover period, the horses are treadmill-exercised for 14 weeks and then the osteochondral fragment is removed (16 weeks after creation). Synovial tissue samples were collected arthroscopically from the MCPJ of eleven adult horses before (pre-OA) and 16 weeks after (OA) experimental induction of OA as well as from the sham-operated joints (sham). RNA was successfully extracted from 28 samples (6 pre-OA, 11 OA, 11 sham)

first: Annette

last: McCoy

first: Mary

middle: K

last: Boyce

first: Murray

middle: P

last: Brown

first: Trumble

last: Troy


title: A longitudinal and transancestral analysis of DNA methylation patterns and disease activity in lupus patients

city: Pittsburgh

first: Amr

last: Sawalha

address: 4401 Penn Avenue

institute: University of Pittsburgh

summary: Epigenetic dysregulation is implicated in the pathogenesis of lupus. We performed a longitudinal analysis to assess changes in DNA methylation in neutrophils collected from 54 lupus patients over 4 years of follow up and across disease activity levels using 229 patient samples.

overall_design: Illumina Infinium MethylationEPIC array of genomic DNA from neutrophils extracted from whole blood from 54 systemic lupus erythematosus (SLE) patients over time for a total of 229 timepoints.

middle: H

first: Patrick

last: Coit


title: Glomerular microRNA data of the kidney podocyte-specific cyclin-G associated kinase (Gak) deficient mice

city: New Haven

first: Xuefei

last: Tian

state: CT

address: 300 Cedar Street

department: Nephrology/Internal Medicine

institute: Yale University School of Medicine

summary: Evidence for reduced expression of cyclin-G associated kinase (GAK) in glomeruli of chronic kidney disease patients was observed in the Nephroseq human database and was found to be associated with the decline in kidney function. To examine the role of GAK,  a protein that functions to uncoat clathrin during endocytosis, we generated podocyte-specific Gak knockout mice (Gak KO) which developed progressive proteinuria and kidney failure with global glomerulosclerosis. We isolated glomeruli from the mutant mice to perform messenger RNA profiling and unearthed evidence for dysregulated podocyte calpain protease activity as an important contributor to this process. Treatment with calpain inhibitor III specifically inhibited calpain-1/-2 activities, mitigated the degree of proteinuria and glomerulosclerosis, and led to a striking increase in survival in the Gak KO mice.  Podocyte-specific deletion of Capns1, essential for calpain-1 and calpain-2 activities, also improved proteinuria and glomerulosclerosis in Gak KO mice. Increased podocyte calpain activity mediated proteolysis of IkB  resulted in increased NF-kBp65 induced Gadd45b expression in the Gak KO mice. Our results suggest that loss of podocyte associated Gak induces glomerular injury secondary to calcium dysregulation and aberrant calpain activation, which when inhibited, can provide a protective role.

overall_design: The freshly glomeruli samples were isolated from the Control mice and Gak KO mice at 3 weeks of age for the microRNA analysis. Each sample contained 3 mice in order to get the sufficient glomeruli samples, and 2 independent experiments were analyzed and summarized.

first: Shuta

last: Ishibe

first: Yan

last: Zhang

first: Kazunori

last: Inoue

first: Zhenhai


title: Cellular proteostasis collapse in mammalian senescence

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

institute: Technion

summary: Proteostasis collapse, the diminished ability to maintain protein homeostasis, has been established as a hallmark of nematode aging. However, whether proteostasis collapse occurs in humans has remained unclear. Here, we demonstrate that proteostasis decline is intrinsic to human senescence. Using transcriptome-wide characterization of gene expression, splicing, and translation, we found a significant deterioration in the transcriptional activation of the heat shock response in stressed senescent cells. Furthermore, phosphorylated HSF1 nuclear localization and distribution were impaired in senescence. Interestingly, alternative splicing regulation was also dampened. Surprisingly, we found a decoupling between different unfolded protein response (UPR) branches in stressed senescent cells. While young cells initiated UPR-related translational and transcriptional regulatory responses, senescent cells showed enhanced translational regulation and endoplasmic reticulum (ER) stress sensing; however, they were unable to trigger UPR-related transcriptional responses. This was accompanied by diminished ATF6 nuclear localization in stressed senescent cells. Finally, we found that proteasome function was impaired following heat stress in senescent cells, and did not recover upon return to normal temperature. Together, our data unraveled a deterioration in the ability to mount dynamic stress transcriptional programs upon human senescence with broad implications on proteostasis control and connected proteostasis decline to human aging.

