title: The role of stromal and immune cells in atrial disease [III]

status: Public on Jul 13 2023

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

summary: In atrial fibrillation, disturbed electrical conduction disrupts the coordinated contraction of the heart’s antechambers, increasing the risk of stroke and heart failure. The rising prevalence of this disease approaches 9% in patients >65 years. Studying freshly isolated human atrial tissue and a new mouse model, we here decipher how immune and stromal cells contribute to the structural tissue remodeling that underlies atrial fibrillation. Single-cell transcriptomes from control and diseased human atria documented macrophage doubling at the expense of endothelial and mural cells. An inflammatory monocyte and a pro-fibrotic SPP1+ macrophage cluster expanded in patients with atrial fibrillation. To experimentally perturb pathways observed in patients, we matched their risk factors Hypertension, Obesity and Mitral valvE Regurgitation (HOMER) in mice. Atrial single-cell transcriptomes obtained in HOMER mice, which developed enlarged, fibrillation-prone atria, recapitulated human cell composition and transcriptome variations. Recruitment drove the expansion of atrial macrophages; accordingly, inhibition of monocyte migration reduced arrhythmia in Ccr2-/- HOMER mice. Deleting Spp1 established macrophage-derived osteopontin as a pleiotropic signal that promotes atrial fibrillation through pro-fibrotic, inflammatory crosstalk with an arsenal of local immune and stromal cells. Taken together, we identify SPP1+ macrophages as targets for immunomodulatory therapy in atrial fibrillation.

overall_design: Single-cell mRNA sequencing was used to investigate the transcriptomic differences between non-cardiomyocytes FACS-purified from left ventricular tissues collected from 4 sham-operated mice and 4 mice exposed to Hypertension, Obesity and Mitral valvE Regurgitation (HOMER).

first: Maarten

last: Hulsmans

first: Maximilian

middle: J

last: Schloss

first: Kamila

last: Naxerova

first: Matthias

last: Nahrendorf


title: The role of stromal and immune cells in atrial disease

country: USA

type: Expression profiling by high throughput sequencing

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: The role of stromal and immune cells in atrial disease [II]

overall_design: Single-cell mRNA sequencing was used to investigate the transcriptomic differences between non-cardiomyocytes FACS-purified from left atrial tissues collected from 2 C57BL/6 bone marrow transplanted (BMT) and 2 Spp1-/- BMT mice exposed to Hypertension, Obesity and Mitral valvE Regurgitation (HOMER).


title: The role of stromal and immune cells in atrial disease [I]

overall_design:
Single-cell mRNA sequencing was used to investigate the transcriptomic differences between non-cardiomyocytes FACS-purified from left atrial tissues collected from 7 patients with persistent atrial fibrillation undergoing surgical mitral valve repair and from 5 control subjects. We also present single-cell transcriptomic data on FACS-purified, left atrial non-cardiomyocytes from 4 sham-operated mice and 4 mice exposed to Hypertension, Obesity and Mitral valvE Regurgitation (HOMER).

**Submitter declares that raw data have not been provided for the human samples due to privacy concerns**

first: I

middle: H

first: George

last: Tolis

first: Serguei

last: Melnitchouk


title: Deep dynamical modelling of developmental trajectories with temporal transcriptomics [SCIFATE_PILOT_DATA]

status: Public on Jul 06 2023

city: London

first: Rory

middle: James

last: Maizels

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Developmental cell fate decisions are dynamic processes driven by the complex behaviour of gene regulatory networks. A challenge in studying these processes using single-cell genomics is that the data provides only a static snapshot with no detail of dynamics. Metabolic labelling and splicing can provide time-resolved information, but current methods have limitations. Here, we present experimental and computational methods that overcome these limitations to allow dynamical modelling of gene expression from single-cell data. We developed sci-FATE2, an optimised metabolic labelling method that substantially increases data quality, and profiled approximately 45,000 embryonic stem cells differentiating into multiple neural tube identities. To recover dynamics, we developed velvet, a deep learning framework that extends beyond instantaneous velocity estimation by modelling gene expression dynamics through a neural stochastic differential equation system within a variational autoencoder. Velvet outperforms current velocity tools across quantitative benchmarks, and predicts trajectory distributions that accurately recapitulate underlying dataset distributions while conserving known biology. Velvet trajectory distributions capture dynamical aspects such as decision boundaries between alternative fates and correlative gene regulatory structure. Using velvet to provide a dynamical description of in vitro neural patterning, we highlight a process of sequential decision making and fate-specific patterns of developmental signalling. Together, these experimental and computational methods recast single-cell analyses from  descriptions of observed data distributions to models of the dynamics that generated them, providing a new framework for investigating developmental gene regulation and cell fate decisions.

overall_design: sci-FATE original protocol test, all mES differentiating celld, fixed in PFA, just to test protocol quality

first: Daniel

last: Snell

first: James

last: Briscoe


title: Deep dynamical modelling of developmental trajectories with temporal transcriptomics


title: Deep dynamical modelling of developmental trajectories with temporal transcriptomics [PROTOCOL_PILOT_DATA]

overall_design: Different protocols (different chemical conversion protocols; different sci-RNA-seq protocols) are multiplexed within one sample and sequenced here using sci-FATE


title: Deep dynamical modelling of developmental trajectories with temporal transcriptomics [EXPERIMENT_DATA]

overall_design: Four replicates from in vitro neural differentiation: replicates 1-3 collected on days 3,4,5,6,7,8. Replicate 4 collected between day 3 and 4 on 5 hour intervals (day 3 + 5, 10, 15, 20hr). All differentiations RA + 500nM SAG, ventral neural tube differentiation


title: Transcriptomic profiling of differentially expressed mRNA, lncRNA, miRNA and circRNA in liver tissue of acetaminophen induced liver injury mice [miRNA_APAP]

status: Public on Sep 01 2023

city: Hangzhou

first: CHAO

last: CHEN

state: Zhejiang

address: The First Affiliated Hospital, College of Medicine, Zhejiang University, NO.79 Qingchun Road, Hangzhou, Zhejiang 310003, China

country: China

institute: zhejiang university

summary: Acute liver failure is a serious clinical manifestation resulting from sudden liver injury, which can be triggered by various factors. One of the most frequent causes of acute liver failure is excessive ingestion of acetaminophen (APAP), which is known to damage hepatocytes directly by reducing glutathione levels in cells, ultimately leading to hepatocyte death.PGE2 can play a dual role in inflammation, either promoting or inhibiting the inflammatory response, depending on the cell type, local concentration, receptor type, and tissue microenvironment. Early studies have shown that PGE2 significantly alleviated acute liver failure induced by galactosamine/lipopolysaccharide, APAP, and carbon tetrachloride. However, the precise mechanism by which PGE2 alleviates APAP-induced acute liver failure remains unclear. The aim of this study is to investigate the mechanisms underlying the protective effects of PGE2 against APAP-induced hepatocyte injury.

overall_design: RNA-seq was conducted on total RNA isolated from livers of AILI mice treated with 500 mg/kg APAP or dmPGE2 300μg/kg for 6 h; n = 3 per group.

first: Chao

last: Chen

first: Xinyu

last: Gu

first: Qingfei

last: Chu

first: Jun

last: Guan

first: Haihong

last: Zhu


title: DOT1L controls NK cell maturation and lineage integrity [RNA-seq D5]

status: Public on Apr 30 2024

city: Clayton

first: Sebastian

last: Scheer

address: 15 Innovation Walk

country: Australia

institute: Monash University

summary: In the innate immune system, natural killer (NK) cells represent a highly important subset of cells with utmost importance in the control of transformed cell and tumour inflammation. Previous studies showed that NK cells can convert into ILC1-like cells in a TGF-β-rich tumour microenvironment (TME). In addition, cancer patients with acute myeloid leukemia (AML) or chronic lymphocytic leukemia (CLL) have increased frequencies of ILC1 cells in peripheral blood mononuclear cells (PBMCs), which show reduced production of the proinflammatory cytokines IFN-γ and TNF in addition to decreased granzyme B production. Here, we identify the histone methyltransferase DOT1L as a critical regulator of NK cell lineage integrity in vitro and in vivo. NK cells from NKp46-conditional DOT1L knockout mice (DOT1L.Ncr1) show increased frequencies of ILC1-like cells (CD49b+ CD49a+), and also express more of the ILC1 markers CD200R, TRAIL, while showing reduced expression of Ly49H. We further identify that the increased ILC1-like phenotype is largely independent of TGFβ. Assessment of transcription factor (TF) availability in the absence of DOT1L shows that the Myocyte-specific enhancer factor (MEF)2C is the highest downregulated TF in the absence of DOT1L. CRISPRCas9-mediated deletion of MEF2C ultimately provides evidence that this TF is limiting NK cell plasticity in vivo.   Our findings provide evidence for a previously unknown role of DOT1L and MEF2C in NK cell biology for maintaining NK cell lineage integrity and may ultimately result in improved therapies for patients with leukemia or other NK cell-lineage dependent malignancies.

overall_design: RNA-seq of enriched splenic NK cells after culturing for 5 days in the presence of 50 ng/ml IL-15; Three replicates each for WT (Ncr1-Cre- DOT1L fl/fl) and DOT1L knockout (DOT1L.Ncr1; Ncr1-Cre+ DOT1L fl/fl).


