title: Epigenome analysis of primary cervical cancer and normal

city: London

first: Andy

last: Feber

address: 72 Huntley St

institute: University College London

summary: Genome wide DNA methylation profiling of cervical cancer samples and normal tissue. The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in cervical cancer samples. Samples included 102 cervical cancer samples and 29 histologicall normal samples.

overall_design: Bisulphite converted DNA from the XX samples were hybridised to the Illumina Infinium 450K Human Methylation Beadchip v1.2

first: Ankur

last: Chakravarthy

first: Ian

last: Reddin

first: Stephen

last: Henderson

first: Cindy

last: Dong

first: Nerissa

last: Kirkwood

first: Maxmilan

last: Jeyakumar

first: Daniela

last: Rothschild-Rodriguez

first: Natalia

last: Gonzalez-Martinez

first: Jacqueline

last: McDermott

first: Xiaoping

last: Su

first: Nagayasau

last: Egawa

first: Christina

last: Fjeldbo

first: Vilde

last: Skingen

first: Mari

last: Halle

first: Camilla

last: Krakstad

first: Afschin

last: Soleiman

first: Susanne

last: Sprung

first: Peter

last: Ellis

first: Mark

last: Wass

first: Martin

last: Michaelis

first: Heidi

last: Lyng

last: Fiegl

first: Helga

last: Salvesen

first: John

last: Doorbar

first: Kerry

last: Chester

first: Andrew

first: Tim

last: Fenton


title: CAN OF SPINACH, a novel long non-coding RNA, affects iron deficiency responses in Arabidopsis thaliana

status: Public on Sep 15 2022

city: Amherst

first: Elsbeth

last: Walker

state: MA

address: 611 N Pleasant St Morrill Science Center IV South

department: Biology

country: USA

institute: University of Massachusetts Amherst

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site selection in Arabidopsis [RNA-seq]

status: Public on Sep 16 2022

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

summary: In eukaryotes, DNA is associated with histones to form nucleosomes, the basic component of the chromatin. This structure presents a physical barrier for nuclear proteins to access DNA and, therefore, its plays a critical role in multiple processes such as transcription, replication and repair. Eukaryotes have evolved multiple chromatin remodelers to control nucleosome position and composition like the SWI/SNF family, which has been studied in detailed in diverse model organisms. We recently uncovered an evolutionarily conserved SWI/SNF complex in plants reminiscent of the mammalian BAF subclass, which incorporates the ATPases MINU and signature subunits TPF. In this study we characterize the impact of TPF depletion in the model plant Arabidopsis and we explore the genomic targets of the BAF complex, as well as its impact on nucleosome position and gene expression. Our results show that TPF mutants have strong developmental phenotypes, suggesting an important role in the complex function. TPF and MINU genomic targets show change in the position of the +1 nucleosome towards the promoter when the complex is mutated. While there is little correlation between this shift and changes in gene expression levels, we find a strong correlation between +1 nucleosome shift and the presence of extended 5´ regions towards the promoter in hundreds of BAF targets, suggesting a change in TSS usage. These additional 5´ UTR regions might alter RNA function and be responsible for the strong developmental phenotypes observed in the TPF and MINU mutants.

overall_design: Total RNA was extracted from inflorescences of Col-0, minu1-2 minu2-1, and tpf1-1 tpf2-1 plants (3 biological replicates per background) and sent to BGI to prepare strand-specific mRNA libraries that were sequenced by DNBSEQ high-throughput platform as PE100 reads.

first: Javier

last: Gallego-Bartolomé

first: Borja

last: Diego-Martin

last: Perez-Alemany


title: Innate immune checkpoint inhibitor resistance is associated with melanoma sub-types exhibiting invasive and de-differentiated gene expression signatures

city: Dunedin

middle: Averill

last: Stockwell

state: Otago

address: Hanover Street

department: Pathology

country: New Zealand

institute: University of Otag

summary: Melanoma is a highly aggressive skin cancer, which, although highly immunogenic, frequently escapes the body’s immune defences. Immune checkpoint inhibitors (ICI), such as anti-PD1, anti-PDL1, and anti-CTLA4 antibodies lead to reactivation of immune pathways, promoting rejection of melanoma. However, the benefits of ICI therapy remain limited to a relatively small proportion of patients who do not exhibit ICI resistance. Moreover, the precise mechanisms underlying innate and acquired ICI resistance remain unclear. Here, we have investigated differences in melanoma tissues in responder and non-responder patients to anti-PD1 therapy in terms of tumour and immune cell gene-associated signatures.

overall_design: RNA was extracted from macrodissected FFPE tissue samples using an Qiagen RNeasy mini prep kit

first: Sultana

middle: M

last: Hossain

first: Gregory

last: Gimenez

last: Tsai

first: Cristin

last: Print

first: Janusz

last: Ryś

first: Bozena

last: Cybulska-Stopa

first: Magda

last: Ratajska

first: Agnieszka

last: Harazin-Lechowska

first: Suzan

last: Almomani

first: Christopher

last: Jackson

first: Aniruddha

last: Chatterjee

first: Michael

last: Eccles


title: Cardiopulmonary Phenotyping of Sex-Based Differences in a Feline Model of HFpEF

city: Utica

first: Nathan

last: Tucker

state: NY

address: 2150 Bleecker St

institute: Masonic Medical Research Institute

summary: In order to better understand sex-related differences of heart failure with preserved ejection fraction (HFpEF), male and female kittens underwent aortic contriction surgery (banding) or sham surgery (normal). Slow progressive pressure overload was then compared between male and female kittens, analyzing structural and functional phenotypes. Transcriptional differences between male and female kittens were investigated via single nuclear RNA sequencing (snRNA-seq) within left ventricle tissue.

overall_design: Compared transcriptional differences in left ventricles between male and female kittens when placed under aortic constriction (banding)

first: Deborah

last: Eaton

first: Remus

last: Berretta

first: Jacqueline

middle: E

last: Lynch

first: Joshua

middle: G

last: Travers

first: Kathleen

middle: C

last: Woulfe

first: Ryan

middle: D

last: Pfeiffer

first: Michelle

middle: L

last: Hulke

first: Edward

last: Lau

first: Huaqing

last: Zhao

first: Alexander

middle: R

last: Hobby

first: Giana

last: Schena

first: Jaslyn

middle: P

last: Johnson

first: Markus

last: Wallner

first: P

middle: Y

last: Lam

first: Timothy

middle: A

last: McKinsey

first: Marla

last: Wolfson

first: Steven

last: Houser


title: The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site selection in Arabidopsis [ChIP-seq]

first: Jaime

last: Pérez

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Immunoprecipitated chromatin from inflorescences of Col-0, TPF2-3xFLAG and 3xFLAG-MINU2 lines were used to build libraries using the Nugen Ultralow V2 kit and sequenced at SE50. For histone ChIPs one replicate was done. For TPF2 and MINU2 ChIPs two independent transgenic lines were used as replicates compared to untransformed Col-0 plants.

first: Javier

last: Gallego-Bartolomé

first: Borja

last: Diego-Martin

last: Perez-Alemany


title: CAN OF SPINACH, a novel long non-coding RNA, affects iron deficiency responses in Arabidopsis thaliana (small RNA-Seq)

first: Elsbeth

last: Walker

summary: We performed small RNA-seq (sRNA-seq) study of Arabidopsis shoots under iron-sufficient (+Fe), iron deficient (-Fe) and iron resupply (Fe resupply) conditions to investigate and identify sRNAs whose expression is regulated by iron deficiency.

overall_design: Comparative small RNA expression profiling analysis of sRNA-seq data for Col-0 Arabidopsis shoots under three conditions

first: Ahmet

last: Bakirbas


title: MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: The BRCA1-associated protein 1 (BAP1) is a ubiquitin carboxy-terminal hydrolase (UCH), which forms a multi-protein complex with different epigenetic factors such as ASXL1-3, and FOXK1/2. At chromatin, BAP1 catalyzes the removal of mono-ubiquitination on histone H2AK119 in collaboration with other subunits within the complex, and therefore functions as a transcriptional activator. However, the crosstalk between different subunits and how these subunits impact BAP1 function remains unclear. Here, we report the identification of the methyl-CpG-binding domain proteins 5 and 6 (MBD5 and MBD6) that bind to the C-terminal PHD fingers of the large scaffold subunits ASXL1-3 and stabilize the BAP1 complex at chromatin. We further identified a previously uncharacterized Drosophila protein, the six-banded (SBA), as the ortholog of human MBD5/6. We demonstrated the core module of the BAP1 complex is structurally and functionally conserved during the evolution from Drosophila (Calypso/ASX/SBA) to human cells (BAP1/ASXL/MBD). Dysfunction of the BAP1 complex induced by the misregulation/mutations in each subunit is frequent in human cancer. In BAP1-dependent human cancers, MBD6 tends to be a dominant form. Depletion of MBD6 leads to a global loss of BAP1 occupancy at chromatin, resulting in a reduction of BAP1-dependent gene expression and tumor growth in vitro and in vivo. In summary, our study has uncovered MBD5/6 as important regulators of the BAP1 complex and transcription, and sheds light on the therapeutic potential of targeting MBD5/6 in human cancer.

overall_design: This study aims to provide mechanistic insight into the function of MBD5/6 in BAP1 complex .

first: Zibo


title: CAN OF SPINACH, a novel long non-coding RNA, affects iron deficiency responses in Arabidopsis thaliana (RNA-Seq)

summary: A whole transcriptome (RNA-seq) study of Arabidopsis shoots under iron sufficient, deficient and resupply conditions was carried out to determine the genes that are iron-regulated in the shoots.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type Col-0 plants under three conditions (+Fe, -Fe and Fe resupply)


title: Slow RNAPII transcription elongation rate, low levels of RNAPII pausing, and elevated histone H1 content at promoters associate with higher m6A deposition on nascent mRNAs

status: Public on Sep 14 2022

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

institute: CBMSO(CSIC/UAM)

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine modification (m6A) fine-tunes RNA fate in a variety of ways, thus regulating multiple fundamental biological processes. m6A writers bind to chromatin and interact with RNA polymerase II (RNAPII) during transcription. To evaluate how the dynamics of the transcription process impact m6A deposition, we studied RNAPII elongation rates in mouse embryonic stem cells with altered chromatin configurations, due to reductions in linker histone H1 content. We found that genes transcribed at slow speed are preferentially methylated and display unique signatures at their promoter region, namely high levels of histone H1, together with marks of bivalent chromatin and low RNAPII pausing. They are also highly susceptible to m6A loss upon histone H1 reduction. These results indicate that RNAPII velocity links chromatin structure and the deposition of m6A, highlighting the intricate relationship between different regulatory layers on nascent mRNA molecules.