overall_design: RNA-Seq and Ribo-Seq for young and senescent WI-38 cells with and without heat shock

first: Niv

last: Sabath


title: Gliogenic neural progenitors from HLA "Super donor" iPSCs trigger functional recovery in spinal cord injury model

first: Tsukasa

last: Sanosaka


title: The role of Salmonella Genomic Island 4 in metal tolerance of Salmonella enterica serovar I 4,[5],12:i:- pork outbreak isolate USDA15WA-1

city: Columbia

first: Sathesh

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: Multidrug-resistant (MDR; resistance to >3 antimicrobial classes) Salmonella enterica serovar I 4,[5],12:i:- strains were linked to a 2015 foodborne outbreak from pork. Strain USDA15WA-1, associated with the outbreak, harbors an MDR module and the metal tolerance element Salmonella Genomic Island 4 (SGI-4). Characterization of SGI-4 revealed that conjugational transfer of SGI-4 resulted in the mobile genetic element (MGE) replicating as a plasmid or integrating into the chromosome. Tolerance to copper, arsenic, and antimony compounds was increased in Salmonella strains containing SGI-4 compared to strains lacking the MGE. Following Salmonella exposure to copper, RNA-seq transcriptional analysis demonstrated significant differential expression of diverse genes and pathways, including induction of numerous metal tolerance genes (copper, arsenic, silver, and mercury). Evaluation of swine administered elevated concentrations of zinc oxide (2,000 mg/kg) and copper sulfate (200 mg/kg) as an antimicrobial feed additive (Zn+Cu) in their diet for 4 weeks prior to and 3 weeks post-inoculation with serovar I 4,[5],12:i:- indicated that Salmonella shedding levels declined at a slower rate in pigs receiving in-feed Zn+Cu compared to control pigs (no Zn+Cu). The presence of metal tolerance genes in MDR Salmonella serovar I 4,[5],12:i:- may provide benefits for environmental survival or swine colonization in metal-containing settings.

overall_design: Transcriptomic profile of multidrug-resistant Salmonella exposed to 0 and 5 mM CuSO4 for 30 and 60 minutes. Transcriptomic changes was observed using RNAseq, three biological replicates were generated for each condition.

first: Bradley

middle: L

last: Bearson

first: Julian

last: Trachse

first: Daniel

last: Shippy

first: Brian

last: Kerr

first: Crystal

last: Loving

last: Brunelle

first: Shelby

last: Curry

first: Nicholas

last: Gabler

first: Shawn

middle: D


title: Expression profile of mouse embryonic stem cells upon knockdown or overexpression of YAP

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

institute: University of Milan

summary: We  looked at the expression profiles of embyonic stem cells (ESCs) 48 hours after YAP siRNAs transfection, to knockdown YAP expression, or after pCAG-YAP transfection, to over-express YAP protein. Total RNA was isolated from three independent experiments and analyzed by RNA-seq.

overall_design: mRNA profile of ESCs knockdown for YAP expression (siRNAs) vs CTR cells (scrambled) and mRNA profile of ESCs overexpressing YAP  (pCAG-YAP plasmid) vs CTR cells (pCAG-GFP). Each condition has three independent biological replicates.

first: Fabiana

last: Passaro

first: Ilaria

last: De Martino

first: Caterina

last: Manzari

first: Graziano

last: Pesole

first: Tommaso

last: Russo


title: Emergence of Dynamic Neuro-Immune Profile During Mid-life Aging in the Female Brain: Implications for Alzheimer’s Disease Risk [Hot flash]

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

summary: Aging and endocrine transition states can significantly impact inflammation across organ systems. Neuroinflammation is a well-documented feature in Alzheimer’s disease (AD). Herein, we investigated neuro-inflammation that emerges during mid-life aging, chronological and endocrinological, in the female brain as an early initiating mechanism driving AD risk later in life.  Analyses were conducted in a translational rodent model of mid-life chronological and endocrinological aging followed by validation in transcriptomic profiles from women versus age-matched men. In the translational model, the neuroinflammatory profile of mid-life aging in females was endocrine and chronological  state specific, dynamic, anatomically distributed and persistent. Microarray dataset analyses of aging human hippocampus indicated a sex difference in neuroinflammatory profile in which women exhibited a profile comparable to the pattern discovered in our translational rodent model, whereas age-matched men exhibited a profile consistent with low neuro-immune activation. Translationally, these findings have implications for therapeutic interventions during mid-life to decrease late-onset AD risk.