title: DOT1L controls NK cell maturation and lineage integrity [CUT&TAG]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic modifiers are promising targets to improve therapies in patients with cancer. Targeting the methyltransferase DOT1L with small molecule inhibitors has shown promising effects on the control of cancerous cells. However, these small molecules are given systemically and may have a profound impact on non-cancerous cells, such as the cells of the immune system. In the innate immune system, natural killer (NK) cells are a critical subset of cells with important roles in controlling transformed cells and tumour inflammation. Previous studies have shown that NK cells can convert into ILC1-like cells in a TGFβ-rich tumour microenvironment (TME). Additionally, cancer patients with acute myeloid leukemia (AML) or chronic lymphocytic leukemia (CLL) have increased frequencies of ILC1 cells in peripheral blood mononuclear cells (PBMCs), which show reduced production of proinflammatory cytokines and decreased granzyme B production. In this study, we identify DOT1L as a critical regulator of NK cell activation and lineage integrity. We generated NKp46-conditional DOT1L knockout mice (DOT1L.Ncr1) and observed increased frequencies of ILC1-like cells (CD49b+ CD49a+, CD62L-) and reduced frequencies of NK cells (CD49b+ CD49a-, CD62L+) in these mice. While the absence of DOT1L increases the sensitivity to TGFβ, the increased expression of CD49a is highly intrinsic and only partially dependent on TGFβ signalling. Functionally, the increased presence of ILC1-like cells in the tumour microenvironment of DOT1L.Ncr1 mice leads to decreased tumour control. Our assessment of the transcriptional program reveals alternative uses of transcription factors, such as the AP-1 family or SMAD2/3, to maintain NK cell activation and lineage integrity. Our findings provide evidence for a previously unknown role of DOT1L in NK cell biology, and demonstrate the importance of maintaining NK cell lineage integrity for effective tumour control. These findings have significant implications for the development of improved therapies for cancer or other NK cell-lineage dependent malignancies.

overall_design: Splenic NK cells of cultured for 5 days in the presence of 50 ng/ml IL-15 prior to performing Cut&Tag.


title: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis [CITE-seq]

status: Public on Apr 12 2024

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

summary:
Atherosclerotic plaques are complex tissues composed of a heterogeneous mixture of cells. However, our understanding of the comprehensive transcriptional and phenotypical landscape of the cells within these lesions is limited.
To characterize the landscape of human carotid atherosclerosis in greater detail, we combined cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-cell RNA sequencing (scRNA-seq) to classify all cell types within lesions (n=21; 13 symptomatic) to achieve a comprehensive multimodal understanding of the cellular identities of atherosclerosis and their association with clinical pathophysiology.
We identified 25 cell populations, each with a unique multi-omic signature, including macrophages, T cells, NK cells, mast cells, B cells, plasma cells, neutrophils, dendritic cells, endothelial cells, fibroblasts, and smooth muscle cells (SMCs). Among the macrophages, we identified 2 proinflammatory subsets enriched in IL1B or C1Q expression, 2 TREM2 positive foam cells (one expressing inflammatory genes), and subpopulations with a proliferative gene signature and SMC-specific gene signature with fibrotic pathways upregulated. Further characterization revealed various subsets of SMCs and fibroblasts, including SMC-derived foam cells. These foamy SMCs were localized in the deep intima of coronary atherosclerotic lesions. Utilizing CITE-seq data, we developed a flow cytometry panel, using cell surface proteins CD29, CD142, and CD90, to isolate SMC-derived cells from lesions. Lastly, we observed reduced proportions of efferocytotic macrophages, classically activated endothelial cells, and contractile and modulated SMC-derived cells, while inflammatory SMCs were enriched in plaques of clinically symptomatic vs asymptomatic patients.
Our multimodal atlas of cell populations within atherosclerosis provides novel insights into the diversity, phenotype, location, isolation, and clinical relevance of the unique cellular composition of human carotid atherosclerosis. These findings facilitate both the mapping of cardiovascular disease susceptibility loci to specific cell types as well as the identification of novel molecular and cellular therapeutic targets for the treatment of the disease.

overall_design: CITE-seq was performed on carotid atherosclerotic plaques from 6 subjects (5 symptomatic)

first: Alexander

last: Bashore


title: Deep dynamical modelling of developmental trajectories with temporal transcriptomics [BACKGROUND_DATA]

overall_design: here, in vitro differentiation cells collected from D3-D8 in one sample, sequenced using sci-RNA-seq, with no metabolic labelling. This data used to define SNPs and background mutation rate for mutation detection in metabolic labelling experiments


title: High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis


title: Deep dynamical modelling of developmental trajectories with temporal transcriptomics [SPECIES_MIXTURE_DATA]

overall_design: ES cells from human and mouse mixed together and sequenced with sci-RNA-seq. This data is used to measure doublet rate by detecting mouse-human hybrid cells.


title: Individual variation in preference behavior in sailfin fish refines the neurotranscriptomic pathway for mate preference

status: Public on Jul 01 2023

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway #C0930, Patterson Lab 607A

institute: University of Texas at Austin

summary: Social interactions can drive distinct gene expression profiles which may vary by social context. Here we use female sailfin molly fish (Poecilia latipinna) to identify genomic profiles associated with preference behavior in distinct social contexts: male-interactions (mate choice) versus female-interactions (shoaling partner preference). We measured behavior of 15 females interacting in a non-contact environment with either two males or two females for 30 minutes followed by whole brain transcriptomic profiling by RNA sequencing. We profiled females that exhibited high levels of social affiliation and great variation in preference behavior to identify an order of magnitude more differentially expressed genes associated with behavioral variation than by differences in social context. Using linear modeling (limma), we took advantage of the individual variation in preference behavior to identify unique gene sets that exhibited distinct correlational patterns of expression with preference behavior in each social context.  By combining limma and weighted gene co-expression network analyses (WGCNA) approaches we identify a refined set of 401 genes robustly associated with mate preference that is independent of shoaling partner preference or general social affiliation. While our refined gene set confirmed neural plasticity pathways involved in moderating female preference behavior, we also identified a significant proportion of discovered that our preference-associated genes were enriched for ‘immune system’ gene ontology categories. We hypothesize that the association between mate preference and transcriptomic immune function is driven by the less well-known role of these genes in neural plasticity which is likely involved in higher-order learning and processing during mate choice decisions.

overall_design: Gene expression profiles (RNAseq) were associated with preference behavior in distinct social contexts: male interactions (mate choice) versus female interactions (shoaling partner preference) in female sailfin molly fish (Poecilia latipinna).

first: Sarah

middle: M

last: Price

first: Molly

last: Schumer

first: Silu

last: Wang

middle: E

last: Cummings


title: Epitope-specific T cell responses after SARS-2 vaccination, including for a hypervaccinated individual

status: Public on Mar 05 2024

city: Erlangen

first: Kilian

last: Schober

state: Bavaria

address: Maximiliansplatz 2

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: Universitätsklinikum Erlangen

summary: Prime-boost vaccinations tailor adaptive immunity. However, chronic antigen exposure can also lead to immune dysfunction. Overall, the benefits and limits of repetitive antigen exposure for vaccinations in humans remain poorly understood. Here we performed in-depth immune profiling in an individual that reports 217 vaccinations (including 134 certified doses) against SARS-CoV-2 in less than two years (Hypervaccinated Individual from Magdeburg, HIM). Antigen-specific antibody and T-cell responses were of higher quantity, while quality was preserved, compared to a three-dose mRNA vaccine control cohort. Hyperimmunization did not lead to adverse events and HIM remains SARS-CoV-2 infection-free. Insights from extreme settings like the one reported here instruct our understanding on the consequences of repetitive antigen exposure on adaptive immunity in humans.

overall_design: Antigen-specific T cells (as well as unspecific T cells as a control) were identified by DNA-baroded pMHC multimers (Dextramers) including the SARS-CoV-2 specificity LTD as well as the EBV specificity RAK. Dextramer+ and - cells were sorted by FACS and subjected to 5' scRNAseq on a 10x Genomics platform including CITEseq for Dextramers and, for some samples, 130 surface proteins; different samples from different donors were labelled with hasthag antibodies

first: Katharina

last: Kocher

first: Carolin

last: Moosmann

first: Felix

last: Drost

first: Christine

last: Schülein

first: Pascal

last: Irrgang

first: Philipp

last: Steininger

first: Jahn

last: Zhong

first: Johannes

last: Träger

first: Bernd

last: Spriewald

first: Christoph

last: Bock

first: Dirk

last: Busch

first: Christian

last: Bogdan

first: Benjamin

last: Schubert

first: Thomas

last: Winkler

first: Matthias

last: Tenbush

first: Ev-Marie

last: Schuster


title: Transcriptomic investigation of the modes of action of polymyxins and colistin/sulbactam combination against carbapenem-resistant Acinetobacter baumannii

city: Shanghai

first: Xingchen

last: Bian

state: Shanghai

address: Fudan university, Huashan hospital

institute: Huashan hospital, Fudan University

summary:
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a Priority 1 (Critical) pathogen urgently requiring new antibiotics. Polymyxins are a last-line option against CRAB-associated infections. This transcriptomic study utilized a CRAB strain to investigate mechanisms of bacterial killing with polymyxin B, colistin, colistin B and colistin/sulbactam combination therapy. After 4 h of 2 mg/L polymyxin monotherapy, all polymyxins exhibited common modes of action which primarily involved disruption to amino acid and fatty acid metabolism. Of the three monotherapies, polymyxin B induced the greatest number of differentially expressed genes (DEGs), including for genes involved with fatty acid metabolism. Gene disturbances with colistin and colistin B were highly similar (89% common genes for colistin B), though effects on gene expression were generally lower (0-1.5-fold in most cases) with colistin B. Colistin alone (2 mg/L) or combined with sulbactam (64 mg/L) resulted in rapid membrane disruption as early as 1 h. Transcriptomic analysis of this combination revealed the effects were driven by colistin and included disturbances in fatty acid synthesis and catabolism and inhibition of nutrient uptake. Combination therapy produced substantially higher fold changes in 72% of DEGs shared with monotherapy, resulting in substantially greater reductions in fatty acid biosynthesis and increases in biofilm, cell wall and phospholipid synthesis. This indicates synergistic bacterial killing with the colistin/sulbactam combination results from a systematic increase in perturbation of many genes associated with bacterial metabolism. These mechanistic insights enhance our understanding of bacterial responses to polymyxin mono- and combination therapy and will assist to optimize polymyxin use in patients.
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a Priority 1 (Critical) pathogen urgently requiring new antibiotics. Polymyxins are a last-line option against CRAB-associated infections. This transcriptomic study utilized a CRAB strain to investigate mechanisms of bacterial killing with polymyxin B, colistin, colistin B and colistin/sulbactam combination therapy. After 4 h of 2 mg/L polymyxin monotherapy, all polymyxins exhibited common modes of action which primarily involved disruption to amino acid and fatty acid metabolism. Of the three monotherapies, polymyxin B induced the greatest number of differentially expressed genes (DEGs), including for genes involved with fatty acid metabolism. Gene disturbances with colistin and colistin B were highly similar (89% common genes for colistin B), though effects on gene expression were generally lower (0-1.5-fold in most cases) with colistin B. Colistin alone (2 mg/L) or combined with sulbactam (64 mg/L) resulted in rapid membrane disruption as early as 1 h. Transcriptomic analysis of this combination revealed the effects were driven by colistin and included disturbances in fatty acid synthesis and catabolism and inhibition of nutrient uptake. Combination therapy produced substantially higher fold changes in 72% of DEGs shared with monotherapy, resulting in substantially greater reductions in fatty acid biosynthesis and increases in biofilm, cell wall and phospholipid synthesis. This indicates synergistic bacterial killing with the colistin/sulbactam combination results from a systematic increase in perturbation of many genes associated with bacterial metabolism. These mechanistic insights enhance our understanding of bacterial responses to polymyxin mono- and combination therapy and will assist to optimize polymyxin use in patients.