overall_design: We analyzed transcription elongation rates in H1-TKO and WT mESCs (two replicates per condition) based on 4sU-DRB sequencing (4sU-DRB-seq) generated at 0, 5, 15 and 45 minutes after RNAPII release from TSS. Mid- and high-coverage experiments are provided. We also analyzed data from mononucleosomal DNA sequencing (MN-Seq) in H1-TKO and WT mESCs (two replicates per condition).

first: Gallego

last: Alicia

first: Fernández-Justel

last: José Miguel

first: Martín-Vírgala

last: Sara

first: Maslon

last: Magdalena M

first: Gómez

last: María


title: Single-cell transcriptomic profiling for inferring tumor origin and mechanisms of therapeutic resistance

city: Boston

first: Moshe

last: Sade-Feldmnan

address: 255 Charles Street GRJ-910

department: Cancer Center

institute: Massachusetts General Hospital

summary: We performed single-cell RNA sequencing on three different tumors isolated from an HNSCC patient who had a mixed response to checkpoint inhibitor therapy. A total of 11,470 single cells were profiled after the removal of cells that did not pass QC: Tumor-1: NPSCC (PR; n=3818; HN19-1); Tumor-2: NPSCC lymph node (PR; n=2870; HN19-2); and Tumor-3: Laryngeal SCC (PD; n=4782; HN19-3).

overall_design: To identify drivers of response and resistance in an HNSCC patient treated with checkpoint inhibitor therapy, two responding and one non-responding tumor (all isolated at the same time) were dissociated and profiled using a 10x Genomics Chromium single-cell VDJ NextGEM v1.1 kit

last: Sade-Feldman

first: Maoxuan

last: Lin

first: Daniel

last: Faden


title: Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β-cells [iPSC scRNAseq]

city: Anderlecht

first: Florian

last: Szymczak

state: Brussels

address: Route de Lennik 808 - CP618

department: Faculty of Medicine

country: Belgium

institute: Université Libre de Bruxelles

summary: IFNa is a key regulator of the dialogue between pancreatic β-cells and the immune system in early type 1 diabetes (T1D). IFNa up-regulates HLA class I expression in human β-cells fostering autoantigen presentation to the immune system. We observed by bulk and single cell RNA sequencing that exposure of human induced pluripotent-derived islet-like cells to IFNa induces expression of HLA class I and of other genes involved in antigen presentation, including the transcriptional activator NLRC5. We next evaluated the global role of NLRC5 in human insulin-producing EndoC-βH1 and human islets cells by RNA sequencing and targeted gene/protein determination. NLRC5 regulates expression of HLA class I expression and related genes and of chemokines. NLRC5 also mediates the effects of IFNa on alternative splicing, a generator of β-cell neoantigens, suggesting that it is a central mediator of the effects of IFNa on β-cells that contribute to trigger and amplify autoimmunity in T1D.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for Islets-like cells exposed, or not, to IFNa

middle: I

last: Alvelos

first: Sandra

last: Marín-Cañas

first: Ângela

last: Castela

first: Décio

last: Eizirik


title: Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β-cells


title: Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β-cells [iPSC bulk RNAseq]

summary: IFNa is a key regulator of the dialogue between pancreatic β-cells and the immune system in early type 1 diabetes (T1D). IFNa up-regulates HLA class I expression in human b-cells fostering autoantigen presentation to the immune system. We observed by bulk and single cell RNA sequencing that exposure of human induced pluripotent-derived islet-like cells to IFNa induces expression of HLA class I and of other genes involved in antigen presentation, including the transcriptional activator NLRC5. We next evaluated the global role of NLRC5 in human insulin-producing EndoC-bH1 and human islets cells by RNA sequencing and targeted gene/protein determination. NLRC5 regulates expression of HLA class I expression and related genes and of chemokines. NLRC5 also mediates the effects of IFNa on alternative splicing, a generator of β-cell neoantigens, suggesting that it is a central mediator of the effects of IFNa on β-cells that contribute to trigger and amplify autoimmunity in T1D.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iPSC-derived islets-like cells exposed, or not, to IFNa


title: Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β-cells [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EndoC-βH1 cells exposed, or not, to IFNa with or without KD of NLRC5


title: Temperature and livestock grazing trigger transcriptome responses in bumblebees along an elevational gradient

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

summary: It is assumed that climate and land-use changes cause increasing stress to pollinators, which play pivotal roles in almost all terrestrial ecosystems, with consequences on population growth, diversity and ecosystem functions. While these responses to global change drivers are well located, the molecular pathways triggering the response are poorly understood. We analysed the transcriptomic response of Bombus lucorum workers in their systematic responses to temperature and livestock grazing, sampled along an elevational gradient from 650 – 1930 m.a.s.l., and from differently managed grassland sites (livestock grazing vs. unmanaged) in and around the National Park Berchtesgaden (German Alps).

overall_design: In total, 81 B. lucorum workers (Lowlands: 30; mid-elevation: 25; highlands: 26) were collected via sweep nets on 16 different study sites (lowlands: 6 study sites from 641-987 m a.s.l.; mid-elevations: 5 study sites from 1140-1420 m a.s.l; highlands: 5 study sites from 1579-1930 m a.s.l.) between end of July and mid of August 2019 between 9 am and 7 pm. We collected 5 workers per study site except for the highest site, where on one site less individuals were found, therefore on another site more individuals were captured.

first: Kristof

last: Brenzinger

first: Thorsten

last: Bischler

first: Fabienne

last: Maihoff

first: Alice

last: Claßen

first: Marcell

middle: K

last: Peters

first: Leonie

last: Schimmer


title: Transcriptome profiling of  miRNA and mRNA  of the cortex in a rat model of Vascular dementia by RNA-sequencing

city: Beijing

first: Kaiyue

last: Zhao

address: 1 Tiantan Xili, Dongcheng District, Beijing

department: Institute of medicinal biotechnology

country: China

institute: Peking union medical college

summary: In this study, we investigated the miRNA and mRNA profiling of the cortex of rat model of vascular dementia (VaD) to analyze the regulatory mechanism in the pathology of VaD involved by miRNAs, transcription factors (TFs), and corresponding target genes. As a validated model of VaD, rats suffering from bilateral common carotid artery occlusion (2VO) were used in the present study and the reliability of this model was examined by the Morris water maze (MWM) test and the Nissl staining. Overall, results showed that rats with 2VO presented declined learning and memory capabilities in the MWM test and neuronal loss in the hippocampus and cortex indicated by Nissl-staining compared to sham rats. DEGs, DEMs, and DETFs were discriminated between rats with 2VO and sham rats in the cortex, illustrated by 13 aberrantly-expressed miRNAs, 805 mRNAs, and 63 TFs. Further network analysis revealed that 7 target genes, 5 miRNAs, and 10 TFs were the key molecule in the miRNA-TF-gene network related to VaD. Gene Ontology (GO) and pathway enrichment analyses of these VaD-related transcripts showed that these differently changed genes mostly got involved in PI3K-Akt signaling pathway, neuroactive ligand-receptor interaction, calcium signaling pathway, and Wnt signaling pathway, along with central locations around cell membrane, exerting function such as growth factor binding, integrin binding, and extracellular matrix structural constituent, with representative biological processes like vasculature development, cell-substrate adhesion, cellular response to growth factor stimulus, and synaptic transmission. In conclusion, these results will help us understand the underlying regulatory mechanisms of miRNA-TF-genes in pathogenesis and provide potential therapeutic targets for the treatment of VaD.

overall_design: miRNA and mRNA profiles of the cortex of 7-week-old rats with 2VO and sham rats.

first: Kai-Yue

first: Li

last: Zeng

first: Zhong-Di

last: Cai

first: Mi-Min

last: Liu

first: Ting

last: Sun

first: Zhuo-Rong

last: Li

first: Rui


title: Lung tuft single cell transcriptomics

city: PHILADELPHIA

first: Andrew

last: Vaughan

state: United States

address: 3800 Spruce Street

institute: University of Pennsylvania

summary: While the lung bears significant regenerative capacity, severe viral pneumonia can chronically impair lung function by triggering dysplastic remodeling. The connection between these enduring changes and chronic disease remains poorly understood.  We recently described the emergence of tuft cells within Krt5+ dysplastic regions after influenza injury. Using bulk and single cell transcriptomics, we characterized and delineated multiple distinct tuft cell populations that arise following influenza clearance. Distinct from intestinal tuft cells which rely on Type 2 immune signals for their expansion, neither IL-25 nor IL-4Ra signaling are required to drive tuft cell development in dysplastic/injured lungs. Furthermore, tuft cells were also observed upon bleomycin injury, suggesting that their development may be a general response to severe lung injury. While intestinal tuft cells promote growth and differentiation of surrounding epithelial cells, in the lungs of tuft cell deficient mice, Krt5+ dysplasia still occurs, goblet cell production is unchanged, and there remains no appreciable contribution of Krt5+ cells into more regionally appropriate alveolar Type 2 cells. Together, these findings highlight unexpected differences in signals necessary for lung tuft cell amplification and establish a framework for future elucidation of tuft cell functions in pulmonary health and disease.

overall_design: Post-influenza tuft cells were sorted from day 28-post influenza lung. Single-Cell RNASeq was performed using the Chromium System (10x Genomics) and the Chromium Single Cell 3’ Reagent Kits v2 (10x Genomics) at the Children’s Hospital of Philadelphia Center for Applied Genomics. As with bulk RNA-Seq, ~3000 EpCam+ Trpm5-GFP+ cells were sorted into PBS + 0.1% BSA from mice at day 28 post-influenza and loaded onto the 10x Chromium system. After sequencing, initial data processing was be performed using Cellranger (v.3.1.0). Cellranger mkfastq was used to generate demultiplexed FASTQ files from the raw sequencing data. Next, Cellranger count was used to align sequencing reads to the mouse reference genome (GRCm38) and generate single cell gene barcode matrices. Post processing and secondary analysis was performed using the Seurat package (v.4.0). First, variable features across single cells in the dataset will be identified by mean expression and dispersion. Identified variable features was then be used to perform a PCA. The dimensionally-reduced data was used to cluster cells and visualize using a UMAP plot. Contaminating non-tuft cells were removed by sub-setting data, requiring counts for Trpm5 > 1. Raw reads and CellRanger output data is deposited at GEO.


title: Injury-induced pulmonary tuft cells are heterogenous, arise independent of key Type 2 cytokines, and are dispensable for dysplastic repair


title: Lung tuft cell transcriptomics

overall_design: Bulk seq. 1000-3000 EpCam+ Trpm5-GFP+ cells from mice at day 43 post-influenza were sorted directly into lysis buffer from Takara SMART-Seq v4 and RNA / cDNA was amplified according to manufacturer’s instructions.  All downstream library preparation and sequencing was performed by the Next-Generation Sequencing Core at the Perelman School of Medicine, University of Pennsylvania.  In brief, libraries were sequenced on a NovaSeq sequencer at 100SR, raw FASTQ files were imported into R and reads mapped with Kallisto, and differential expression performed by Limma. Raw data is deposited at GEO.