overall_design: Female rats were aged to 6 months before OVX and followed with E2 estrogen or estrogen prevention treatments

first: Shang

last: Yuan

first: Yin

last: Fei

first: Mishra

last: Aarti


title: Methylation pattern profile of mouse embryonic stem cells upon knockdown of YAP, during neuroectodermal differentiation

type: Methylation profiling by high throughput sequencing

summary: We analyzed by BS-seq the methylation pattern of CTR and YAP knockdown cells in undifferentiated (T0) embryonic stem cells (ESCs) vs cells differentiated toward neuroectodermal fate at day 4 of differentiation (T4). Two biological duplicates for each condition.

overall_design: Methylation pattern of ESCs knockdown for YAP expression (siRNAs) vs CTR cells (scrambled). Samples were analysed in undifferentiated (T0) and Differentiated (T4) conditions.

first: Anna

last: D'erchia


title: Single-cell RNA sequencing of mesenchymal stromal cells from primary donor-matched tissue sources reveals functional heterogeneity in immune activity and cell motility

city: Ithaca

first: Gerlinde

last: Van de Walle

state: NY

address: 235 Hungerford Hill Road

department: Microbiology and Immunology

institute: Cornell University

summary: The efficacy of mesenchymal stromal cell (MSC) therapy is thought to depend on the intrinsic heterogeneity of MSC cultures isolated from different tissue sources as well as individual MSCs isolated from the same tissue source, neither of which is well understood. The horse model, in contrast to human and mouse, allows for simultaneous sample collection from multiple tissues of the same animal, which circumvents the inter-donor variation in MSC cultures observed in other models. In the present study, we performed single-cell RNA sequencing (scRNA-seq) on primary equine MSCs that were collected from three donor-matched tissue sources; adipose tissue (AT), bone marrow (BM), and peripheral blood (PB). We observed both inter- and intra-source heterogeneity across the three sources of equine MSCs.

overall_design: Mesenchymal stem cells were derived from 3 donor-matched tissues; adipose tissue, bone marrow, and peripheral blood and subjected to single cell RNA sequencing

first: Rebecca

last: Harman

first: Roosheel

middle: S

last: Patel

first: Jennifer

last: Fan

first: Jee

middle: E

last: Park

first: Brad

middle: R

last: Rosenberg


title: Immune cells transcriptome

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: RNA seq of dendritic (CD86+), mast (FCER+) and other  cells (CD86-FCER-) derived from DMSO, SR1 (500nM), UM171 (35nM) exposed cord blood cells culture (at day 7)

overall_design: CD34+ cord blood cells (3 independent pool)  were cultured in stemspan media (4 cytokines) in presence of compounds for 7 days and sorted for CD86, CD34 or FCER1 expression. RNA were extracted from sorted subsets and sequences were obtained with an illumina HiSeq 2000 sequencer.

first: Jalila

last: Chagraoui

first: Céline

last: Moison


title: Genomic architecture and evolution of a seasonal reaction norm [Hi-C]

first: Karin

middle: Revka Loek

last: van der Burg

address: 215 Tower Road, Corson Hall

department: EEB

summary: Here we used artificial selection to assimilate a seasonal wing color phenotype from a naturally plastic population of butterflies. Using SNP association and RNAseq we mapped three genes responsible for wing color fixation, including the color pattern supergene cortex. Combined with endocrine and chromatin accessibility assays, we found that the rapid transition of wing coloration from an environmentally determined trait to a fixed, genetic trait occurred through selection on cis-regulatory alleles of genes with wing-specific functions, not by changes in environmental detection or hormone signaling.

overall_design: We used mRNA-seq and ATAC-seq to measure mRNA levels and chromatin accessibility levels in four developmental stages, 3 replicates each

first: James

middle: J

last: Lewis

first: Benjamin

last: Brack

first: Richard

last: Fandino

first: Anyi

last: Mazo-Vargas

first: Robert

last: Reed


title: YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation

first: Federico

last: Zambelli

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

overall_design: Refer to individual Series


title: Paracardial fat remodeling affects systemic metabolism through alcohol dehydrogenase 1.