overall_design: We have six groups including colistin, polymyxin B, colistin B, sulbactam, colistin combined with sulbactam and control. Each group have three replicates.

first: Mengyao

last: Li

first: Xiaofen

last: Liu

first: Yan

last: Zhu

first: Jian

first: Phillip

last: Bergen

first: Wanzhen

first: Xin

first: Meiqing

last: Feng

first: Jing

last: Zhang


title: Fc-FcgR interactions shift alveolar macrophage metabolism to promote Mycobacterium tuberculosis restriction in mice

status: Public on May 31 2023

city: Cambridge

first: Bryan

middle: B

last: Bryson

state: MA

address: 77 Massachusetts Avenue

department: Department of Biological Engineering

institute: Massachusetts Institute of Technology

summary: The mechanistic basis for humoral immune control of Mtb remains poorly understood. We use single-cell RNA-sequencing to explore the impact of antibody treatment on cellular states in vivo.

overall_design: Using single-cell RNA-sequencing, we profile CD45+ and infected Mtb+ cells in B6 mice 5 days post-infection following treatment with different antibodies.

first: Patricia

last: Grace

first: Joshua

last: Peters

first: Sarah

last: Fortune

first: Galit

last: Alter


title: Whole transcriptome sequencing of 50 laryngeal squamous cell carcinoma and paired adjacent normal tissues

status: Public on May 24 2023

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout transcriptome sequencing to identify lncRNA, mRNA, and circRNA that associated with LSCC progression.Transcriptome sequencing were performed on a cohort of LSCC tissues (50 samples) and paired adjacent normal mucosa tissues (50 samples).

overall_design: Expression of lncRNA, mRNA and circRNA in 50 LSCC and 50 paired adjacent normal mucosa tissues was examination by high throughout sequencing.

first: Wei

last: Gao

first: Binquan

last: Wang

first: Qinli

last: Zhao

first: Xiwang

last: Zheng


title: Jurkat T cells

status: Public on May 01 2023

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

institute: Yale University School of Medicine

overall_design: Refer to individual Series


title: HiC and H3K27ac HiChIP of clonal Jurkat T cells infected HIV-1 model NL4-3-D6-drEGFP

summary: HIV-1 integration introduces ectopic transcription factor binding sites into host chromatin. We postulate that the integrated provirus serves as an ectopic enhancer that recruits additional transcriptional factors to the integration locus, increases chromatin accessibility, changes 3D chromatin interactions, and enhances both retroviral and host gene expression. We used 4 well-characterized HIV-1-infected cell line clones having unique integration sites and low to high levels of HIV-1 expression. Using single-cell DOGMA-seq, which captured the heterogeneity of HIV-1 expression and host chromatin accessibility, we found that HIV-1 transcription correlated with HIV-1 accessibility and host chromatin accessibility. HIV-1 integration increased local host chromatin accessibility within ~5–30 kb distance. CRISPRa and CRISPRi-mediated HIV-1 promoter activation and inhibition confirmed integration site-dependent HIV-1-driven changes of host chromatin accessibility. HIV-1 did not drive chromatin confirmation changes at the genomic level (by Hi-C) or the enhancer connectome (by H3K27Ac HiChIP). Using 4C-seq to interrogate HIV-1-chromatin interactions, we found that HIV-1 interacted with host chromatin ~100–300 kb from the integration site. By identifying chromatin regions having both increased transcription factor activity (by ATAC-seq) and HIV-1-chromtain interaction (by 4C-seq), we identified enrichment of ETS, RUNT, STAT, and ZNF transcription factor binding that may mediate HIV-1-host chromatin interactions. Our study found that HIV-1 promoter activity increased host chromatin accessibility, increased HIV-1-host chromatin interactions in an integration site dependent manner, within the existing chromatin boundaries without impacting broader host chromatin structure.

overall_design: Unstimulated Jurkat CD4+ T cells with or without an HIV-1 provirus were profiled.

first: Jack

last: Collora


title: Single Cell Multiome of isogenic HIV-1-infected Jurkat T cells


title: HIV-1 LTR targeting 4C-seq


title: ATAC-seq of isogenicHIV-1 infected Jurkat T cell lines


title: RIP-PEN-SHAPE-MaP for 15.5K-interacted RNAs

status: Public on Apr 10 2023

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

summary: RNA secondary structure is crucial for RNA mentalism, including transcription, splicing, translation, RNA-binding protein interaction as well as turnover. The kink-turn (K-turn) structure motif is is an RNA three-dimensional (3D) structure that exists in all three primary phylogenetic domains and plays vital roles in RNA metabolism. In order to investigate the K-turn secondary structure in vivo, we combined SHAPE-Map and our RIP-PEN-seq to profile the RNA structure of 15.5K-interacted RNAs.

overall_design: The 15.5K-interacted RNAs were first isolated by 15.5K-specific antibody and followed by on-beads modification with SHAPE reagent NAI-N3 or DMSO (negative control). After RNA isolation and DNase I-treatment, the 15.5K-interacted RNAs were ligated to 3’ and 5’ randomized RNA adaptors. Then the ligated products were subjected to rRNA, snRNA and some high-abundance snoRNA depletion utilizing an RNase H-based strategy. Following the reverse transcription under SHAPE-MaP conditions, the libraries were amplified with Illumina small RNA indexed PCR primers.

first: Bin

last: Li

first: Anrui

last: Liu

first: Lianghu

last: Qu

first: Jianhua


title: PEN-seq for identifying non-coding RNAs and their expression in 15.5K-knockdown HEK293T cells

type: Non-coding RNA profiling by high throughput sequencing

summary: 15.5K is a RNA binding protein involved in the Minor Spliceosome. Here, we used shRNAs to knock down 15.5K in HEK293T cells to analysis the function of 15.5K in ncRNA expression.

overall_design: Total RNA from negative control HEK293T (shNC) cells and two 15.5K-knockdown  (sh15.5K-1 and sh15.5K-2) cells  were ligated to RNA adaptors, followed by rRNA and snRNA depletion. After reverse transcription and library amplification, inserts between 20-500bp were size selected and subjected to Illumina sequencing.

first: Shurong

first: Wujian

first: Peng

last: Yu

first: Di

first: Jie

last: Zhou

first: Ping

last: Zhang

first: Chang

first: Qiao

last: Lin

first: Xiaoqin

first: Qiaojuan

last: Huang

first: Hui


title: Sex differences in the effects of caloric restriction (CR) on hepatic gene expression in mice

status: Public on Apr 26 2023

city: Edinburgh

first: William

middle: P

last: Cawthorn

address: 47 Little France Crescent

department: University/BHF Centre for Cardiovascular Science

institute: The University of Edinburgh

summary: The effects of caloric restriction (CR) on glucose homeostasis and metabolic function differ between males and females. To investigate if hepatic function contributes to these sex differences, we collected liver samples from male and female C57BL/6NCrl mice that were fed ad libitum (AL) or underwent caloric restriction (CR; receiving 70% of daily AL intake) from 9-13 weeks of age. Livers were then analysed by bulk RNA-seq.

overall_design: The goal of this study was to determine how caloric restriction (CR) influences the hepatic transcriptome and if this differs between males and females. The experiment included five ad libitum (AL)-fed females, six CR females, six AL males and five CR males. Mice were fed AL or CR from 9-13 weeks of age. To minimise effects resulting from differences in fasting duration, mice in both the AL and CR groups were fasted for ~8 hours prior to necropsy and liver sampling.

first: Yoshiko

last: Ikushima

first: Hiroshi

last: Kobayashi

first: Kuan-Chan

last: Chen


title: sub-PEN-seq for identifying novel non-coding RNAs and their expression in cultured cells II

first: Jian-Hua

summary: Small RNAs between 20-500nt were least explored. Here we used RNase H-based rRNA depletion and a serial of strategies to developed sub-PEN-seq method for identifying novel non-coding RNAs in Subcellular RNAs.

overall_design: Subcellular RNA were ligated to  RNA adaptors, followed by rRNA and snRNA depletion. After reverse transcription and library amplification, inserts between 20-500bp were size selected and subjected to Illumina sequencing.

first: Bin

first: Anrui

last: Wu

first: Lianghu


title: Viral reprogramming of host transcription initiation

status: Public on Feb 01 2024

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center


title: High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing [10X Visium]

status: Public on Jan 17 2024

city: St. Louis

first: Haojia

state: MO

address: 4523 Clayton Ave, MSB Rm 820

institute: Washington University in St Louis

summary: Spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ. We applied direct RNA hybridization-based in situ sequencing (ISS, Cartana) to compare male and female healthy mouse kidneys and the male kidneys injury and repair timecourse of ischemic reperfusion injury (IRI). A pre-selected panel of 200 genes were used to identify the dynamics of cell states and their spatial distributions during injury and repair. We developed a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting atlas allowed us to resolve distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. Projection of snRNA-seq dataset from the same injury and repair samples allowed us to impute the spatial localization of genes not directly measured by Cartana.