title: H3K18la marks active tissue-specific enhancers [RNA-Seq]

city: Schwerzenbach

first: Ferdinand

last: von Meyenn

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: We profiled the genome-wide distribution of H3K18la in samples originating from 6 different in vitro and in vivo mouse samples, representing 3 tissues: embryonic stem cells, macrophages and skeletal muscle as well as in human skeletal muscle and compared them to the profiles of other well-established histone modifications as well as gene expression patterns. Globally, we found that H3K18la profiles resemble H3K27ac profiles better than any other investigated hPTM, including H3K4me3, but that they do not copy them. For all samples, H3K18la marked active CGI promoters of highly expressed genes which were remarkably shared across the different mouse tissues and which contained many housekeeping genes. Promoter H3K18la levels correlated positively to both H3K27ac and H3K4me3 levels as well as to gene expression levels. In addition, we found that H3K18la is enriched at tissue-type specific, active enhancers, which are particularly tissue-type-specific, especially when compared to the H3K18la-marked promoter regions. Accordingly, enhancer H3K18la levels correlate positively to the expression of their nearest genes. Additionally, genes closest to enhancers with high H3K18la levels predominantly consist of tissue-type specific marker genes. Overall, we showed that H3K18la is not only a marker for active promoters, but that it also marks active enhancers, and this both in embryonic tissues and differentiated tissues, and both in mouse and in human.

overall_design: RNAseq on mouse myoblast and myotube samples was performed to correlate genome-wide H3K18la profile changes to gene expression changes during cell state transitions. RNAseq on mouse myoblasts treated with sodium-L-lactate was performed to investigate whether lactate can stimulate myogenic differentiation through histone lactylation

first: Eva

last: Galle

first: Adhideb

last: Ghosh

first: Magdalena

last: Engl


title: Transcriptomic Analysis of Naïve mESC, Primed mESC and EpiLC

summary: Pluripotency is a transient feature during early embryonic development, which enables the epiblast cells to generate all the somatic lineages of the organism. Studies using mouse embryo and embryonic stem cell (ESC) indicates that embryonic pluripotency is highly dynamic with a spectrum of pluripotent states. To better understand and characterise the different pluripotent states (Naïve, Primed and EpiLC), we have generated RNA-seq datasets.

overall_design: Transcriptome profiling of Naïve mESC, Primed mESC and EpiLC using RNA sequencing


title: H3K18la marks active tissue-specific enhancers [Cut & Tag mouse]

overall_design: We profiled various mouse (embryonic stem cells (ESC), gastrocnemius (GAS), post-ischemia macrophages (PIM), primary myoblasts (MB), primary myotubes (MT) and bone marrow-derived macrophages (BMDM) and human samples (vastus lateralis) for various histone post-translational modifications

first: Chee-Wai

last: Wong

first: Thibaut

last: Desgeorges

first: Katrien

last: De Bock


title: Cellular landscapes of non-diseased human cardiac valves from end-stage heart failure-explanted heart

status: Public on Sep 13 2022

first: Jiangping

last: Song

address: 167A Beilishi Road, Xi Cheng District

institute: State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases

summary: Exploring the mechanisms of valvular heart disease (VHD) at the cellular level may be useful to identify new therapeutic targets; however, the comprehensive cellular landscape of non-diseased human cardiac valve leaflets remains unclear. The cellular landscapes of non-diseased human cardiac valve leaflets (five aortic valves, five pulmonary valves, five tricuspid valves, and three mitral valves) from end-stage heart failure patients undergoing heart transplantation were explored using single-cell RNA sequencing (scRNA-seq)

overall_design:
To identify the cellular composition of human cardiac valves, 18 valve specimens were collected from seven HTx recipients. Of these, five were AV samples, five were PV samples, five were TV samples, and three were MV samples. The determination of each sample’s non-diseased state was based on the clinical history, echocardiography, and histological characterization of the corresponding valves. The freshly collected valves were digested enzymatically to prepare the single-cell suspension, and scRNA-seq was performed using the 10x Genomics Chromium platform. Then, the sequencing reads were demultiplexed, mapped to the GRCh38 human genome, and counted by unique molecular identifier.

>>>Submitter states: Raw sequence data were provided at China Genomic Sequence Archive (GSA) at accession no. HRA002977.<<<

first: Songren

last: Shu

first: Mengxia

last: Fu

first: Xiao

last: Chen


title: Single-cell RNA-seq in AT2 cell-ablated mouse lungs

city: Durham

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

state: NC

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

summary: We performed single-cell RNA-seq using the chemistry of 10x Genomic Chromium v3.1 in mouse lungs following AT2 cell ablation.

overall_design: Single-cell RNA-seq of mouse lungs at day 3 after AT2 cell ablation and control.

first: Arvind

last: Konkimalla

first: Yoshihiko

last: Kobayashi

first: Ann Marie

last: Pendergast


title: Liver Transcriptomics Reveals microRNA Features of the Host Response in a Mouse Model of Dengue Virus Infection

city: Guangzhou

first: zheng

last: wenjiang

state: Guangdong

department: The First Clinical Medical School

institute: Guangzhou University of Chinese Medicine

summary:
Background: Organ dysfunction, especially liver injury, caused by dengue virus (DENV) infection has been associated with fatal cases in dengue patients around the world. However, the pathophysiological mechanisms of liver involvement in dengue remain unclear. There is accumulating evidence that miRNAs are playing an important role in regulating viral pathogenesis, and it can help in diagnostic and anti-viral therapies development.   Methods: We collected liver tissues of DENV-infected for small RNA sequencing to identify significantly different express miRNAs during dengue virus infection, and the identified target genes of these miRNAs were annotated by biological function and pathway enrichment.  Results: 31 significantly altered miRNAs were identified, including 16 up-regulated and 15 down-regulated miRNAs. By performing a series of miRNA prediction and signaling pathway enrichment analyses, the down-regulated miRNAs of mmu-miR-484, mmu-miR-1247-5p and mmu-miR-6538 were identified to be the crucial miRNAs. Further analysis revealed that the inflammation and immune responses involving Hippo, PI3K-Akt, MAPK, Wnt, mTOR, TGF-beta, Tight junction, and Platelet activation were modulated collectively by these three key miRNAs during DENV infection. These pathways are considered to be closely associated with the pathogenic mechanism and treatment strategy of dengue patients.  Conclusion: The miRNAs identified by sequencing, especially miR-484 may be the potential therapeutic targets for liver involvement in dengue patients which involves the regulation of vascular permeability and expression of inflammatory cytokines.
In this study, RNA-Seq analysis of liver tissues from a mouse model after DENV infection was performed to identify differential miRNA expression profiles, predicted target genes, and analyzed the biological functions and pathways involved in the regulation of differential miRNAs, contributing to the understanding of the mechanisms of liver tissue involvement after DENV infection.

overall_design: Comparative microRNA expression profiling analysis of RNA-seq data for the liver tissues of dengue virus-infected mice and control mice.

first: Wenjiang

last: Zheng

first: Ting

last: Wang

first: Chengxin

last: Liu

first: Qian

last: Yan

first: Shaofeng

last: Zhan

first: Yong

last: Jiang

first: Xiaohong

first: Geng

last: Li


title: Analysis of Kozak sequences variants of haploinsufficient genes

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

summary: We conceived that the availability of base editors and the possible presence of suboptimal Kozak sequences in the human genome could provide an elegant approach to modulate translational efficiency for the molecular compensation of some haploinsufficient disorders. Moreover, such an approach would be independent of the type of alteration inactivating the defective allele and, therefore, highly suitable for gene therapy protocols. To find base conversions upregulating translational efficiency, we systematically screened 5261 (4621 unique) variants of Kozak sequences for translational strength. We designed these variants in the main AUG context of 230 previously annotated haploinsufficient genes. Analysis of our library of Kozak variants, bearing the conversions that base editors can reproduce, proved that weak Kozak sequences are present at about a 20% frequency in our gene sample. We validated the variants of five genes and base edited one of them in a cell model, providing proof of principle of the approach, which we called BOOST (Base editing cOrrection of haplOinSufficiency by Translational enhancement).

overall_design: HEK293T cells transduced independently with 2 Kozak variants libraries were sorted into 4 gates according to the EGFP/mCherry ratio as a measure of Kozak strength. After cell sorting, the Kozak sequences from the 4 subpopulations (gates) were amplified and sequenced, for a total of 8 samples: 4 gates with library A, 4 gates with library B (reduced synthesis error rate)

first: Alessandro

last: Quattrone

first: Chiara

last: Ambrosini

first: Eliana

last: Destefanis


title: Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-B-selection pre-T cells [TCRa-seq]

first: Jeremy

last: Ratiu

state: North Carolina

address: 328 Jones Bldg, Box 3010

department: Immunology

institute: Duke University

summary: The transcription factor Zfp335 is esstential for the survival of post-B-selection DN4 thymocytes. We utilized TCRa repertoire sequencing to assess alterations to survival duration for Zfp335-deficient DP thymocytes.

overall_design: DP thymocytes were FACS-sorted (Live Lin- CD4+ CD8+) from Zfp335-fl/fl or Zfp335-fl/fl E8III-cre positive 7 week old male and female mice. Each sample was from one individual mouse. Following sorting, total RNA was isolated and libraries were prepared as follows: 5ng total RNA was reverse transcribed with Trac-specific reverse transcription primer and template switch oligo containing a Unique Molecular Identifier (UMI) using SmartScribe RT (Takara Bio). cDNA was purified and TCRa transcripts were amplified with a TSO-specific nested Trac-specific primers using Q5 polymerase (NEB). Each sample was dual indexed then all samples pooled and Illumina-compatible adaptors were added using the NEBNext Ultra II DNA library prep kit. 300x300bp sequencing was performed on an Illumina MiSeq instrument.


title: H3K18la marks active tissue-specific enhancers

first: Ferdinand

last: von Meyenn

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Effect of divergence in fertility on mRNA profling in spermatozoa of bulls

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: The aim of this study was to examine changes in the mRNA transcriptional profile of spermatozoa in Holstein-Friesian bulls. Spermatozoa from bulls divergent for feritlity status were used for this study with 10 High fertility bulls and 10 Low fertility bulls. RNA was extracted and subsequently subjected to miRNAseq analysis. 6 miRNA were identified as differentially expressed in the spermatozoa between bulls of high and low feritlity status.