city: Columbus

first: Federica

last: Accornero

state: Ohio

address: 473 W 12th Ave

department: Physiology and Cell Biology

institute: The Ohio State University

summary:
Affymetrics expression data from pCF and iVF tissues of WT C57 male mice
Affymetrics microarrays to detail the transcriptomic differences between pCF and iVF

overall_design: mRNA from pCF and iVF depots of WT mice was extracted and then hybridized on Affymetrix microarray.

first: Ouliana

last: Ziouzenkova

middle: M

last: Petrosino

first: Jacob

middle: Z

last: Longenecker

first: Srinivasagan

last: Ramkumar

first: Xianyao

last: Xu

first: Lisa

last: Dorn

first: Anna

last: Bratasz

first: Lianbo

last: Yu

first: Santosh

last: Maurya

first: Vladimir

last: Tolstikov

first: Valerie

last: Bussberg

first: Paul

last: Janssen

first: Muthu

last: Periasamy

first: Michael

last: Kiebish

first: Gregg

last: Duester

first: Johannes

last: von Lintig


title: Genome-wide maps of YAP target chromatin loci in mouse pluripotent stem cells

first: Federico

last: Zambelli

summary: ChIP-seqs were performed to detect YAP direct target genes in mouse embryonic stem cells.

overall_design: Chromatin immunoprecipitated with an anti-YAP antibody and relative input samples. Biological duplicates, run in quadruplicate.

first: Fabiana

last: Passaro

first: Ilaria

last: De Martino

first: Margherita

last: Mutarelli

first: Davide

last: Cacchiarelli

first: Dario

last: Antonini

first: Tommaso

last: Russo


title: Cardiac specific deletion of natriuretic peptide receptor A induces different myocardial expression of circular RNA and mRNA involved with metabolism in mice

city: 西安

first: Jun

state: Shaanxi

address: North of Wei 32nd Road, and east of Xitai Road, High-tech Zone

department: Clinical Experimental Center

institute: Xi'an International Medical Center Hospital

summary: Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are not only important biological markers, but also regulators of cardiac functions. The natriuretic peptide A receptor (NPRA), also called NPR1 or guanylyl cyclase A (GC-A), binds with ANP or BNP ligand and fulfils transmembrane signalling transduction by elevating the intracellular levels of cGMP. However, the comprehensive effects and mechanisms downstream to NPRA are still largely to be elucidated. Here, the cardiac expressing profiles of mRNA in the mice with myocardium-specific deletion of NPRA were analyzed. It was found that differently expressed mRNAs were detected and proved by Gene Ontology (GO) and pathway analysis to be mainly related to the metabolic process. Moreover, circular RNAs (circRNAs) were scrutinized, and subsequently a possible regulatory network consisting of circRNAs- MicroRNAs (miRNAs) -mRNAs was predicted and constructed by ceRNA (competing endogenous RNA) analysis. In conclusion, NPRA plays possible roles in cardiac metabolism, which might be mediated by circRNAs via endogenous competition mechanisms.

overall_design: The cardiac expressing mRNA profiles in the C57BL/6 mice (NPRA+/+) and C57BL/6 mice with myocardium-specific deletion of NPRA (NPRA-/-)  were sequenced by Illumina HiSeq instrument, and differently expressed mRNAs were detected. Then,a high throughout screening for the different expression of circRNAs between the NPRA-deficient mice and the matched littermates.

first: Baoying

last: Chen

first: Pan

last: Chang


title: Targeted deletion of astrocytic Nhe1 stimulates Wnt/β-catenin-mediated BBB repair and angiogenesis after ischemic stroke