overall_design: Kidney spatial transcriptomics data were generated by RNA hybridization-based in situ sequencing (ISS, Cartana) and 10X Visium

first: Benjamin

last: Humphreys


title: Gene expression and intron retention analysis of 15.5K-knockdown human cells

summary: 15.5K is a RNA binding protein involved in the Minor Spliceosome. Here, we used shRNAs to knock down 15.5K in HEK293T cells to analysis the function of 15.5K in gene expression and intron retention.

overall_design: We analysed RNA from negative control HEK293T (shNC) cells and two 15.5K-knockdown  (sh15.5K-1 and sh15.5K-2) cells. For each condition, mRNA-seq analysis was conducted in triplicate from three independent expriments. We compare 15.5K-knockdown cells vs WT cells.

first: Shurong

first: Wujian

last: Zheng

first: Peng

first: Di

first: Jie

first: Ping

first: Jianhua


title: RIP-PEN-seq for 15.5K in Hepa1-6 cells

last: Yang

summary: Here, we developed a RNA ImmunoPrecipitation coupled with sequencing of Paired-Ends of NcRNAs (RIP-PEN-seq) method to identify the full-length sequences of ncRNAs bound by 15.5K protein and discover a novel class of backward K-turn RNAs.

overall_design: Analysis of 15.5K binding ncRNAs in Hepa1-6 cells.

first: Chang

first: Qiao

first: Xiaoqin

first: Qiaojuan

first: Hui


title: RIP-PEN-seq for 15.5K in HEK293T cells

first: Jian-Hua

overall_design: Analysis of 15.5K binding RNAs in HEK293T cells.

first: Bin

last: Li

first: Anrui


title: PEN-seq for identifying novel non-coding RNAs and their expression in cultured cells

summary: Small RNAs between 20-500nt were least explored. Here we used RNase H-based rRNA depletion and a serial of strategies to developed PEN-seq method for identifying novel non-coding RNAs in total RNAs.

overall_design: Total or subcellular RNA were ligated to small RNA-seq adapors, followed by rRNA and snRNA depletion. After reverse transcription and library amplification, inserts between 20-500bp were size selected and subjected to Illumina sequencing.

last: Liu

first: Lianghu


title: Transcriptomic analysis of lpcat1/2 mutant and wild type plants

status: Public on Mar 30 2023

city: Wuhan

first: Qiang

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

summary: To explore the transcriptional regulations in lpcat1/2 mutant and wild type plants grown on 1/2 MS media (control), or 1/2 MS media containing 20ug/ml lyso-PAF or 20ug/ml lyso-PAF plus 50 µM ONO

overall_design: Total RNA were extracted from wild type and lpcat1/2 mutant root tissue under each condition

first: Jiao

last: Zou


title: Effect of drought stress on gene expression of maize leaves

status: Public on Mar 31 2023

city: Ithaca

first: yuan

last: jiang

address: 306 Tower Rd

institute: cornell university

summary: To investigate the different drought response between the different maize lines, we screened drought-tolerant line W9706 and drought-susceptible line B73 to compare the  transcriptome

overall_design: Comparative gene expression profiling analysis of RNA-seq data for W9706 and B73

first: yaping

last: yuan


title: LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis [RNA-seq]

status: Public on Mar 28 2023

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: The lncRNA EPR (a.k.a BC030870) is highly enriched in the gastrointestinal tract in mice and, more specifically, in the large intestine. We generated conditional EPR knock-out in large intestine e and analyzed genome-wide the gene expression changes by RNA-Seq. Total RNA was extracted from the proximal colon of six control (EPR fl/fl) and six knock-out (EPR cKO) mice. Libraries were constructed and sequenced. Results indicate that EPR knock-out predominantly leads to down-regulation of genes implicated in mucus biogenesis. These results help in explaining the phenotype displayed by EPR cKO mice that is characterized by higher susceptibility to intestinal inflammation and cancer formation.

first: P

last: Briata

first: E

last: Zapparoli

first: G

last: Bucci

first: A

last: Inga

first: F

last: Chiacchiera

first: L

last: Caputo

first: R

last: Gherzi


title: Retinoic acid enhances HIV-1 reverse transcription and transcription in macrophages via mTOR-modulated mechanisms

status: Public on Dec 31 2023

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

summary: The intestinal environment facilitates HIV-1 infection via mechanisms involving the gut-homing vitamin A-derived retinoic acid (RA), which transcriptionally reprograms CD4+ T cells for increased HIV-1 replication/outgrowth. Consistently, colon-infiltrating CD4+ T cells carry replication-competent viral reservoirs in people with HIV-1 (PWH) receiving antiretroviral therapy (ART). Intriguingly, integrative infection in colon macrophages, a pool replenished by monocytes, represents a rare event in ART-treated PWH, thus questioning the effect of RA on macrophages. Here, we demonstrate that RA enhances R5 but not X4 HIV-1 replication in monocyte-derived macrophages (MDMs). RNA sequencing, gene set variation analysis, and HIV interactor NCBI database interrogation reveal RA-mediated transcriptional reprogramming associated with metabolic/inflammatory processes and HIV-1 resistance/dependency factors. Functional validations uncover post-entry mechanisms of RA action including SAMHD1-modulated reverse transcription and CDK9/RNA polymerase II (RNAPII)-dependent transcription under the control of mammalian target of rapamycin (mTOR). These results support a model in which macrophages residing in the intestine of ART-untreated PWH contribute to viral replication/dissemination in an mTOR-sensitive manner.

overall_design: Monocyte-derived macrophages (MDMs) from 6 HIV-uninfected donors; 2 conditions: M-CSF . M-CSF + ATRA

first: Jonathan

last: Dias

first: Amélie

last: Cattin

first: Laurence

middle: R

last: Marchand

first: Augustine

last: Fert

first: Tomas

last: Wiche Salinas

first: Christ-Dominque

last: Ngassaki Yoka

first: Etiene

last: Moreira Gabriel

first: Jean-Pierre

last: Routy

first: Petronela

last: Ancuta


title: Pioneer transcription factors coordinate active and repressive gene expression states to regulate cell fate

status: Public on Jan 10 2024

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

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


title: LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis

first: gabriele

last: bucci


title: Anti-cancer action of imidazopyridine BAG1 compounds in steriod hormone receptor-positive breast and prostate cancer

status: Public on Mar 13 2023

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

summary: Transcriptomics analyses to study the effect of the imidazopyridine X15695 on proliferation of estrogen receptor positive (ER+) breast and androgen receptor positive (AR+) prostate cancer cells. The effect of X15695 was analyzed on vehicle or steroid hormone-treated breast and prostate cancer cells.

overall_design: RNA-seq was carried out with breast cancer (MCF-7, T47D) and prostate cancer (LNCaP) cells treated with hormone and the compound X15695. MCF-7 and T47D cells were treated with 10 nM 17-β-estradiol (E2) or dihydrotestosterone (DHT) for the LNCaP cells, 1 µM X15695 (for the MCF-7 and T47D cells) or 5 µM for LNCaP cells and X15695 together with E2 or DHT for the breast or prostate cancer cells.

first: Andrew

last: Cato

last: Gourain

first: Mengwu

last: Pan


title: Pan-cancer tumor-specific antigens and membrane targets from transposable elements

status: Public on Jan 20 2023

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: We charted the transcription start sites (TSSs) landscape globally to determine the expressed isoform of each gene and validate the precence of transposable element-derived transcript. Cryptic promoters within transposable elements (TEs) are transcriptionally reactivated in tumors to create novel TE-gene chimeric transcripts, which can produce immunogenic antigens. We performed the most comprehensive screen to date for these TE exaptation events in 33 TCGA tumortypes,675 cancer cell lines, and 11,686 GTEx adult tissue transcriptomes and identified 201,068 TE-exapted candidates with the potential to generate shared tumor-specific TE-chimeric antigens (TS-TEAs). Resultant whole lysate and HLA-pull down mass spectrometry data confirmed that TS-TEAs are presented on cancer cell surfaces. In addition, we highlight the tumor-specific membrane proteins transcribed from TE promoters that can expose novel epitopes on the extracellular surface of cancer cells. Here, we showcase the high pan-cancer prevalence of TS-TEAs and atypical membrane proteins that can be therapeutically exploited through immunotherapy approaches.

overall_design: nanoCAGE libraries was generated for variuos cancer cell lines across different cancer types.

first: Nakul

last: Shah

first: Hyo

middle: S

last: Jang

first: Yonghao

last: Liang

first: Ting

last: Wang


title: Transcriptional Profiles of Pulmonary Artery Endothelial Cells in Pulmonary Hypertension

status: Public on Dec 27 2023

city: Providence

first: Navneet

last: Singh

state: Rhode Island

address: 593 Eddy Street, POB Suite 334

department: Medicine

institute: Brown University

summary: Pulmonary arterial hypertension (PAH) is characterized by endothelial cell (EC) dysfunction. There are no data from living patients to inform whether differential gene expression of pulmonary artery ECs (PAECs) can discern disease subtypes, progression and pathogenesis. We aimed to further validate our previously described method to propagate ECs from right heart catheter (RHC) balloon tips and to perform additional PAEC phenotyping. We performed bulk RNA sequencing of PAECs from RHC balloons. Using unsupervised dimensionality reduction and clustering we compared transcriptional signatures from PAH to controls and other forms of pulmonary hypertension. Select PAEC samples underwent single cell and population growth characterization and anoikis quantification.  Fifty-four specimens were analyzed from 49 subjects. The transcriptome appeared stable over limited passages. Six genes involved in sex steroid signaling, metabolism, and oncogenesis were significantly upregulated in PAH subjects as compared to controls. Genes regulating BMP and Wnt signaling, oxidative stress and cellular metabolism were differentially expressed in PAH subjects. Changes in gene expression tracked with clinical events in PAH subjects with serial samples over time. Functional assays demonstrated enhanced replication competency and anoikis resistance. Our findings recapitulate fundamental biological processes of PAH and provide new evidence of a cancer-like phenotype in ECs from the central vasculature of PAH patients. This “cell biopsy” approach may provide insight into EC heterogeneity within the lung and a therapeutic screening approach in PAH.