overall_design: In total 20 spermatozoa RNA samples were analysed. 10 samples were derived from bulls which ranked for high fertility status (High, n=10) and 10 samples were derived from low fertility status bulls (Low, n=10).  Total RNA was extracted from a pool of frozen-thawed semen from three different ejaculates per bull.

first: Eimear

last: Donnellan

first: Jean-Philippe

last: Perrier

first: Miriam

last: Štiavnická

first: Caitríona

last: Collins

first: Elaine

last: Dunleavy

first: Eli

last: Sellem

first: Naomi

last: Bernecic

first: Patrick

last: Lonergan

first: David

last: Kenny

first: Sean

last: Fair


title: Comprehensive assessment of miniature CRISPR-Cas12f nucleases for gene disruption

status: Public on Sep 12 2022

first: Changchang

last: Xin

state: Beijing

address: No.5 Yiheyuan Road Haidian District,Beijing,P.R.China

institute: Peking University

summary: Because of their smallness, the recently developed CRISPR-Cas12f nucleases can be effectively packaged into adeno-associated viruses for gene therapy. However, a systematic evaluation of the editing outcomes of CRISPR-Cas12f is lacking. In this study, we apply a high-throughput sequencing method to comprehensively assess the editing efficiency, specificity, and safety of four Cas12f proteins in parallel with that of Cas9 and two Cas12a proteins at multiple genomic sites. Cas12f nucleases achieve robust cleavage at most of the tested sites and mainly produce deletional fragments. In contrast, Cas9 and Cas12a show relatively higher editing efficiency at the vast majority of the tested sites. However, the off-target hotspots identified in the Cas9- and Cas12a-edited cells are negligibly detected in the Cas12f-edited cells. Moreover, compared to Cas9 and Cas12a nucleases, Cas12f nucleases reduce the levels of chromosomal translocations, large deletions, and integrated vectors by 2- to 3-fold. Therefore, our findings confirm the editing capacity of Cas12f and reveal the ability of this nuclease family to preserve genome integrity during genome editing.

overall_design: We employed primer-extension-mediated sequencing (PEM-seq) to study the gene-editing outcomes for various CRISPR-Cas nuclease, include: SpCas9, AsCas12a, LbCas12a, Un1Cas12f1_ge4.1, CasMINI,CasMINI_ge4.1, AsCas12f1, PlmCas12e, and PlmCas12e-R1-v2. Twelve different editing site were targeted for each nuclease.

first: Jianhang

last: Yin

first: Shaopeng

last: Yuan

first: Liqiong

last: Ou

first: Jiazhi

last: Hu


title: Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-B-selection pre-T cells [RNA-seq]

first: Jeremy

last: Ratiu

summary: The transcription factor Zfp335 is esstential for the survival of post-B-selection DN4 thymocytes. We utilized RNA-seq to profile the alterations to the transcriptional profiles of Zfp335-deficient DP thymocytes

overall_design: DP thymocytes were FACS-sorted (Live Lin- CD4+ CD8+) from Zfp335-+/+ E8III-cre or Zfp335-fl/fl E8III-cre positive 7 week old female mice. Each sample was from one individual mouse. Following sorting, total RNA was isolated and libraries were prepared and sequenced at BGI genomics.

first: Ratiu

last: Jeremy


title: H3K18la marks active tissue-specific enhancers [Cut & Tag human]

first: Ferdinand

last: von Meyenn

overall_design: We profiled human (female) vastus lateralis muscle for 5 different histone post-translational modifications to investigate the role and profile of H3K18la in human muscle. Specifically, we profiled H3K4me3, H3K27ac, H3K27me3, H3K9me3 and H3K18la in biological duplicates.

first: Eva

last: Galle

first: Adhideb

last: Ghosh

first: Jonathan Ruiz

last: Ruiz


title: FIONA1-mediated methylation of the 3'UTR of FLC affects FLC transcript levels and flowering in Arabidopsis

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

country: Denmark

institute: University of Copenhagen

summary: Characterizing the FIONA1 protein in Arabidopsis revealing its methyl transferase activity influencing level of FLC transcripts plus the pleiotropic phenotype obsersed in fio mutants

overall_design: Comparative Nanopore direct RNA sequencing elucidating the m6A methylation landscape in Arabidopsis WT and fio1-1 and fio1-5 mutant seedlings.

first: Petri

last: Louise

first: Wenkel

last: Stephan

first: Kruusvee

last: Valdeko

first: Sun

last: Bin


title: Identification of ESRP1 targets in the epidermis

city: Philadelphia

first: Russ

last: Carstens

state: PA

address: 412 Curie Blvd

department: Medicine

summary: The epithelial splicing regulatory proteins, ESRP1 and ESRP2 are essential for mammalian development through regulation of a global program of alternative splicing of genes involved in maintenance of epithelial cell function. To further inform our understanding of the molecular functions of ESRP1 we performed enhanced crosslinking immunoprecipitation coupled with high throughput sequencing (eCLIP) in epithelial cells of mouse epidermis. The genome-wide binding sites of ESRP1 were integrated with RNA-Seq analysis of alterations in splicing and total gene expression that result from epidermal ablation of Esrp1 and Esrp2.  These studies demonstrated that ESRP1 functions in splicing regulation occur primarily through direct binding in a position-dependent manner to either promote exon inclusion or skipping. In addition, we also identified widespread binding of ESRP1 in 3’ and 5’ untranslated regions (UTRs) of genes involved in epithelial cell function, suggesting that its post-transcriptional functions extend beyond splicing regulation.

overall_design: Crosslinking immunoprecipitation of ESRP1 from mouse epidermis, for nucleotide level resolution of ESRP1:RNA interactions

first: Natoya

middle: J

last: Peart


title: Next-generation sequencing analysis of wild-type and PGRN-/- mouse neutrophils challenged with Candida albicans [RNA-seq]

city: ChongQing

first: Jiayu

last: Liu

address: No. 1 Yi xue yuan Road, Yuzhong  District，ChongQing

department: School of Medical Laboratory

institute: Chongqing Medical University

summary: To investigate the effect of Progranulin on neutrophils phagocytosis and killing of Candida albicans, we designed RNA-Seq analysis of wild-type and PGRN-/- neutrophils challenged with Candida albicans in vitro at one time point.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type and PGRN-/- neutrophils challenged with Candida albicans for 6 hours.

first: Ju

last: Cao


title: Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses [FAIRE-seq]

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

summary: In Drosophila, the ecdysone steroid hormone is essential for coordinating developmental timing across physically separated tissues. Ecdysone directly impacts genome function through its receptor, a heterodimer of the EcR and Usp proteins. Ligand binding to EcR triggers a transcriptional cascade, including activation of a set of primary response transcription factors. The hierarchical organization of this pathway has left the direct role of EcR in mediating ecdysone responses obscured. Here, we investigate the role of EcR in controlling tissue-specific ecdysone responses, focusing on two tissues that diverge in their response to rising ecdysone titers: the larval salivary gland, which undergoes programmed destruction, and the wing imaginal disc, which initiates metamorphosis. We find that EcR functions bimodally, with both gene repressive and activating functions, even at the same developmental stage. We find that EcR DNA binding profiles are highly tissue-specific, and transgenic reporter analyses demonstrate that EcR plays a direct role in controlling enhancer activity. Despite a strong correlation between tissue-specific EcR binding and tissue-specific open chromatin, we find that EcR does not control chromatin accessibility at genomic targets. We conclude that EcR contributes extensively to tissue-specific ecdysone responses. However, control over access to its binding sites is subordinated to other transcription factors.

overall_design: FAIRE from WT wings, legs, and salivary glands, and wings constitutively expressing EcR-RNAi at -6hAPF.

first: Mary

last: Leatham-Jensen

first: Daniel

last: McKay


title: Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses [RNA-seq]

overall_design: Developmental timecourse of RNAseq from wings and salivary glands in wildtype (WT) tissues and tissues constitutively expressing EcR-RNAi.


title: Next-generation sequencing analysis of wild-type and PGRN-/- mouse macrophages challenged with Candida albicans [RNA-seq]

summary: To investigate the effect of progranulin on macrophages phagocytosis and killing of Candida albicans, we designed RNA-Seq analysis of wild-type and PGRN-/- macrophages challenged with Candida albicans in vitro at one time point.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type and PGRN-/- macrophages challenged with Candida albicans for 6 hours.


title: Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-B-selection pre-T cells

first: Jeremy

last: Ratiu


title: Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-B-selection pre-T cells [scRNA-seq]

summary: The transcription factor Zfp335 is esstential for the survival of post-B-selection DN4 thymocytes. We utilized 10x Genomics v3 platform to profile the transcriptomes of

overall_design: DN4 thymocytes were FACS-sorted (Live Lin- CD4- CD8- CD44- CD25-) from Zfp335-fl/fl or Zfp335-fl/fl E8III-cre positive 6 week old mice. Each sample was a pool of one male and one female mouse. Following sorting, scRNA-seq libraries were prepared using the 10x Chromium system with v3 chemistry targeting 7,000 cells per sample.


title: Artificial Immune Receptors as novel tools to engineer inflammation sensing regulatory T cells for cell therapy

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

summary: Engineered regulatory T cell (Treg) therapy is a promising strategy to treat patients suffering from inflammatory diseases and autoimmunity. In this study, we introduce a new class of synthetic sensors, named Artificial Immune Receptors (AIRs), for murine and human Treg cells that provide new features to this cell type. AIRs bind inflammatory ligands of the TNF-receptor superfamily and translate this environmental signal into a T cell receptor (TCR)-like program, leading to activation and proliferation of the Treg cells. In a preclinical graft-versus-host-disease model, AIR-Treg cells recognizing lymphotoxin-beta-receptor ligands protect significantly better than Treg cells with only a natural TCR repertoire. Expression and signaling of a human AIR construct in human Treg cells prove that the concept can be translated. Inflammation sensing AIR-Treg cells could be an off-the-shelf Treg cell therapy approach without the knowledge of a specific antigen driving the inflammatory process.

overall_design: murine regulatory T-cells were cultured with anti-CD3/CD28 stimulation and IL2 for 2 days,then transduced with MSCV retroviral vector containing ORFS for anti-CD19 CAR as control or DR3,LTBR or TNFR2 AIR.