first: Gulnaz

last: Begum

state: PA

address: 3501 5th Ave

department: Neurology

summary: Roles of reactive perivascular astrocytes in dysregulation of the blood-brain barrier (BBB) function and cerebral perfusion are not well defined. Here, we investigated transformation of reactive astrocyte function for vascular repair after ischemic stroke by targeted deletion of astrocytic Na+/H+ exchanger isoform 1 in Gfap-CreERT2+/-;Nhe1f/f (Nhe1 Astro-KO) mice. Control Gfap-CreERT2+/-;Nhe1f/f (wild-type) mice displayed BBB damage (elevated endothelial transcytosis and intracellular vesicles) and persistent cerebral hypoperfusion in an ischemic stroke model (transient middle cerebral artery occlusion). In contrast, Nhe1 Astro-KO mice exhibited significantly less endothelial transcytosis and vesicle formation, and increased angiogenesis and cerebral blood perfusion (CBF) post-stroke. Bulk RNA-sequencing transcriptome analysis of isolated GFAP+ reactive astrocytes from wild-type and Nhe1 Astro-KO ischemic brains revealed that ~177 genes were differentially upregulated, with the Wnt7a mRNA among the top upregulated genes, along with additional Wnt pathway genes (Wnt7b, Fzd9, Fzd10, and Ndp). Abundant Wnt7a/b and β-catenin protein expression was detected in cerebral vessels of Nhe1 Astro-KO ischemic brains but not in the wild-type brains. Selective activation of Wnt/β-catenin pathway in cerebral vessels of Nhe1 Astro-KO ischemic brains was further validated using the Wnt reporter line TCF/LEF::H2B-eGFP; Gfap-CreERT2+/-;Nhe1f/f mice. Lastly, the role of Wnt/β-catenin pathway in resistance of Nhe1 Astro-KO mice to stroke-mediated BBB damage was tested by administration of Wnt/β-catenin inhibitor XAV-939. Taken together, we report that transforming reactive astrocyte function by upregulating astrocytic Wnt/β-catenin signaling activity is a novel mechanism to reduce the BBB endothelial damage, stimulate vascular repair, and restore cerebral blood flow after ischemic stroke.

overall_design: Examination of effect of deletion of Nhe1 in astrocytes on post-stroke recovery

first: Dandan

last: Sun

first: Ansuman

last: Chattopadhyay

first: Sri

last: Chaparala


title: Physiological and transcriptomic analyses of manganese toxicity response in Stylosanthes leaves

city: Haikou

first: Zhijian

email: jchen@scau.edu.cn, zjchen@catas.cn

address: Xueyuanlu 4

institute: Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences

summary: Despite its necessity, manganese (Mn) can causes phytotoxicity when present in excess. Stylo (Stylosanthes) is a dominant tropical legume with high Mn adaptability, but its Mn tolerance mechanisms are not well documented. This study integrated both physiological and transcriptome analyses of stylo in response to excess Mn toxicity. Results showed that stylo growth was decreased by excess Mn higher than 200 µM, as reflected by reductions in leaf chlorophyll and plant dry weight. Increases in enzyme activities of peroxidase (POD), ascorbate peroxidase (APX) and phenylalanine ammonia-lyase (PAL) and concentrations of secondary metabolites, including total phenols, flavonoids, tannins and anthocyanidins, were observed in stylo leaves at high Mn stress. Transcriptome analysis in stylo leaves resulted in identification of 2,471 up-regulated and 1,623 down-regulated genes under excess Mn toxicity. Among them, a set of differentially expressed genes (DEGs) involved in secondary metabolism, including PAL, chalcone synthase (CHS), chalcone isomerase (CHI) and flavonol synthase (FLS), were up-regulated in stylo under Mn toxicity, which were closely associated with the accumulation of secondary metabolites, suggesting that activation of secondary metabolism and corresponding gene expression might be important for stylo adaptation to Mn toxicity. Furthermore, a group of DEGs encoding transcription factors, such as genes belonged to C2H2 zinc finger transcription factor, WRKY, MYB and AP2 family, may be involved in stylo responses to Mn toxicity. Taken together, this study suggests that enhancing defense response and secondary biosynthesis pathway is adaptive strategy of stylo during Mn exposure, which might be regulated by complex transcriptional regulatory networks.

overall_design: Stylo (Stylosanthes guianensis) seedlings were transferred to Hoagland's nutrient solution. After 30 d of normal growth, the uniform seedlings were transplanted into fresh Hoagland’s nutrient solution supplied with 5 and 400 μM MnSO4. After 10 d of Mn treatments, leaves were harvested for RNA-seq analysis.

first: Yidan

last: Jia

first: Xinyong

last: Li

first: Lijuan

last: Luo


title: Genn expression influenced by Akt1 knock out in mouse ErbB2 mammary tumor cells

city: Wynnewood

first: Richard

middle: G

last: Pestell

state: Pennsylvania

address: 100 E Lancaster Ave LIMR R234

department: Pennsylvania Cancer and Regenerative Medicine Center

institute: Baruch S. Blumberg Institute

summary: Analysis of ErbB2 mammary tumor cells derived from Akt1 wild type and knockout MMTV-ErbB2 transgenic mice using Affymetrix Mouse 430A v2.0 GeneChip arrays.