overall_design: To profile bulk gene expression of human pulmonary artery endothelial cells (PAECs) harvested from the tips of right heart catheter balloon tips, we submited PAECs for bulk RNA sequencing and performed comparitive analysis.

first: Carsten

last: Eickhoff

first: Augosto

last: Garcia-Agundez

first: Paul

last: Bertone

first: Sunita

last: Paudel

first: Dhananjay

middle: T

last: Tambe

first: Leslie

middle: A

last: Litzky

first: Katherine

last: Cox-Flaherty

first: James

last: Klinger

first: Sean

middle: F

last: Monagahn

first: Christopher

last: Mullin

first: Mandy

last: Pereira

first: Thomas

last: Walsh

first: Mary

last: Whittenhall

first: Troy

last: Stevens

first: Elizabeth

middle: O

last: Harrington

first: Corey

last: Ventetuolo


title: Germinalmatrix-Intraventricular Hemorrhage induced Early Gene Expression Profile in Subventricular zone (SVZ) of developing rabbit forebrain

status: Public on Dec 31 2022

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

summary: Intraventricular hemorrhage (IVH) remains a major neurological complication of prematurity that results in cerebral palsy, hydrocephalus, and cognitive deficits. No effective therapy exists to prevent these disorders in infants with IVH. IVH triggers inflammation, cellular infiltration and white matter injury following neurobehavioural deficits.

overall_design: In this study, we have assessed early gene expression profile after hemorrhage in SVZ tissue from rabbit forebrain with without hemorrhagic pups.

first: Dina

last: Finkel

first: Selvakumar

last: Subbian

first: Edmund

last: La Gamma

first: Govindaiah

last: Vinukonda


title: VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis

status: Public on Jan 16 2023

city: Columbus

first: Genevieve

last: Kendall

state: OH

address: 700 Children's Drive, WA5014

institute: Nationwide Children's Hospital / The Ohio State University

summary: Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the new fusion of transcriptional coactivators, VGLL2-NCOA2, found in infantile rhabdomyosarcoma. To delineate VGLL2-NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities, we implemented a cross-species comparative oncology approach with zebrafish, mouse allograft, and patient samples. We found that VGLL2-NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2-NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2-NCOA2 developmental targets, including a RAS family GTPase, arf6/ARF6. In VGLL2-NCOA2 zebrafish, mouse allograft, and patient tumors, arf6/ARF6 is highly expressed and is absent from mature skeletal muscle. Moreover, ARF6 is overexpressed in adult and pediatric sarcoma subtypes. Our data indicate that VGLL2-NCOA2 is an oncogene which leverages developmental programs for tumorigenesis, and that the reactivation or persistence of arf6/ARF6 could represent a therapeutic opportunity.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Examination of RNA-seq transcriptional profiles from zebrafish tumors derived from mosaic human VGLL2-NCOA2 expression, and a comparison to mature  zebrafish skeletal muscle and CIC-DUX4 generated zebrafish tumors. Examination of C2C12 mouse myoblasts stably transfected with human VGLL2-NCOA2, and allografted to generate tumor models. These are compared to allografts of C2C12-empty controls.

last: Amatruda

first: Olivier

last: Delattre

first: Franck

last: Tirode

first: Matthew

last: Cannon

first: Lin

last: Xu

first: Sarah

last: Watson

first: Didier

last: Surdez


title: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes

status: Public on Dec 23 2022

city: Munich

first: Karin

last: Hrovatin

address: Ingolstädter Landstraße 1

department: Institute of Computational Biology

institute: Helmholtz Munich

summary:
Mouse pancreatic islet scRNA-seq integrated atlas encompassing different ages, sexes, chemical stress leading to dedifferentiation, and diabetes models with corresponding treatments.

Two datasets (sub-series) were newly generated for the atlas.

overall_design:
The atlas integrates data from nine studies and 56 samples with over 300,000 pancreatic islet cells, including over 100,000 beta cells, across different conditions (sex, age, chemical stress, diabetes status). The atlas object with raw and processed expression, annotations, and integrated embedding is contained in GSE211799_adata_atlas.h5ad.gz. Two datasets newly generated for the atlas are in sub-series.
We mapped an external dataset (GSE137909), not contained in the atlas, on top of the atlas and provide the integrated latent embedding  in GSE211799_adata_referenceMapping_GSE137909.h5ad.gz

In both anndata integration objects we describe individual anndata fields under uns key field_descriptions.

Code associated with the manuscript: https://github.com/theislab/mm_pancreas_atlas_rep

cellxgene portal entry: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070

first: Aimée

last: Bastidas-Ponce

first: Luke

last: Zappia

first: Mostafa

last: Bakhti

first: Maren

last: Büttner

first: Ciro

last: Sallino

first: Michael

last: Sterr

first: Anika

last: Böttcher

first: Adriana

last: Migliorini

first: Heiko

last: Lickert

first: Fabian

last: Theis


title: scRNA-seq of pancreatic islets from adult male mice with Fltp-reporter sorting and pancreatic head-tail separation

summary: Single-cell RNA sequencing of pancreatic islets from adult male mice. To disect islet heterogeneity we sorted cells based on anatomical location and maturity marker (Fltp).

overall_design: We used the Fltp reporter mouse line FltpZV (Gegg, et al., 2014; https://doi.org/10.7554/elife.03842) in male mice with the age of 4 months. Pancreas head and tail were anatomically separated prior islet isolation. Islets from six FltpZV/+  mice were pooled. Fltp Venus reporter positive and negative cells were sorted. Four libraries were generated based on anatomical region and cell sorting.


first: Weihua

last: Huang

overall_design: In this study, we have assesed early gene expression profile after hemorrhage in SVZ tissue from rabbit forebrain with without hemorrhagic pups.

first: Dina

last: Finkel

first: Edmund

last: La Gamma

first: Govindaiah

last: Vinukonda


title: scRNA-seq of pancreatic islets from male and female aged mice with Fltp-reporter sorting

summary: Single-cell RNA sequencing of pancreatic islets from aged male and female mice. To disect islet heterogeneity we included both sexes and sorted cells based on maturity marker (Fltp).

overall_design: Islets of Langerhans isolated from the Fltp lineage tracing mouse model Fltp iCre mTmG (Lange, et al. 2012; https://doi.org/10.1016/j.diff.2011.11.003) in male and female mice older than 2 years. We sorted Fltp negative (tomato positive), Fltp lineage positive (GFP positive), and Fltp transient (double positive) populations and generated separate libraries for each population. Male and female mice were pulled together after sorting.


title: Effects of dopamine on HIV latently-infected U1 macrophage cell line

status: Public on Dec 21 2022

city: San Diego

first: Maria

middle: Cecilia

last: Marcondes

state: CA

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

summary:
U1 monocytic cell line was cloned from U937 cells that survived an infection with Human Immunodeficiency Virus HIV-1 and bear integration sites, serving as one of the most studied HIV latent models.
Under the hypothesis that the hyperdopaminergic environment of the brain of substance users affects HIV-infected cells and latency, we tested the effects of Dopamine and two dopamine receptors that were identified as able to signal changes ininnate immune cells, DRD1 and DRD4.

overall_design: U1 cells were exposed for 24 hrs to Dopamine 1uM, SKF 38393 (1uM DRD1 selective agonist), and PD 168077 (1uM DRD4 selective agonist). The concentrations were pre-determined in dose-response experiments, and

middle: C

first: Liana

middle: V

last: Basova


title: Single-Cell RNA Sequencing Reveals the Difference of Human Normal and Degenerative Nucleus Pulposus Tissue Profiles and Cellular Interactions

status: Public on Dec 11 2022

city: Zhanjiang

first: Zhencong

last: Li

address: 57 South Renmin Avenue, Xiashan District, Zhanjiang City, Guangdong Province, China

institute: Affiliated Hospital of Guandong Medical University

summary: Background: The nucleus pulposus is a constituent structure of the human intervertebral disc, and its degeneration can cause Intervertebral disc degeneration (IDD). However the cellular molecular mechanisms involved remain elusive.     Methods: Through bioinformatics analysis, the single-cell transcriptome sequencing expression profiles of human normal nucleus pulposus cells (NNP) and human degenerative nucleus pulposus cells (DNP) were compared to clarify the transcriptome differential expression profiles of human normal and human degenerative nucleus pulposus cells. The single-cell sequencing results of the two samples were analyzed using bioinformatics methods to compare the differences in histiocytosis between human normal nucleus pulposus and human degenerated nucleus pulposus, map the histiocytes of NNP and DNP, perform cell differentiation trajectories for the cell populations of interest and predict cell function, and explore their heterogeneity by pathway analysis and Gene ontology analysis.    Results: Nine cell types were identified, which were Chondrocyte1, Chondrocyte2, Chondrocyte3, Chondrocyte4, Chondrocyte5, Endothelial, Macrophage, Neutrophil, and T cells. Analysis of the proportion of chondrocytes in different tissues revealed that chondrocyte 1 accounted for a higher proportion of normal nucleus pulposus cells and highly expressed COL2A1 compared with degenerated nucleus pulposus cells; chondrocyte 2, chondrocyte 3, chondrocyte 4, and chondrocyte 5 accounted for a higher proportion of degenerated nucleus pulposus cells compared with normal nucleus pulposus cells. Among them, chondrocyte 2 was an inhibitory calcified chondrocyte with high expression of MGP, Chondrocytes 3 were fibrochondrocytes with high expression of COL1A1, Chondrocytes 4 are chondrocytes that highly express pain inflammatory genes such as PTGES, Chondrocytes 5 were calcified chondrocytes with high expression of FN1. (Chondrocytes 4 and chondrocytes 5 were found for the first time in a study of single-cell transcriptome sequencing of disc tissue.) Cell trajectory analysis revealed that chondrocyte 1 was at the beginning of the trajectory and chondrocyte 3 was at the end of the trajectory, while chondrocyte 5 appeared first in the trajectory relative to chondrocyte 2 and chondrocyte 4.    Conclusion: After functional identification of the specifically expressed genes in five chondrocytes, it was found that chondrocyte 1 was a chondrocyte with high expression of COL2A1, COL9A2, COL11A2, and CHRDL2 in a high proportion of normal nucleus pulposus cells, and chondrocyte 3 was a fibrochondrocyte with high expression of COL1A1, COL6A3, COL1A2, COL3A1, AQP1, and COL15A1 in an increased proportion during nucleus pulposus cell degeneration. Through cell trajectory analysis, it was found that chondrocytes 5 specifically expressing FN1, SESN2, and GDF15 may be the key cells leading to degeneration of nucleus pulposus cells. Chondrocytes 2 expressing MGP, MT1G, and GPX3 may play a role in reversing calcification and degeneration, and chondrocytes 4 expressing PTGES, TREM1, and TIMP1 may play a role in disc degeneration pain and inflammation.