first: Sebastian

last: Bittner

first: Makrus

last: Feuerer

first: Nicholas

last: Strieder


title: Chemotherapy-induced complement signaling modulates immunosuppression and metastatic relapse in breast cancer

city: Tel Aviv

first: Nour

last: Ershaid

state: Israel

address: Postal code 2373,

country: Israel

institute: Tel Aviv University

summary: Mortality from breast cancer is almost exclusively a result of tumor metastasis and resistance to therapy and therefore understanding the underlying mechanisms is an urgent challenge. Chemotherapy, routinely used to treat breast cancer, induces extensive tissue damage, eliciting an inflammatory response that may hinder efficacy and promote metastatic relapse. Here we show that systemic treatment with doxorubicin, but not cisplatin, following resection of a triple-negative breast tumor induced the expression of complement factors in lung fibroblasts and modulated an immunosuppressive metastatic niche that supported lung metastasis. CAF-derived complement signaling mediated the recruitment of myeloid-derived suppressor cells (MDSCs) to the metastatic niche, thus promoting T cell dysfunction. Pharmacological targeting of complement signaling in combination with chemotherapy alleviated immune dysregulation and attenuated lung metastasis. Our findings suggest that combining cytotoxic treatment with blockade of complement signaling in triple-negative breast cancer patients may attenuate the adverse effects of chemotherapy, thus offering a promising approach for clinical use.

overall_design: Lung fibroblasts from early-stage metastatic lungs were sorted and RNA was isolated and analyzed with nCounter Mouse Inflammation v2 Panel, providing gene expression analysis for 248 inflammation-related mouse genes (and 6 internal reference controls), (NanoString Technologies).

first: Lea

last: Monteran

first: Hila

last: Doron

first: Yael

last: Zait

first: Yeela

last: Scharff

first: Shahar

last: Ben-Yosef

first: Camila

last: Avivi

first: Iris

last: Barshack

first: Amir

last: Sonnenblick

first: Neta

last: Erez


title: Reprogramming of naïve B cells in pancreatic cancer subverts humoral immunity

city: Chapel Hill

first: William

last: Kim

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

summary: RNAseq analysis for the differential gene expression pattern between non-tumor bearing and tumor bearing WT and BEBi3-/- mice.

overall_design: Naïve B cells isolated from spleens non-tumor bearing and tumor bearing WT and BEBi3-/- mice and processed for RNA isolation followed by downstream RNAseq library preparation

first: Bhalchandra

last: Mirlekar

first: Mi

last: Zhou

first: Yuliya

last: Pylayeva-Gupta


title: Roles of ESRPs in maintenance of epidermal transcriptome

first: Russ

last: Carstens

overall_design: Comparative analysis of transcriptome - gene expression (DeSeq2) and alternative splicing (Majiq) in the epidermis is response to loss of ESRPs

first: Natoya

last: Peart


title: Epigenetic and genetic change through cell cycling under selumetinib treatment

status: Public on Sep 11 2022

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Here we apply single cell bisulfite sequencing to detect epigenetic and genetic changes that occur in BRAF V600E cells that escape G1 arrest and return to the cell cycle during treatment with the MEK inhibitor selumetinib. We detect no major changes in DNA methylation, but find that cells in G2 are enriched in large amplifications and deletions that we ascribe to abnormal mitotic chromosome segregation.

overall_design: COLO205 cells were treated with 1uM selumetinib for 48 hours then fixed with glyoxal and stained for cyclin B1. 48 cyclin B1 negative and 48 positive cells were sorted into individual wells and subjected to a standard single cell bisulfite sequencing protocol.

first: Prasanna

last: Channathodiyil

first: Jon

last: Houseley


title: CD169 is a marker of IFN-γ-stimulated inflammatory macrophages in brain tumor [CT2A]

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Therapies against glioblastoma multiforme (GBM) have been largely ineffective due to the infiltration of immunosuppressive tumor-associated macrophages (TAMs). Recent studies demonstrated that TAMs can also be immune-activating. However, markers differentiating these heterogeneous macrophage populations have not been established. In this study, we identified a subset of macrophages expressing CD169 that promote an anti-tumoral microenvironment in GBM. Using single-cell transcriptome analysis, we found that CD169+ macrophages in human and mouse gliomas produced proinflammatory chemokines, leading to the accumulation of T cells and NK cells. Depletion of CD169+ macrophages shortened the survival of mice with gliomas and reduced the function of antitumor lymphocytes. We show that IFN-γ produced by NK cells was critical for the accumulation of CD169+ macrophages into gliomas. Additionally, CD169 expression on macrophages increased the phagocytosis of apoptotic glioma cells. Our finding suggests that the CD169+ subset of TAMs promotes antitumor immune responses against GBM.

overall_design: We analyzed glioma infiltrated immune cells by single cell RNA sequencing (scRNAseq) with 10X genomics.   For CT2A tumor in C57BL/6 WT mice, mice were injected with 100000 tumor cells. CD45.2+ immune cells were sorted from brain tumors and analyzed at 10 dpi.

first: Hyun-Jin


title: Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses [CUT&RUN]

first: Christopher

last: Uyehara

overall_design: EcR CUT&RUN from wings, salivary glands, and legs in EcR-GFSTF (GFP-FlAsH-Streptactin-TEV-FLAG) / Df(2R)BSC313.

first: Mary

last: Leatham-Jensen

first: Daniel

last: McKay


title: Murine CD4+ T cells: naive vs. experimental autoimmune uveitis

status: Public on Sep 10 2022

city: Tianjin, China

first: hong

last: nian

address: 251 Fukang Road, Nankai District

institute: Tianjin Medical University Eye Hospital

summary: miRNA expression profiling of CD4+ T cells comparing naïve mice and experimental autoimmune uveitis (EAU) mice. EAU was induced by immunization of retinal antigen (IRBP1-20) in complete Freund’s adjuvant (CFA). CD4+ T cells were isolated and purified from the spleen and draining lymph nodes 13 days after immunization.

overall_design: Naïve CD4+ T cells vs. EAU CD4+ T cells. 6 control, 6 EAU, independently harvested. RNAs from CD4+ T cells of six mice were pooled as one sample. One sample was generated from naïve CD4+ T cells and one sample was from EAU CD4+ T cells. Totally, 2 samples were collected and analyzed.

first: Hong

last: Nian


title: Transcription factor Zbtb1 interacts with bridging factor Lmo2 and maintains the T-lineage differentiation capacity of lymphoid progenitor cells

city: Isehara

first: Hiroyuki

last: Hosokawa

address: 143 Shimokasuya

country: Japan

institute: Tokai Univ

summary: Hematopoietic stem and progenitor cells are able to differentiate into all blood cell types.  Regulatory mechanisms underlying pluripotency in progenitors, such as the ability of lymphoid progenitor cells to differentiate into T-lineage, are not fully understood.  We have previously reported that Lmo2, a bridging factor in large transcriptional complexes, is essential to retain the ability of lymphoid progenitors to differentiate into T-lineage.  However, biochemical characterization of Lmo2 protein complexes in physiological hematopoietic progenitors has remained obscure.  In this study, we identified around 600 of Lmo2 interacting molecules in a lymphoid progenitor cell line by two-step affinity purification with LC-MS/MS analysis.  Among them, we found that Zbtb1 and Cbfa2t3 are functionally important binding partners of Lmo2.  CRISPR/Cas9-mediated acute disruption of Zbtb1 or Cbfa2t3 in a lymphoid progenitor line or BM-derived primary hematopoietic progenitors caused significant defects in the initiation of T cell development when Notch signal is activated.  Transcriptome analysis of Zbtb1- or Cbfa2t3-deficient lymphoid progenitors reveled that Tcf7, one the earliest Notch-target genes, is a common target of both factors.  ChIP-seq analysis clearly showed that Lmo2, Zbtb1 and Cbfa2t3 co-bind to the Tcf7 upstream enhancer region, where is occupied by Notch intracellular domain/RBPJ transcriptional complex after Notch stimulation, in lymphoid progenitors.  Moreover, transduction of Tcf7 restored the defect in the T-lineage potential of Zbtb1-deficient lymphoid progenitor cells.  Thus, in lymphoid progenitors, Lmo2/Zbtb1/Cbfa2t3 complex directly binds to the Tcf7 locus and maintains responsiveness to the Notch-mediated inductive signaling for the T-lineage program.

overall_design:
ChIP-seq of LP cells for Zbtb1 and Cbfa2t3
RNA-seq of LP cells with CRISPR/Cas9-mediated disruption of LMO2, Zbtb1, Cbfa2t2 or Cbfa2t3.

first: Maria

last: Koizumi

first: Ken-Ichi

last: Hirano

first: Yuichi

last: Kama

first: Yusuke

last: Endo


title: single cell-RNA sequencing for Immune cells from mouse brain tumor post control diet

first: Chae Won

last: Kim

address: 291, Daehak-ro, Yuseong-gu  E7 Rm 5101

summary: To identify the effect of high-salt diet on immune cells of brain tumor microenvironment, we isolated immune cells of brain from mice fed with control diet or high-salt diet.

overall_design: Examination of transcriptional changes on brain immune cells post control diet and GL261 intracranial injection

first: ChaeWon

first: HeungKyu


title: Sustained infiltration of neutrophils into the CNS results in increased demyelination in a viral-induced model of multiple sclerosis

status: Public on Sep 09 2022

city: Salt Lake City

first: Amber

last: Syage

state: Utah

address: 2000 Circle of Hope

department: Pathology

institute: University of Utah

summary: Intracranial inoculation of the neuroadapted JHM strain of mouse hepatitis virus (JHMV) into susceptible strains of mice results in acute encephalomyelitis and chronic immune-mediated demyelination similar to the human demyelinating disease multiple sclerosis (MS). JHMV infection of transgenic mice in which expression of the neutrophil chemoattractant chemokine CXCL1 is under the control of a tetracycline-inducible promoter active within GFAP-positive cells results in sustained neutrophil infiltration in the central nervous system (CNS) that correlates with an increase in spinal cord demyelination. We used single cell RNA sequencing (scRNAseq) and flow cytometry to characterize molecular and cellular changes within the CNS associated with increased demyelination in transgenic mice compared to control animals. These approaches revealed the presence of activated neutrophils as determined by increased expression of mRNA transcripts associated with increased neutrophil effector functions, such as CD63, MMP9, S100a8, S100a9, and ASPRV1, as well as by altered neutrophil morphology and protein expression. Collectively, these findings reveal insight into changes in the profile of neutrophils associated with increased white matter damage in mice persistently infected with a neurotropic coronavirus.