overall_design: Three akt1(+/+) erbb2 mammary tumor cell lines were compared to three akt1(-/-) erbb2 mammary tumor cell lines.

first: Xuanmao

last: Jiao

first: Xiaoming

last: Ju

first: Sankar

last: Addya

first: Mattew

middle: C

last: Casimiro


title: Genomic architecture and evolution of a seasonal reaction norm [ATAC-seq]

first: Karin

last: van der Burg

first: James

last: Lewis

first: Benjamin

last: Brack

middle: A

last: Fandino

first: Anyi

last: Mazo-Vargas

first: Robert

last: Reed


title: Genomic architecture and evolution of a seasonal reaction norm [RNA-seq]


title: Bone marrow, spleen and  lymph node Tregs;  WT anti-CD25 long-term hematopoietic stem cells

city: Singapore

first: Ying

state: --- Select a state ---

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Regulatory T cells (Tregs) are a subpopulation of T cells critical for maintaining bone marrow  homeostasis and regulate stromal cell function via IL-10

overall_design: Live CD4+ CD8α− Foxp3+ NK-1.1− (Tregs) were sorted from these tissues (bone marrow, inguinal lymph node, and spleen) of 6-8-week-old Foxp3GFP mice and resuspended in Buffer RLT. RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 3 biological replicates per tissue. Live Lin−Sca-1+c-Kit+Flt3-CD150+CD48− (long-term hematopoietic stem cells) were sorted from 10-12-week-old B6 mice treated with anti-CD25 or IgG1 and resuspended in Buffer RLT. RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 4 biological replicates per treatment condition.

first: Virginia

last: Camacho

first: Victoria

last: Matkins

first: Sweta

last: Patel

first: Jeremie

last: Lever

first: Zhengqin

last: Yang

first: Ashley

last: Landyut

first: Emma

last: Dean

last: George

first: Henry

first: Paul

middle: B

last: Ferrell

first: Craig

last: Maynard

first: Casey

last: Weaver

first: Heth

last: Turnquist

last: Welner


title: Gene expression profiles in the retina from RTBDN knockout mice versus wild type controls by RNA-seq

city: Bethesda

first: Jianguo

last: Fan

state: MD

address: 6 Center Drive Rm 108A

institute: National Eye Institute

summary: Retinas from RTBDN knockout mice versus wild type controls were used to prepare total RNA for RNA-sequencing.

overall_design: Differential mRNA expression between RTBDN knockout mice and age matched C57bl6/J control mice was quantified by RNA-seq data analysis using the Tuxedo package (i.e. the Tophat-Cufflinks pipeline)

first: Graeme

last: Wistow


title: Genome-wide identification of AP-2α targets in bladder cells by RNA-seq

city: Changsha

first: Jianlin

last: Zhou

state: Hunan

address: 36 Lushan road

department: College of Life Science

institute: Hunan Normal University


title: Genomic architecture and evolution of a seasonal reaction norm

first: Karin

last: van der Burg


title: Genome-wide identification of AP-2α targets in bladder cells by RNA-seq (Control vs AP-2α OE)

summary: TFAP2A (AP-2α) is a member of the transcription factor AP-2 family, functions as a tumor suppressor by regulating the expression of various cancer-related genes; its expression is positively correlated with chemosensitivity and survival of cancer patients.

overall_design: UM-UC-3 cells were infected with a lentivirus expressing empty vector or AP-2α cDNA for 48 h and then the cells were selected with puromycin (1 µg/mL).  Cells infected with empty vector (control) and AP-2α cDNA were sequenced by Illumina HiSeq2000.

first: Ji


title: Genome-wide identification of AP-2α by ChIP-chip in breast cancer cell line MCF7

type: Genome binding/occupancy profiling by genome tiling array

summary: The AP-2 family of transcription factors is involved in the regulation of embryonic development, cell proliferation and tumorigenesis. To date, five members of the AP-2 family have been identified: AP-2α, AP-2β, AP-2γ, AP-2δ and AP-2ε. All AP-2 proteins bind as homo- or heterodimers to the consensus sequence of 5'- GCCNNNGGC-3' and directly regulate transcription of their target genes. Among these, AP-2α is the best-characterized gene.