overall_design: A total of two human samples were analyzed including one human normal nucleus pulposus tissue and one human degenerative nucleus pulposus tissue

first: Dongping

last: Ye

first: Libing

last: Dai

first: Yude

last: Xu

first: Hao

last: Wu

first: Wei

last: Luo

first: Yiming

last: Liu

first: Xiguan

last: Yao

first: Peigeng

last: Wang

first: Haixiong

last: Miao

first: Jiake

first: Weiguo

last: Liang


title: The regional distribution of resident immune cells shapes distinct immunological environments along the murine epididymis

status: Public on Nov 30 2022

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Previously, the epididymal regions were demonstrated to react strikingly different to inflammatory stimuli. We therefore aimed at untangling the heterogeneity of extravascular CD45+ cells throughout epididymal regions and identifying their transcriptional profile. Using an unbiased scRNASeq approach, 12 distinct populations were identified in total showing striking differences in their distribution along the epididymal duct. Our data indicate that resident immune cell populations are strategically positioned within the organ to provide distinct immunological environments required to maintain tissue integrity and to adequately tackle invading pathogens ascending through the urogenital tract. This study provides an important common research platform and starting point for future functional studies of distinct populations under physiological and pathological conditions.

overall_design: scNRASeq of extravascular CD45+ cells separately isolated from the four main epididymal regions (Initial segment, caput, corpus, cauda) in mice

first: Christiane

last: Pleuger

last: Guenther

first: S

last: Epelman

first: C

last: Kantores

last: Bhushan

first: A

last: Meinhardt


title: Single cell RNA-seq data for iPSC differentiation into Syndetome

status: Public on Apr 18 2023

city: Los Angeles

first: Wensen

last: Jiang

address: 127 S San Vicente Blvd

department: Board of Governors Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: We developed a protocol to differentiate iPSC into iPSC-derived Tenocytes (Syndetome)

overall_design: We collected cells at each stage for scRNA-seq, then optimze Syndetome with WNT inhibitor and sent for scRNA-seq, then applied to 83i cells and sent for scRNA-seq

first: Angela

last: Papalamprou

first: Victoria

last: Yu

first: Dmitriy

last: Sheyn


title: Lymphatic endothelial cell identity is controlled by a GATA2 bound enhancer [ChIP-seq]

status: Public on Nov 21 2022

city: Adelaide

first: Natasha

last: Harvey

state: SA

address: UniSA CRI Building, North Terrace

institute: Centre for Cancer Biology

summary: Transcriptional enhancer elements are responsible for orchestrating the temporal and spatial control over gene expression that is crucial for programming cell identity during development. Here, we describe a novel enhancer element important for regulating Prox1 expression in lymphatic endothelial cells. This evolutionarily conserved enhancer is bound by key lymphatic transcriptional regulators including GATA2, FOXC2, NFATC1 and PROX1. CRISPR-Cas9 genome editing of this enhancer element revealed that deletion of only 5 nucleotides encompassing the GATA2 binding site has a dramatic impact on lymphatic vascular development; mice homozygous for this deletion die soon after birth exhibiting profound lymphatic vascular defects. Lymphatic endothelial cells in enhancer mutant mice exhibit reduced levels of genes characteristic of lymphatic endothelial cell identity and acquire characteristics of hemogenic endothelium, including the capacity to generate hematopoietic cells. These data reveal the first transcriptional enhancer element important for regulating Prox1 expression and lymphatic endothelial cell identity and suggest that Prox1 is important for repressing hemogenic cell identity in the lymphatic endothelium.

overall_design: Genome wide investigation of transcription factor binding in human lymphatic endothelial cells using key TFs in lymphatic valve development

first: Jan

last: Kazenwadel

first: Luis

last: Arriola


title: Lymphatic endothelial cell identity is controlled by a GATA2 bound enhancer

overall_design: Refer to individual Series


title: Cytoplasmic Location of Translation Controls Protein Output

status: Public on Nov 15 2022

city: New York

first: Christine

last: Mayr

state: NY

address: 417 E 68th Street

department: Cancer Biology and Genetics

institute: MSKCC


title: Microglia care for neurons through tunneling nanotubes [Dataset 1 Neurons mRNA-seq]

status: Public on Dec 01 2023

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

institute: University Hospital Bonn

summary: We report the transfer of alpha-s-ynuclein aggregates from neurons to microglia and examined transcriptomic changes following protein extraction. By obtaining RNA samples, we performed differential expression analysis and generated gene ontology enrichment and network analysis.

overall_design: mRNA sequencing of Neurons from mice treated with and without aSyn cocultured in the presence of microglia

first: Hannah

last: Scheiblich

first: Frederik

last: Eikens

first: Lena

last: Wischhof

first: Sabine

last: Opitz

first: Kay

last: Jüngling

first: Csaba

last: Cserép

first: Tracy

last: Bellande

first: Balázs

last: Pósfai

first: Charlotte

last: Geck

first: Jasper

last: Spitzer

first: Alexandru

last: Odainic

first: Stephanie

last: Schwartz

first: Donato

last: Di Monte

first: Daniele

last: Bano

first: Ádám

last: Dénes

first: Eike

last: Latz

first: Ronald

last: Melki

first: Hans-Christian

last: Pape

first: Michael

last: Heneka


title: SHARE-seqV2 for single-cell epigenomic and transcriptomic mapping of human hematopoiesis at scale

status: Public on Oct 04 2022

first: Sai

last: Ma

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: A growing body of single-cell multi-omic tools enables a better understanding of gene regulation underlying development and disease. Tools mapping chromatin and gene expression (such as SHARE-seq) are limited in sensitivity and scalability. Here, we describe SHARE-seqV2 and its associated cloud-computing resource, enabling single-cell analysis at improved quality, robustness, and scale. We apply SHARE-seqV2 across various cell lines, primary tissues, and immune cells, demonstrating a generalizable platform for single-cell multi-omics.

overall_design: SHARE-seqV2 to profile chromatin accessibility and gene expression in the same cell from cell lines (HEK and 3T3), mouse colon, cultured HSC, and primey BMMC.

first: Jason

last: Buenrostro


title: Advanced physiological maturation of iPSC-derived human cardiomyocytes using an algorithm-directed optimization of defined media components

status: Public on Oct 05 2022

city: Toronto

first: Neal

middle: I

last: Callaghan

state: Ontario

address: 661 University Ave

department: Institute of Biomedical Engineering

institute: University of Toronto

summary: Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) hold tremendous promise for in vitro modeling to assess native myocardial function and disease mechanisms as well as testing drug safety and efficacy. However, current iPSC-CMs are functionally immature, resembling in vivo CMs of fetal or neonatal developmental states. The use of targeted culture media and organoid formats have been identified as potential high-yield contributors to improve CM maturation. This study presents a novel iPSC-CM maturation medium formulation, designed using a differential evolutionary approach with oxidative capacity as an objective metric for iterative optimization. Relative to gold-standard reference formulations, our approach significantly matured morphology, Ca2+ handling, electrophysiology, and metabolism, which was further validated by multi-omic screening, for cells in either pure or co-cultured microtissue formats. Together, these findings not only provide a reliable workflow for highly functional iPSC-CMs for downstream use, but also demonstrate the power of high-dimensional optimization processes in evoking advanced biological function in vitro.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iPSC-derived cardiomyocytes treated with 4 different media formulations, and for iPSC-derived biowire tissues cultured in C16 or RPMI+B27 media, with or without electrical stimulation

first: Lauren

middle: J

last: Durland

first: Wenliang

last: Chen

first: Uros

last: Kuzmanov

first: Maria

middle: Z

last: Miranda

first: Zahra

last: Mirzaei

middle: G

last: Ireland

first: Erika

middle: Y

last: Wang

first: Karl

last: Wagner

first: Michelle

last: Kim

first: Julie

last: Audet

first: J

last: Santerre

first: Anthony

last: Gramolini

first: Filio

last: Billia

first: Milica

last: Radisic

first: Seema

last: Mital

first: James

last: Ellis

first: Peter

middle: H

last: Backx

first: Craig

last: Simmons


title: RNAseq of CD14 T cells from female Rheumatoid arthritis patients [NeumRA_CD14]

status: Public on Sep 27 2022

city: Gothenburg

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

summary: RNAseq of CD14 cells from 60 female RA patients activated with LPS for 2 hours. Patients were collected crossectionally from the Rheumatology clinic during 2019-2020. Age md 64, range 23-76 years, Disease duration md 10, range 1-45 years.