overall_design: Double-tg mice and single-tg (male and female, 6-8 weeks) were injected intracranially (i.c.) in the right brain hemisphere with 250 plaque forming units (PFU) of JHMV and CD45-positive (CD45+) cells were flow sorted from the brains of JHMV-infected mice at day post-infection (p.i.). FACS sorted CD45+ cells then underwent single-cell RNA-sequencing analysis

first: Dominic

last: Skinner

first: Gema

last: Olivarria

first: Colleen

last: Stone

first: Bailey

last: Hoglin

first: Thomas

last: Lane


title: Mutations in BCOR, a novel co-repressor of OTX2/CRX, cause pediatric inherited retinal degeneration

city: Montreal

first: Awais

last: Javed

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

summary: Many transcription factors regulating the production, survival and function of photoreceptor cells in the retina have been identified, but little is known about transcriptional co-regulators in retinal health and disease. Here we show that BCL6 co-repressor (BCOR), a polycomb repressive complex I factor mutated in various cancers, negatively regulates photoreceptor gene expression. Using proteomics and promoter assays, we find that BCOR interacts with the photoreceptor transcription factors OTX2 and CRX, and reduces their ability to activate the promoters of photoreceptor-specific genes, such as Rhodopsin and Nrl. CUT&RUN sequencing further shows that BCOR shares genome-wide binding profiles with CRX/OTX2, consistent with a general co-repression activity. Finally, we identify missense variants in the human BCOR gene in six families with early-onset X-linked inherited retinal degeneration (IRD). Together, this work uncovers BCOR as a co-repressor of OTX2/CRX essential for photoreceptor cell biology and survival.

overall_design: RNA-seq of BCOR knockdown in mouse retina/CUT&RUN sequencing of BCOR and Otx2/Crx during retinal development and adult stages.

first: Maéva

last: Langouët

first: Christine

last: Jolicoeur

first: Pierre

last: Mattar

first: Micah

last: Gearhart

first: Stephen

last: Daiger

first: Mette

last: Bertelsen

first: Lisbeth

last: Tranebjærg

first: Nanna

last: Rendtorff

first: Karen

last: Grønskov

first: Catherine

last: Jespersgaard

first: Rui

last: Chen

first: Zixi

last: Sui

first: Hui

last: Li

first: Najmeh

last: Alirezaie

first: Jacek

last: Majewski

first: Vivian

last: Bardwell

first: Ruifang

first: Robert

last: Koenekoop

first: Michel

last: Cayouette


title: Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses

first: Christopher

last: Uyehara

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

overall_design: Refer to individual Series


title: The Global Protein-RNA Interaction map of Epithelial Splicing Regulatory Protein 1 defines a post-transcriptional program that is essential for epithelial cell function

first: Russ

last: Carstens

institute: University of Pennsylvania


title: RNA-Seq analysis of Candida glabrata wild-type and Cgset4Δ mutant in the presence and absence of the cell wall targeting echinocandin antifungal drug, caspofungin.

city: Hyderabad

first: Rupinder

last: Kaur

state: Telangana

address: Inner Ring road

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

summary: To determine the effect of caspofungin (CSP) treatment and/or loss of the SET domain-containing CgSet4 protein on the transcriptional response of log-phase C. glabrata cells. RNA-Seq analysis was conducted on CAA medium-grown log-phase Candida glabrata wild-type (wt) and CgSET4-deleted (Cgset4D) cells in the presence and absence of caspofungin.

overall_design: The study was designed to profile the transcriptomes of C. glabrata wild-type and Cgset4Δ strains grown in the regular CAA medium (CAA) and caspofungin-containing CAA medium (CSP; 0.25 µg/ml) for 1 hour via RNA-Sequencing approach. The experiment was performed with two biological replicate samples for each strain/condition.

first: Priyanka

last: Bhakt

first: Mayur

last: Raney


title: P300-mediated adaptive conversion of glioma stem cells to vascular-like cells in response to therapeutic stress promotes tumor recurrence [RNA-seq_sorted GEC GPC]

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Purpose: The goal of the study is to determine the transcriptional changes associated with non-radiated cells, radiated cells, and sorted non-radiated, and radiation-induced endothelial and pericyte-like cells to establish the identity of the vascular-like cells

overall_design: RNA-sequencing of sorted glioma derived endothelial-like and pericyte-like cells pre- and post-radiation

first: Sree

last: Muthukrishnan

first: Harley

last: Kornblum


title: P300-mediated adaptive conversion of glioma stem cells to vascular-like cells in response to therapeutic stress promotes tumor recurrence [RNA_seq_IR]

summary: Purpose: The goal of the study is to determine the global transcriptomic changes occuring post-radiation in cultured patient-derived gliomaspheres

overall_design: Bulk RNA-sequencing of gliomaspheres post-radiation.


title: P300-mediated adaptive conversion of glioma stem cells to vascular-like cells in response to therapeutic stress promotes tumor recurrence [RNA_seq IR_C646]

summary: Purpose: The goal of the experiment is to determine if blocking P300 HAT activity with a small molecule inhibitor C646 reverses the radiation-induced changes in gliomaspheres

overall_design: RNA-sequencing of gliomaspheres pre-treated with C646 for 48 hours and radiated at a dose of 8 Gy


title: P300-mediated adaptive conversion of glioma stem cells to vascular-like cells in response to therapeutic stress promotes tumor recurrence [ATAC_Seq_IR]

summary: Purpose: The goal of the experiment is to determine chromatin accessibility changes induced by radiation in gliomaspheres by ATAC-sequencing

overall_design: ATAC-sequencing of control and 2-day radiated gliomaspheres


title: Next-generation sequencing analysis of wild-type and PGRN-/- mouse macrophages and neutrophils challenged with Candida albicans

first: Jiayu

last: Liu


title: P300-mediated adaptive conversion of glioma stem cells to vascular-like cells in response to therapeutic stress promotes tumor recurrence


title: scRNA-seq analysis of CD45+ cells isolated from mouse lung tumor models

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Fibrocytes are defined as monocytic cells expressing collagen-1. Single-cell RNA-seq identifies a novel fibrocyte specific marker signature.

overall_design: FACS sorted CD45+ cells from C57BL/6 mice lung and followed by single cell RNA sequencing (scRNA-seq)

first: Rajkumar

last: Savai

first: Andreas

last: Weigert

first: Guenther

last: Stefan


title: Induction of natural IgE by glucocorticoids

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

institute: Seoul National University

summary: Allergy is one of the most prevalent chronic diseases, affecting hundreds of millions of people worldwide. In allergy, environmental allergens induce B cells to undergo class switch recombination and produce Immunoglobulin E (IgE) antibodies. IgE is a key molecule that mediates allergic responses by coating mast cell or basophil surfaces and inducing degranulation upon binding a specific allergen. IgE can also be spontaneously produced in the absence of exogenous allergens, yet the origin, regulation, and functions of such “natural” IgE still remains largely unknown. Here, we discovered that glucocorticoids, which are steroid stress hormones, enhance IgE isotype class switching in B cells both in vivo and ex vivo without antigenic challenge. Such IgE class switching is promoted by B cell-intrinsic glucocorticoid receptor signaling that reinforces CD40 signaling and synergizes with the IL-4/STAT6 pathway. In addition, we found that rare B cells in the mesenteric lymph nodes are responsible for the production of glucocorticoid-inducible IgE. Furthermore, we showed that locally produced glucocorticoids in the gut may induce natural IgE during perturbations of gut homeostasis such as dysbiosis. Notably, mice preemptively treated with glucocorticoids were protected from subsequent IgE-mediated pathogenic anaphylaxis in vivo. Together, our results suggest that glucocorticoids, classically considered to be broadly immunosuppressive, have a selective immunostimulatory role in B cells.

overall_design: RNA-seq data for B cells from ex vivo culture and mLNs in vivo

first: Erica

middle: V

last: Lin

first: Jun

last: Hong

first: Ruslan

last: Medzhitov


title: P300-mediated adaptive conversion of glioma stem cells to vascular-like cells in response to therapeutic stress promotes tumor recurrence [scRNA-seq in vivo]

summary: Purpose: The goal of the study is to determine the phenotypic and functional states of glioma cells induce in response to a standard glioblastoma therapy, ionizing radiation.  Methods: We performed single-cell RNA-sequencing  on non-radiated and radiated tumor cells isolated from patient-derived xenografts. Tumor-bearing mice were exposed to a single dose of radiation ( 8 Gy) and cells were isolated and FACS sorted to obtain cell suspensions for assessing gene expression. Single cell suspensions and cDNA library preparation was done using 10x Genomics Chromium single cell reagent kit v3 according to manufacturer's protocol. cDNA samples were sequenced on 1 lane of NovaSeq 6000 S2 flowcell. Reads were mapped to HumanGRCh38 genome using Cell Ranger v.3.0.2. Seurat package v3.1.1 was used for integrated analysis by Canonical correlation analysis method with 75 dimensions . PCA was used for dimensional reduction, and Cell clustering was performed using shared nearest neighbor method.  Each cell cluster was annotated by a combination of the following methods 1) canonical marker expression 2) Gene Set Enrichment Analysis (GSEA) of cluster specific markers determined by Find Markers function in Seurat and 3) Co-expression modules obtained by Louvain community detection clustering method. Trajectory analysis was done with monocle 3 (version 0.2.1.3) by converting Seurat object to monocle. Results: We identified 14 clusters in non-radiated tumors and 15 clusters in radiated tumors.

overall_design: Gene expression profiles of single cells from patient-derived xenografts post-radiation.


title: High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci [Cut&Run]

city: Bethesda

first: Zachary

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Chromatin organization and enhancer-promoter contacts are critical for establishing unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate transcriptional regulation by non-coding genome in human retina, we mapped chromatin contacts at high resolution and integrated this data with histone marks and super-enhancers (SEs). Retinal SEs exhibited abundant local interactions and reside in topologically associated domains (TADs) with weak boundary insulation. Notably, intra-TAD positioning of SEs correlated with the biological function of their target genes in the retina. We also identified regulatory landscapes of retinopathy genes and uncovered candidate genes for risk variants associated with age-related macular degeneration and glaucoma. Our studies of high-resolution genomic architecture of the human retina provide new insights into genetic control of tissue-specific functions, suggest paradigms for missing heritability, and enable the dissection of multifactorial disease phenotypes.

overall_design: High resolution Hi-C, ATAC-seq, and Cut&Run (H3K4me3, H3K9me3) performed on adult human retina samples.

first: Marchal

last: Claire

first: Singh

last: Nivedita

first: Batz

last: Zachary

first: Advani

last: Jayshree

first: Jaeger

last: Catherine

first: Corso-Diaz

last: Ximena

first: Swaroop

last: Anand


title: CD169 is a marker of IFN-γ-stimulated inflammatory macrophages in brain tumor [WG vs TG]

first: Heung Kyu

last: Lee

overall_design: We analyzed glioma infiltrated immune cells by single cell RNA sequencing (scRNAseq) with 10X genomics. C57BL/6 background CD169-DTR wild type or hetero type mice were treated with diphtheria toxin and intracranially injected with GL261 mouse glioma cell line. Cells in tumor were isolated at 10 days after inoculation and sorted CD45-positive immune cells were analyzed.