overall_design: We performed chromatin immunoprecipitation (ChIP) and DNA microarray (chip) analysis to identify the transcriptional targets of AP-2α in living MCF7 cells.


title: Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage

city: New York

first: Chi-Shuen

last: Chu

address: 1230 York Ave

institute: The Rockefeller University

overall_design: ChIP-sequencing of human OCI-Ly7 cells.


title: Expression data from isolated epidermis from cFLIPko/TNFKO, TNFKO and cFLIPKO mice.

status: Public on Dec 07 2020

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: To gain further insights into the role of TNF for the inflammatory response in epidermal cFLIP KO skin, we  performed gene expression profiling to compare epidermal RNA isolated from TNF KO, cFLIP KO and cFLIP KO/TNF KO animals after 3 days tamoxifen application.

overall_design: Treated skin of 4 animals per group was isolated. Epidermis and dermis was separated. Epidermal RNA was isolated and pooled.

first: Maria

last: Feoktistova

first: Roman

last: Makarov

first: Martin

last: Leverkus

first: Amir

last: Yazdi

first: Diana

last: Panayotova-Dimitrova


title: Study of differentiation of human adipocytes using SGBS cells in vitro

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

country: France

institute: UMR1078 - Université de Bretagne Occidentale

summary: This data set consists of a time series of transcriptional profiles of differentiating human adipocytes in vitro a for different fructose concentration

overall_design: In this study the adipogenesis process of human SGBS pre-adipocyte cells in vitro was monitored by obtaining gene expression profiles at beginning of experiment and at different time points after induction of differentiation for different fructose and glucose concentration. The resulting transcriptomic data set includes six time points (0, 6, 48, 96, 192, 384 hours), with three to six replicates per time point. The platfom used for the profiling was Illumina Human HT-12 v4 Expression BeadChip (Ilumina, Inc., San Diego, CA).

first: Vijayalakshmi

last: Varma

first: Marie-Pier

last: Scott-Boyer

first: Patrick

last: Descombes

first: Jim

last: Kaput


title: DNA methylation during human adipogenesis and impact of fructose

summary: This data set consists of a time series of DNA methylation profiles of differentiating human adipocytes in vitro a for different fructose concentration

overall_design: Genome-wide methylation of single CpG sites and global transcriptomics in SGBS pre-adipocytes at 0, 24, 48, 96, 192 and 384 hours post induction were analyzed in response to 0, 2.5, 5, and 10mM fructose during adipogenesis (3 to 6 replicates).


title: Genome-wide identification of AP-2α targets in bladder cells by RNA-seq (Control vs AP-2α KD)

overall_design: SV-HUC-1 cells were infected with a lentivirus expressing scramble shRNA or AP-2α shRNA for 48 h and then the cells were selected with puromycin (1 µg/mL).  Cells infected with scramble shRNA (control) and AP-2α shRNA were sequenced by Illumina HiSeq2000.


title: OX40 regulates double-negative regulatory T cells dependently of its effects on conversion and function

city: Beijing

first: Kai

last: Liu

address: No. 95 Yong-an Road

institute: Beijing Friendship Hospital, Capital Medical University

summary:
Methods: To better understand the role of OX40 in the regulation of double-negative regulatory T cells (DNT), OX40 deficiency and wild-type DNT converted from naïve CD4 T cells were compared in a transcriptome sequencing study. Total RNA was isolated from FACS-separated DNT. Transcriptome sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Sequences were aligned to the reference genome with TopHat and processed with Cufflinks, which quantifies each transcript in each sample using reference annotations produced by the University of California Santa Cruz UCSC. Differentially expressed genes with a fold change of >=2.0 and padj < 0.05 between OX40 deficiency and control DNT were submitted to GO and KEGG enrichment analysis, which uses unbiased methods to assess pathway enrichment.
Results: Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that OX40 knockout are involved in regulatory function of DNT; including suppressive function, apoptosis, proliferation, and so on. Compared to control DNT, OX40 knockout DNT exhibited up-regulation of 52 genes and down-regulated of 46 genes. The most enriched GO term were Signal Transduction, Protein Binding, and Banding.

overall_design: Double-negative regulatory T cells were converted from wild-type and OX40 knock mouse. mRNA profiles were generated and compared by deep sequencing in duplicate using Illumina HiSeq.

first: Dong

last: Zhang