overall_design: 60 women with  rheumatoid arthritis, CD4 cells  from human PBMC isolated by positive selection on Easysep (cat. #17858), stimulated with LPS (Sigma Aldrich L2880, 5ug/ml) for 2h

first: Karin

middle: M

last: Andersson

first: Malin

last: Erlandsson

first: Nina

last: Oparina

first: Eric

last: Malmhäll-Bah


title: The trichloroethylene metabolite S-(1,2-dichlorovinyl)-l-cysteine inhibits lipopolysaccharide-induced inflammation transcriptomic pathways and cytokine secretion in a macrophage cell model

status: Public on Jul 08 2022

city: Ann Arbor

first: Kelly

last: Bakulski

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

summary: Macrophage cells play a critical role in the innate immune response during infection. Previous studies have reported that the trichloroethylene (TCE) metabolite S-(1,2-dichlorovinyl)-l-cysteine (DCVC) inhibits cytokine secretion in pathogen stimulated placental membranes, but little is known about the mechanism for these effects, including which cell types or transcriptomic pathways are impacted. We tested the hypothesis that DCVC inhibits lipopolysaccharide (LPS) stimulated inflammation pathways in differentiated (macrophage like) THP-1 cells. THP-1 cells were differentiated with phorbol 12-myristate 13-acetone (PMA) for 24 h and then treated with 1, 5, or 10 µM DCVC for 24 h. After an additional 4 h incubation with lipopolysaccharide (LPS), RNA was harvested, and RNA sequencing and cytokine analysis was performed. There were 1,399 differentially expressed genes in the cells co-treated with DCVC and LPS compared to LPS alone. Major pathways impacted include the inflammatory response, response to cytokines, and leukocyte activation. Finally, DCVC significantly reduced LPS-stimulated IL-1β, IL-6, and TNF-α secretion. These findings suggest that TCE could potentially modify important macrophage functions during infection.

overall_design: 4 treatment groups with 6 replicates: Control, LPS (100ng/mL), DCVC (5µM), and LPS (100ng/mL) + DCVC (5µM)

first: Sean

last: Harris

first: John

last: Dou

first: Ethan

last: Houskamp

first: Eleanor

last: Sheeres

first: Emily

last: Schellenboom

first: Olivia

last: Harlow

first: Rita

last: Loch-Caruso

first: Erica

last: Boldenow


title: Single-molecule chromatin architectures of human centromeres and telomeres

status: Public on May 10 2022

city: Seattle

first: Andrew

middle: Ben

last: Stergachis

state: WA

address: 1959 NE Pacific St

department: Medical Genetics

institute: University of Washington

summary: Centromeres and telomeres are essential structural components of eukaryotic genomes, and alterations in their structure and function contribute to various human diseases. Currently, our understanding of the chromatin architecture underlying centromeres and telomeres is limited owing to their highly repetitive DNA content. To overcome this, we applied long-read single-molecule chromatin fiber-sequencing (Fiber-seq) to a human cell line with a complete telomere-to-telomere (T2T) reference genome, resulting in single-nucleotide precise mapping of chromatin accessibility, nucleosome positioning, and transcription factor occupancy across 1.7 million intact ~16kb chromatin fibers - resolving the chromatin architecture for ~97% of human telomeric and centromeric DNA. We identify that the centromeric kinetochore binding region contains highly atypical chromatin that juxtaposes highly accessible and tightly compacted DNA - a feature unique to the kinetochore. This structure mirrors the alpha-satellite DNA repeat and appears driven via clustered CENP-B occupancy at hypo-CpG methylated repeats. In addition, telomeres often contain several kilobases of non-nucleosomal chromatin, and the transition between nucleosome-bound chromatin and the telomere cap is highly heterogeneous and often punctuated by CTCF-bound elements. Our findings uncover non-standard chromatin architectures as the predominant organizational structure of telomeres and the kinetochore binding region, and provide a framework for future studies of complete human epigenomes.

overall_design:
Single-molecule chromatin fiber-sequencing (Fiber-seq) of CHM13 cells using a complete reference genome.
Single-molecule chromatin fiber-sequencing (Fiber-seq) of GM12878 cells using a complete reference genome.

first: Danilo

last: Dubocanin

first: Adriana

middle: E

last: Sedeño-Cortés

first: Jane

last: Ranchalis

first: Taylor

last: Real

middle: B


title: Mutant p53 drives an immune cold tumor immune microenvironment in oral squamous cell carcinoma

status: Public on May 04 2022

city: Houston

first: Roberto

last: Rangel

state: Texas

address: 1515 Holcomb Blvd

department: Head and Neck Surgery

institute: The University of Texas MD Anderson Cancer Center

summary: The critical role of the tumor immune microenvironment (TIME) in determining response to immune checkpoint inhibitor (ICI) therapy underscores the importance of understanding cancer cell–intrinsic mechanisms driving immune-excluded (“cold”) TIMEs. One such cold tumor is oral cavity squamous cell carcinoma (OSCC), a tobacco-associated cancer with mutations in the TP53 gene which responds poorly to ICI therapy. Because altered TP53 function promotes tumor progression and plays a potential role in TIME modulation, here we developed a syngeneic OSCC models with defined Trp53 (p53) mutations and characterized their TIMEs and degree of ICI responsiveness. We observed that a carcinogen-induced p53 mutation promoted a cold TIME enriched with immunosuppressive M2 macrophages highly resistant to ICI therapy. p53-mutated cold tumors failed to respond to combination ICI treatment; however, the combination of a programmed cell death protein 1 (PD-1) inhibitor and stimulator of interferon genes (STING) agonist restored responsiveness. These syngeneic OSCC models can be used to gain insights into tumor cell–intrinsic drivers of immune resistance and to develop effective immunotherapeutic approaches for OSCC and other ICI-resistant solid tumors.

overall_design: We generated gene expression profiles of stable p53-knockdown (KD) and non-targeting control-shRNA ROC1 tumor cells to determine the role of mutant p53 T122N in the expression of inflammatory cytokines and chemokines involved in oral cancer. From each group we run triplicate samples and genes differentially expressed were evaluated.

first: Jeffrey

middle: N

last: Myers


title: Identification of the toxic 6mer seed consensus for human cancer cells

status: Public on Feb 16 2022

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: 6mer seed toxicity is a novel cell death mechanism that kills cancer cells by triggering death induced by survival gene elimination (DISE). It is based on si- or shRNAs with a specific G-rich nucleotide composition in position 2-7 of their guide strand. An arrayed screen of 4096 6mer seeds on two human and two mouse cell lines identified a consensus GGGGGC as the most toxic seed. We have now tested two additional cell lines, one human and one mouse, confirming the GGGGGC consensus as the most toxic average 6mer seed for human cells while slightly less significant for mouse cells. RNA Seq and bioinformatics analyses suggested that an siRNA containing the GGGGGC seed (siGGGGGC) is toxic to cancer cells by targeting GCCCCC seed matches in the 3' UTR of a set of genes critical for cell survival. We have identified several genes targeted by this seed and demonstrate direct and specific targeting of GCCCCC seed matches, which is attenuated upon mutation of the GCCCCC seed matches in these 3' UTRs. Our data show that siGGGGGC kills cancer cells through its miRNA-like activity and points at artificial miRNAs, si- or shRNAs containing this seed as a potential new cancer therapeutics

overall_design: PC3 or HeyA8 cells were transfected with different siRNAs at 1nM and 24 or 48hrs after transfection RNA was isolated and subjetced to lareg RNA Seq analysis

first: Monal

last: Patel

first: Elizabeth

middle: T

last: Bartom


title: Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation [ARID2 and PBRM1 ChIP-seq]

status: Public on Mar 22 2022

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Histone proteolysis is a poorly understood phenomena by which the N-terminal tail of histones are irreversible cleaved by intracellular proteases. During development histone PTMs are known orchestrate gene expression and ultimately cell fate decision, therefore it will be key to decipher underlying mechanisms that lead to proteolysis during cellular differentiation. Previous reports have found that histone H2A is cleaved at the C-terminus, and here we found that the N-terminal is also proteolytically clipped and removed by the lysosomal protease Cathepsin L. Using quantitative mass spectrometry (MS), we identified L23 to be the primary site for this protease, with this clipped H2A (cH2A) form representing ~1% of the total H2A reaching a maximum after 4 days of differentiation. Using Chip-seq, we found reduced proteolysis, lead to increase acetylated H2A at promoter regions in differentiated ES cells.  We also report novel readers of acetylated H2A during in pluripotency as we identified members of the pBAF complex to recognize different forms of H2A acetylation. Moreover, our data showed that this recognition is abolished upon proteolysis. All in, our data suggest that proteolysis serve as a quick mechanism to silence genes involve in pluripotency and destabilize the nucleosome core particle as indicated by protein degradation studies.

overall_design:
AID2 and PBRM1 ChIP-seq in mESCs differentiation with CTSL KD.

Please note that peaks were detected for each sample against the corresponding input control and is linked to the corresponding *rep1 ChIP sample records.

first: Mariel

last: Coradin

first: Benjamin

middle: A

last: Garcia


title: Mapping Human Transient Transcriptomes Using Single Nucleotide Resolution 4sU Sequencing (SNU-Seq)

status: Public on Apr 01 2022

city: Oxford

last: Mellor

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: Genomes are pervasively transcribed leading to stable and unstable transcripts that define functional regions of genomes and contribute to cellular phenotypes. Defining comprehensive nascent transcriptomes is pivotal to understand gene regulation, disease processes, and the impact of extracellular signals on cells. However, currently employed methods are laborious, technically challenging and costly. We developed single-nucleotide resolution 4sU-sequencing (SNU-Seq), involving pulse labelling, biotinylation and direct isolation of nascent transcripts. Artificial poly-(A)-tailing of the 3’ most nucleotide of nascent transcripts ensures oligo-d(T) primer-based library preparation and sequencing using commercial 3’ RNA-Seq kits. We show that SNU-Seq is a cost-effective new method generating even read profiles across transcription units. We used SNU-Seq to identify transcription elongation parameters, to map usage of polyadenylation (PAS) sites and novel enhancers. Remarkably, 4sU labelled nascent RNA accumulates short ~100nt transcripts that map to the 5’ end of genes. We show that isolation of these short nascent RNA and sequencing the 5’ and 3’ ends using size-selected SNU-Seq (ssSNU-Seq) provides highly sensitive annotations of mapped and novel TSSs, promoter-proximal pause/termination sites. Thus, SNU-seq and ssSNU-seq combined yield comprehensive transcriptomics data at low cost with high spatial and temporal resolution.