first: Hyun-Jin

last: Kim


title: High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci [ATAC-seq]


title: Histone H3 lysine 27 acetylation (H3K27ac) profile of primary CLL cells transduced with a retrovirus expressing mutated NOTCH1

status: Public on Sep 08 2022

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: In chronic lymphocytic leukemia (CLL), NOTCH1 is the most commonly mutated gene at diagnosis and it is associated with a poor outcome. The mechanisms underlying how NOTCH1 contributes to disease progression, resistance to treatment and Richter’s transformation remain largely unknown. The main goal of this study is to compare the chromatin activation profile of primary CLL cells transduced with the intracellular part of NOTCH1 lacking of the PEST domain vs. cells transduced with an empty vector. Additionally, patients with the Trisomy 12 abnormality are included in this study to clarify the role of the mutations in this specific sub-group of CLL patients that are strongly associated with NOTCH1 mutations.

overall_design: Primary CLL cells from 5 patients were isolated through cell sorting 4 days post transduction with a NOTCH1ΔPEST or an empty retroviral vector. Patients P1 and P4 have the Trisomy 12 abnormality.

first: M

last: Mangolini

first: A

last: Maiques-Diaz

first: S

last: Charalampopoulou

first: I

last: Martin-Subero

last: Ringshausen


title: P300-mediated adaptive conversion of glioma stem cells to vascular-like cells in response to therapeutic stress promotes tumor recurrence [scRNAseq in vitro]

first: Riki

last: Kawaguchi

summary: Purpose: The goal of the study is to determine the phenotypic and functional states of glioma cells induce in response to a standard glioblastoma therapy, ionizing radiation.  Methods: We performed single-cell RNA-sequencing  on a patient-derived gliomasphere line isolated from a primary glioblastoma tumor. Cells were exposed to a single dose of radiation ( 8 Gy) for 2- and 7-days to elaborate their gene expression profile. Single cell suspensions and cDNA library preparation was done using 10x Genomics Chromium single cell reagent kit v3 according to manufacturer's protocol. cDNA samples were sequenced on 1 lane of NovaSeq 6000 S2 flowcell. Reads were mapped to HumanGRCh38 genome using Cell Ranger v.3.0.2. More than 600 million reads were obtained for each sample. Average number of genes detected was 5875 (SE±357). Confident read mapping rates were 81.2-87.4% with over 86.8% of reads in cells. Seurat package v3.1.1 was used for integrated analysis by Canonical correlation analysis method with 75 dimensions . PCA was used for dimensional reduction, and Cell clustering was performed using shared nearest neighbor method.  Each cell cluster was annotated by a combination of the following methods 1) canonical marker expression 2) Gene Set Enrichment Analysis (GSEA) of cluster specific markers determined by Find Markers function in Seurat and 3) Co-expression modules obtained by Louvain community detection clustering method. Trajectory analysis was done with monocle 3 (version 0.2.1.3) by converting Seurat object to monocle. Results: We identified 14 distinct clusters in all samples, and found dynamic alterations in frequency and size of clusters between non-radiated and radiated cells. Louvian community detection and co-expressed gene module analysis revealed that clusters expressing mitotic and DNA repair modules were diminshed, whereas clusters expressing stemness, mesenchymal and vasculogenesis modules increased post-radiation. Conclusion: Radiation therapy induces diverse functional states in glioma cells.

overall_design: Gene expression profiles of single cells from gliomaspheres post-radiation.

first: Sree

last: Muthukrishnan

first: Harley

last: Kornblum


title: Effect of melatonin on gene expression of Hepatocelluar Carcinoma HepG2  cells

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary:
To explore the role of melatonin in hepatocellular carcinoma,we performed high-throughput mRNA sequencing (mRNA-seq) with HepG2 cells treated with 1 mM melatonin for 24 h and 48 h separately.
We then performed gene expression profiling analysis using data obtained from RNA-seq of HepG2 cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells treated with melatonin or with DMSO

first: Lu

last: Bai

first: Yang

last: Wang


title: ScRNA-seq of CD45 positive cells

first: Stefan

last: Günther

summary: Bone marrow derived cell were isolated from C57BL/6 mice tibia and femur using an aseptic technique. The bone marrow was flushed out of the bone marrow cavity by using a 26-gauge needle with 10ml PBS. Subsequently cell suspension was passed through a 70µm nylon mesh. After a 10 min centrifugation step at 500 x g, cells were incubated in 2ml red cell lysis buffer for red blood cell removal. After 4 min incubation time, lysis was stopped by adding 23 ml PBS. Cells were resuspended in PBS and FACS sorted for CD45 cells using an AriaIII-sorter and 7-AAD as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics).

overall_design: Single cell RNAseq library preparation was done using standard protocol. Sequencing was done on Nextseq500 and raw reads were aligned against the mouse genome (mm10) and counted by StarSolo (44) followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy (45). Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 214 cells in total that did not express more than 200 genes or had a mitochondrial content less than 3%. Further, we filtered genes if they were detected in less than 30 cells (<0.3%). Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding (McInnes & Healy, https://arxiv.org/abs/1802.03426) and cell clustering via community detection (Traag et al., https://arxiv.org/abs/1810.08473), were based on the initial PCA. Final data visualization was done by cellxgene package.

first: Rajkumar

last: Savai

first: Andreas

last: Weigert

last: Guenther


title: Topoisomerase 1 dependent R-loop deficiency drives accelerated replication and genomic instability

city: Jerusalem

first: Dan

last: Sarni

address: Givart Ram

institute: The Hebrew University of Jerusalem

summary: DNA replication is a complex process tightly regulated to ensure faithful genome duplication, and its perturbation leads to DNA damage and genomic instability. Replication stress is commonly associated with slow and stalled replication forks. Recently, accelerated replication has emerged as a non-canonical form of replication stress. However, the molecular basis underlying fork acceleration is largely unknown. Here we show that mutated HRAS activation leads to increased topoisomerase 1 (TOP1) expression leading to aberrant replication fork acceleration and DNA damage by decreasing RNA-DNA hybrids or R-loops. In these cells, restoration of TOP1 expression or mild replication inhibition rescues the perturbed replication and reduces DNA damage. Furthermore, TOP1 or RNaseH1 overexpression induces accelerated replication and DNA damage, highlighting the importance of TOP1 equilibrium in regulating R-loop homeostasis to ensure faithful DNA replication and genome integrity. Altogether, our results reveal a novel mechanism of oncogene-induced DNA damage induced by aberrant replication fork acceleration.

overall_design: RNA-seq profiles of immortalized human fibroblasts (FSE-hTert) infected with ER:HRASG12V with or without  4-OHT treatment for 2 or 4 days (3 biological replicaes per condition)

first: Sonia

last: Barroso

first: Alon

last: Shtrikman

first: Michal

last: Irony-Tur Sinai

first: Yifat

middle: S

last: Oren

first: Andres

last: Aguilera

first: Batsheva

last: Kerem


title: Cervimycin resistant Staphylococcus aureus strains display a vancomycin intermediate resistant phenotype

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary: Resistance to antibiotics is an emerging problem and necessitates novel antibacterial therapies. Cervimycins A‒D are natural products of Streptomyces tendae HKI 0179 with promising activity against multidrug resistant staphylococci and vancomycin resistant enterococci. We studied the mode of action of cervimycin C and D by selection of cervimycin resistant (CmR) Staphylococcus aureus strains. Genome sequencing of CmR mutants revealed amino acid exchanges in the essential histidine kinase WalK, the Clp protease proteolytic subunit ClpP or the Clp ATPase ClpC, and the heat shock protein DnaK. Interestingly, all characterized cervimycin resistant mutants harbored a combination of mutations in walK and clpP or clpC. Mutations in the Clp system abolished ClpP or ClpC activity, and the deletion of clpP rendered S. aureus but not B. subtilis cervimycin resistant. The essential gene walK was the second mutational hotspot in the cervimycin resistant S. aureus mutants, which decreased WalK activity in vitro and generated a vancomycin intermediately resistant phenotype, with a thickened cell wall, a slower growth rate, and reduced cell lysis. Transcriptomic and proteomic analysis revealed massive alterations in the CmR strains , with major alterations in the heat shock regulon, the metal ion homeostasis and the carbohydrate metabolism. Taken together, compensatory mutations in cervimycin resistant mutants induced a VISA  phenotype in S. aureus, suggesting cell wall metabolism or the ClpCP proteolytic system as primary target of the polyketide antibiotic

overall_design: 3 replicates of wildtype S. aureus SG511 Berlin, SG511 derived cervimycin resistant mutants and reverted mutants


title: Gene expression profile of primary CLL cells transduced with a retrovirus expressing mutated NOTCH1

first: Irina

last: Mohorianu

summary: In CLL, NOTCH1 is the most commonly mutated gene at diagnosis and it is associated with a poor outcome. The mechanisms underlying how NOTCH1 contributes to disease progression, resistance to treatment and Richter’s transformation remain largely unknown. The main goal of this study is to compare the gene expression profile of primary CLL cells  transduced with the intracellular part of  NOTCH1 lacking of the PEST domain vs cells transduced with an empty vector. Additionally,  patients  with the Trisomy 12 abnormality are included in this study to clarify the role of the mutations in this specific sub-group of CLL patients that are strongly associated with NOTCH1 mutations.

overall_design: primary CLL cells from 13 patients were isolated through cell sorting 4 days post transdusction with a NOTCH1ΔPEST or an empty retroviral vector

first: Maurizio

last: Mangolini

first: Gabriele

last: Adam

first: Ingo

last: Ringshausen


title: Gene expression profile of primary CLL cells transduced with a mutated NOTCH1

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

overall_design: Refer to individual Series


title: Th17 cells from lupus-prone mice compared to healthy controls

status: Public on Sep 07 2022

city: Nashville

first: Kelsey

last: Voss

address: 21st Ave

department: PMI

institute: Vanderbilt University Medical Center

summary: To investigate gene expression profiles in Th17 cultures between healthy control versus lupus-prone mice

overall_design: Naïve CD4 T cells were isolated from age-matched female mice and differentiated into Th17 cells for 5 days.

first: Jeffrey

last: Rathmell


title: Chromatin accessibility of transcription factor Bach2 in mouse NK cells (ATAC-seq)

first: Shasha

last: Li

state: MO

address: 660 S Euclid Avenue

department: Rheumatology

institute: Washington University in St.Louis

summary: Transcription factor Bach2 has been reported to regulate the development and function of multiple immune cells including T cells and B cells. As a transcription repressor, Bach2 plays its role by repressing the expression of downstream targets. We are interested in whether Bach2 will affect NK cell development and what's the relationship between Bach2 and other transcription factors in regulating NK cell function. Here we try to explore the chromatin accessibility of Bach2 by ATAC-seq. We compared enriched peaks in mouse NK cell from Bach2 conditional knockout mice and control mice.

overall_design: Fresh splenic NK cells were sorted into CD3-CD19-NK1.1+NKp46+ cells. ATAC-seq libraries were generated using the omni-ATAC protocol. All ATAC libraries were barcoded, pooled and sequenced using 75bp paired-end read to a depth of at least 30 million.

first: Changxu

last: Fan

first: Xiaoyun

last: Xing

first: Ting

last: Wang

first: Wayne

last: Yokoyama


title: Gene expression profile of primary CLL cells transduced with a mutated form on NOTCH1 following IgM stimulation

summary: In CLL, NOTCH1 is the most commonly mutated gene at diagnosis and it is associated with a poor outcome. The mechanisms underlying how NOTCH1 contributes to disease progression, resistance to treatment and Richter’s transformation remain largely unknown. Data suggests a link between BCR activation and NOTCH1 signalling so the main goal of this study is to compare the gene expression profile of primary CLL cells  transduced with the intracellular part of  NOTCH1 lacking of the PEST domain vs cells transduced with an empty vector following IgM stimulation.

overall_design: Primary CLL cells were isolated through cell sorting 4 days post transusction with a NOTCH1ΔPEST or an empty retroviral vector. The cells were then stimulated with a F(ab')2 Anti-human IgM for 48 hours


title: RNA-seq and methyl-seq of A20 mouse cells using a novel TETact activation of CD4

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary:
Stably silenced genes that display a high level of CpG dinucleotide methylation are refractory to the current generation of CRISPR dCas9-based activation systems. To counter this, we created an improved activation system by coupling the catalytic domain of DNA demethylating enzyme TET1 with transcriptional activators (TETact). To evaluate the specificity of our TETact system, we conducted RNA-seq on A20 cells containing the TETact-v3 system targeting the CD4 promoter, along with non-targeting control TETact-v3 cells as well as wildtype A20. A20 is a BALB/C B cell lymphoma cell line that does not normally express CD4. Non-transduced A20 showed a very similar gene expression profile with the control TETact-v3 cells. Importantly, comparing of TETact-v3 cells targeting CD4 promoter to with cells expressing non-targeting sgRNA revealed CD4 as the sole significantly upregulated gene. Expression of the other genes in the CD4-targeting samples correlated strongly with the control sample. Together these experiments reveal the exquisite specificity of the TETact system.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Two biological replicates were prepared of wild-type A20 cells, A20 cells with CD4 activators and A20 cells with non-targeting activators. RNA-seq and whole genome methyl-seq profiles were prepared of all six samples.

Refer to individual Series


title: RNA-seq of A20 mouse cells using a novel TETact activation of CD4

summary: Stably silenced genes that display a high level of CpG dinucleotide methylation are refractory to the current generation of CRISPR dCas9-based activation systems. To counter this, we created an improved activation system by coupling the catalytic domain of DNA demethylating enzyme TET1 with transcriptional activators (TETact). To evaluate the specificity of our TETact system, we conducted RNA-seq on A20 cells containing the TETact-v3 system targeting the CD4 promoter, along with non-targeting control TETact-v3 cells as well as wildtype A20. A20 is a BALB/C B cell lymphoma cell line that does not normally express CD4. Non-transduced A20 showed a very similar gene expression profile with the control TETact-v3 cells. Importantly, comparing of TETact-v3 cells targeting CD4 promoter to with cells expressing non-targeting sgRNA revealed CD4 as the sole significantly upregulated gene. Expression of the other genes in the CD4-targeting samples correlated strongly with the control sample. Together these experiments reveal the exquisite specificity of the TETact system.

overall_design: Two biological replicates were prepared of wild-type A20 cells, A20 cells with CD4 activators and A20 cells with non-targeting activators. RNA-seq profiles were prepared of all six samples.

first: Hannah

last: Coughlan


title: Diabetes exacerbated sepsis-induced intestinal injury by promoting M1 Macrophage Polarization via miR-3061/Snail1 signaling.

city: Shenzhen

first: Xinjin

last: Chi

state: Guagndong

address: No. 628, Zhenyuan Road, Guangming New District

institute: he Seventh Affiliated Hospital of Sun Yat-Sen University

summary: Sepsis is a severe clinical syndrome related to an exaggerated host immune response to infection as well as systematic inflammation and serious tissue damage. Sepsis-induced intestine injury is one of the most frequent and serious complications of sepsis. This study aimed to identify new mechanisms in sepsis-induced intestine injury through transcriptome profiling (RNA-seq).

overall_design: A total of 5 C57BL/6 mice were randomly divided into 2 groups: CLP group (n=3), Sham group (n=2).The disinfected abdomen was incised 1 cm at midline to expose the cecum. Silk thread was subsequently used to ligate the proximal third of the cecum. Then punctured with a 22G needle once a time and extruded fecal matter. Finally, the cecum was inserted back into abdomen and the incision was sutured. After surgery, 4ml/100g normal saline was injected subcutaneously for fluid resuscitation. In addition, bupivacaine and Butorphanol Tartrate was used for postoperatively analgesia. The cecum was only exposed and then returned to the abdomen in the two sham groups. The serum and intestinal tissue were collected at 12h after surgery. Examination of 2 different groups in RAW264.7 cells. GL group (n=2), Sham group (n=2). RAW264.7 cells in GL group were stimulated with high glucose and LPS.

first: Fang

last: Tan

first: Yuling

last: Cao


title: Whole genome enzymatic methyl-seq of A20 mouse cells using a novel TETact activation of CD4

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

overall_design: Two biological replicates were prepared of wild-type A20 cells, A20 cells with CD4 activators and A20 cells with non-targeting activators. Whole genome enzymatic methyl-seq profiles were prepared of all six samples.

first: Wing

middle: F

last: Chan

first: Rhys

last: Allan

first: Timothy

last: Johanson


title: circRNA Microarray analysis of  hippocampus from mouse treated by HFD

city: Xi'an

first: Yan

last: Niu

state: Shaanxi

address: Xi tai road #777

department: Clinical Experimental Center

institute: Xi'an International Medical Center Hospital

summary:
To explore the potential mechanism linking circRNAs in Obesity-associated cognitive impairment induced by a longtime high-fat diet.
The male mouse  was treated by HFD up to16 weeks . Then the hippocaum tissues was isloated and circRNA Microarray analysis was applied. The expression profiles of  hippocaum from mouse treated with HFD changed and  2 circRNA (mmu-circRNA-004797,mmu-circRNA-21040) from this signature was quantified by real-time PCR, confirming high-fat diet can change the profiles of circRNAs of hippocaum from mouse and may participated in the obesity associated cognitive impairment.

overall_design: 6-week-old mice were randomly divided into two groups, fed with standard diet (STD) and high-fat diet(HFD), respectively. Hippocampal tissue was isolated for circRNA detection after 16 weeks of high-fat feeding

first: Jun

last: Yu


title: Association between lncRNAs in plasma exosomes and diabetic  retinopathy

status: Public on Sep 06 2022

city: Ningbo

first: Peng

last: Shu

state: Zhejiang

address: No1288 of Lushan East Street,Beilun District

department: Molecular laboratory

institute: Bielun People's Hospital,Ningbo

summary:
Long noncoding RNA (lncRNA) in plasma exosomes is a potential non-invasive diagnostic biomarker for diabetic retinopathy (DR). However, the changes in plasma exosomal lncRNAs and diagnostic relevance in patients with DR patients remain unclear.
A case–control study with type 2 diabetes mellitus (T2DM) and patients with comorbid   DR were enrolled, and their clinical information and blood samples were collected.

overall_design: Plasma exosomes were extracted, and the relative expression levels of representative differentially expressed exosomal lncRNAs were determined. A logistic regression model was used to analyze the relationships of DR with relative lncRNA expression and DR-related factors, and receiver operating characteristic (ROC) curve analysis was used to evaluate the value of exosomal lncRNAs for DR diagnosis.

first: Qingqing

last: Ye

first: Lian

first: Zhoujie

last: Shao

first: Miao

last: Xu

first: Li

first: Qianqian

last: Yan

first: Bin

last: Huang

first: Tian

last: Zhao


title: A Human Induced Pluripotent Stem Cell Array-Based Genome Wide Association Study Identifies Virus Susceptibility Locus and Variants

city: New York

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

country: USA

institute: Weill Cornell Medical College

summary: RNA-sequencing was used to compare the global gene expression profiles in WT and NDUFA4-/- iPSCs, iPSCs carrying non-risk (T/T; T/T) and risk (G/G; C/C) alleles, and WT_Δ and NDUFA4Δ iPSCs.

overall_design: RNA-Seq; 48 samples.

last: Han

first: Liuliu

last: Yang

first: Jiajun

last: Zhu

first: Tuo

last: Zhang

first: Jenny

middle: Z

last: Xiang


title: Timecourse of SARS-CoV-2 Infection with New York & Washington Isolates

city: Provo

first: Brett

middle: E

last: Pickett

state: UT

department: Microbiology and Molecular Biology

institute: Brigham Young University

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that was first reported in Wuhan, China in December of 2019 and has since caused a global pandemic resulting in millions of deaths and tens of millions of patients testing positive for infection. Analysis of different viral strains has identified a D614G change in the spike protein that is correlated with the virus becoming more transmissible. While studies have shown G614 viruses to be more transmissible, the effects of this mutation on the host response, especially on the cellular level, are yet to be fully elucidated. In this experiment we infected NHBE cells with the Washington (D614) strain or the New York (G614) strains of SARS-CoV-2. We generated RNA sequencing data at three different time points to improve our understanding of how the intracellular host response differs between infections with these two strains. We analyzed these data with a bioinformatics pipeline that identifies differentially expressed genes, enriched Gene Ontology terms and dysregulated signaling pathways. We detected over 2,000 differentially expressed genes, over 600 Gene Ontology terms, and 29 affected pathways between the two treatments. Many of these entities play a role in immune signaling and response. When comparing the different strains and different time points we found more overall similarities between matched time points than across different time points with the same strain. When specifically comparing the affected pathways, we saw that the 24hr time point of the New York strain was more similar to the 12hr time point of the Washington strain with a large number of pathways related to translation being inhibited in both strains at these time points. These results suggest that D614G substitution in the spike protein, combined with other nonsynonymous changes in the viral gene products cause distinct responses in infected host cells, especially relating to how quickly translation is dysregulated after infection. These observed differences in the intracellular host response to infection could play a role in driving the increase in pathogenicity and mortality seen in the New York outbreaks versus the Washington outbreaks at the beginning of the SARS-CoV-2 pandemic.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the New York 1-PV08001/2020 and USA-WA1/2020 isolates of SARS-CoV-2 in NHBE cells at 6, 12, and 24hpi.

first: Tiana

last: Scott

first: Antonio

last: Solis-Leal

first: J

middle: B

last: Lopez

first: Richard

last: Robison

first: Bradford

last: Berges