overall_design:
To develop SNU-Seq and size-selected SNU-Seq for measuring nascent transcription at high resolution.
There are 3 different sample types reported here; SNU-seq, size-selected SNU-seq, and TT-seq. There are 11 different samples. All samples are from HEK293 cell and are spike-in controlled with 3 thiolablled 1kb long fragments from yeast with a 42% GC content. TT-seq samples are a time series - 10,15, 20 mins labelling with 4sU with 1 reapeat (samples 4 to 9) or cells untreated or treated with alpha amanitin during a 5 min pulse label with 4sU (samples 10 and 11). For samples 4 to 11 libraries were prepared using the NEBNext II Ultra Directional RNA library and sequenced on the Illumina NextSeq 500 platform using the High-Output Nextseq 500 kit. For each sample 4 to 9 there are 4 processed files (two repeats (A and B) and reads on the forward (F) and reverse (R) strand) and 16 raw samples per time point with R1 and R2 series representing the paired-ends. For samples 10 and 11 there is one repeat, 2 processed files and 8 raw files per sample with R1 and R2 representing the paired ends. SNU-seq samples were thiolabelled for 10 minutes with 4sU and after adding a polyA track to the 3' end, sequenced from the 3' polyA tail using the Quant-Seq Lexogen 3' mRNA kit on the Ion Proton platform. There are two raw data files representing two repeats (17 and 18). There are six processed files representing the merged data on each strand for the full SNU-seq read out primed from the artifical polyA tail, the 3 prime read on each strand (SNU-seq readout) and the 3 prime read after removal of internal polyA tracks >8nts. Size-selected SNU-seq samples (ssSNU-seq) were labelled as for the SNU-seq but the polyadenylation step was omitted. Instead 50-100bp thiolabelled RNA fragments were selected from the nascent thiolabelled RNA using a gel, adaptors ligated to the 5' or 3' ends and sequenced using an NEBNext Small RNA library kit on the Illumina platform.There are 4 raw data files and four processed files, two for the 5' ends and two for the 3' ends on each strand. In summary there are 24 processed files and 70 raw data files.

first: Philipp

last: Lorenz

first: Anna

last: Lamstaes

first: Shidong

last: Xi

first: Struan

last: Murray


title: Lariat mapping of a DBR1 CRISPR KO cell line

status: Public on Feb 03 2022

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St, Box G

department: Molecular Biology, Cell Biology and Biochemistry

institute: Brown University

summary: We used CRISPR in HEK293T cells to create two DBR1 knockout cell lines (C19 and C22). After high-throughput sequencing of total RNA extracted from these cells, we performed lariat read mapping using the method described in "Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo" (Taggart et al, 2012). We found lariats in the two DBR1- cell lines to be ~20-fold enriched relative to the levels observed in the HEK293T control samples.

overall_design: Lariat mapping of wild type and DBR1- HEK293T cells

first: Allison

last: Taggart

first: Rachel

last: Soemedi

first: Luke

last: Buerer


title: Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation [H2AK9ac ChIP-seq]

status: Public on Dec 31 2021

overall_design: H2AK9ac ChIP-seq in mESCs differentiation with CTSL KD.


title: Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation [RNA-seq]

overall_design: RNA-seq in mESCs differentiation with CTSL KD.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes for advanced gastric cancer with different ferroptosis-related-scores

status: Public on Nov 29 2021

city: Harbin

first: Yingwei

last: Xue

address: 150, Haping St, Nangang District

department: Department of Gastrointestinal Oncology

institute: Harbin Medical University Cancer Hospital

summary: Gastric cancer is one of the leading causes of cancer mortality worldwide. We compared transcriptomic profiles of gastric cancer with different ferroptosis-related-scores to identify the prognostic significance of ferroptosis-related-score in gastric cancer.

overall_design: High-throughput sequence profiles from 231 gastric tumors and paired normal 230 gastric tissues from gastric cancer patients


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes for advanced gastric cancer with different tumour-stroma-scores

summary: Gastric cancer is one of the leading causes of cancer mortality worldwide. We compared transcriptomic profiles of  advanced gastric cancer with different tumour-stroma-scores to identify the prognostic significance of tumour-stroma-score in advanced gastric cancer.

overall_design: High-throughput sequence profiles from 38 gastric tumors and paired normal 38 gastric tissues from gastric cancer patients


title: Transcriptional changes associated with endoplasmic reticulum stress in the eye imaginal disc of Drosophila melanogaster

status: Public on Sep 20 2021

first: Brian

middle: Scott

last: Brown

address: 540 1st Avenue, SKI 5-2

department: Department of Cell Biology

institute: NYU School of Medicine

summary: We obtained transcriptional profiles of third instar eye imaginal disc nuclei with or without endoplasmic reticulum stress using next generation sequencing (NGS). We employed an isolation of nuclei tagged in specific cell type (INTACT) protocol (Ma and Weake, J. of Vis. Exp., 2014) to label nuclear membranes of GMR-GAL4-expressing cells with EGFP. The experimental group also expressed a mutant allele of the membrane visual protein rhodopsin (Rh-1(G69D)), which is known to cause endoplasmic reticulum stress and initiate Unfolded Protein Response (UPR) signaling. The goal of this study was to characterize the transcriptional changes associated with endoplasmic reticulum stress responses in a commonly used platform, the eye imaginal disc.

overall_design: Comparison of isolated nuclear transcriptomes from third instar control eye imaginal discs and third instar eye imaginal discs overexpressing the misfolded protein Rh-1(G69D), a potent inducer of endoplasmic stress

middle: S

first: Hyung

last: Ryoo


title: IFNγ induces a dynamic and complex transcriptional, chromatin and enhancer landscape

status: Public on Oct 12 2021

city: SEVENOAKS

middle: Rita

state: Kent

address: 99 Solefields Road

department: Department of Biochemistry

summary: Aims and methods: To analyze how IFNγ induces coding and non-coding nascent transcriptional changes, SNU-seq is used to measure genome-wide changes in nascent transcription in untreated, 0.5hr, 2hr and 24hr IFNγ treated Hep3B cells. SNU-seq identifies the last transcribed nucleotide at near single-nucleotide resolution. 3'-end RNA-seq is used to examine RNA levels. ChIPmentation and ATAC-seq are used to assess the differential chromatin landscape upon IFNγ treatments, measuring H3K27ac, H3K4me3 and CTCF genome-wide changes as well as DNA accessibility in untreated, 0.5hr, 2hr and 24hr IFNγ treated Hep3B cells. Higher-order chromatin structure is investigated upon IFNγ treatments using Capture-C to measure promoter interactions of three gene promoters; IRF1, STAT1, and CD274. Results:  3'-end RNA-seq reveals IFNγ stimulated genes. SNU-seq identifies dynamic transcription at genes and non-coding intergenic regions and is used to demonstrate differential APA upon IFNγ treatments. By measuring transcription at nucleosome depleted regions, differential enhancer activity was demonstrated. IFNγ induces hundreds of methylation changes and thousands of acetylation changes over 24hrs. Unlike H3K4me3 which is deposited at late timepoints, H3K27ac is dynamically deposited. This acetylation is sometimes sustained throughout 24hrs but is often transiently deposited. CTCF shows very few binding changes throughout the timecourse. IFNγ induces significant changes in promoter:enhancer interactions at IRF1 and STAT1. The CD274 promoter loops to the nearest gene promoter; PLGRKT.

overall_design: SNU-seq, 3'-end RNA-seq and ATAC-seq were performed in triplicate in untreated, 0.5hr, 2hr and 24hr treated Hep3B cells. ChIPmentation was performed in duplicate in untreated, 0.5hr, 2hr and 24hr treated Hep3B cells. Capture-C was performed in duplicate in untreated, 0.5hr, 2hr and 24hr treated Hep3B cells, capturing the IRF1, STAT1 and CD274 promoter.

middle: R

first: Phil

first: Jane


title: Distinct transcriptional profiles of Leptospira borgpetersenii serovar Hardjo strains JB197 and HB203 cultured at different temperatures

status: Public on Apr 28 2021

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

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

institute: University of Missouri

summary: Leptospirosis is a global zoonotic, neglected tropical disease. Interestingly, a high level of species specificity (both bacteria and host) plays a major role in the severity of disease presentation which can vary from asymptomatic to multi-organ failure. Pathogenic Leptospira colonize the kidneys of infected individuals and are shed in urine into the environment where they can survive until they are contracted by another host. This study looks at two strains of L. borgpetersenii, HB203 and JB197 which are genetically very similar, and identical by serotyping as serovar Hardjo, yet HB203 causes a chronic infection in the hamster while JB197 causes organ failure and mortality. To better characterize bacterial factors causing different disease outcomes, we examined the gene expression profile of these strains in the context of temperatures that would reflect natural Leptospira life cycles (environmentally similar 29oC and 37oC which is more indicative of host environment). We found vast differences in gene expression both between the strains and within strains between temperatures. Characterization of the transcriptome of L. borgpetersenii serovar Hardjo strains JB197 and HB203 provides insights into factors that can determine acute versus chronic disease in the hamster model of infection. Additionally, these studies highlight strain to strain variability within the same species, and serovar, at different growth temperatures, which needs to be considered when serovars are selected and propagated for use as bacterin vaccines used to immunize domestic animal species.

overall_design: L. borgpetersenii serovar Hardjo strains JB197 and HB203 were isolated from the kidneys of experimentally infected hamsters and maintained at 29°C and 37°C. RNAseq revealed distinct gene expression profiles; 440 genes were differentially expressed (DE) between JB197 and HB203 at 29°C, and 179 genes were DE between strains at 37°C. Comparison of JB197 cultured at 29oC and 37oC identified 135 DE genes while 41 genes were DE in HB203 with those same culture conditions. The consistent DE of ligB, which encodes the outer membrane virulence factor LigB, was validated by immunoblotting and 2D-DIGE. Differential expression of lipopolysaccharide was also observed between JB197 and HB203.

first: Ellie

last: Puts

first: Luis

middle: V

last: Fernandes

last: Brunelle

first: John

middle: D

last: Lippolis

first: David

middle: P

last: Alt

first: Darrell

middle: O

last: Bayles

first: Richard

middle: L

last: Hornsby

first: Jarlath

last: Nally


title: Progenitor cell diversity in the developing mouse neocortex

status: Public on Mar 01 2021

first: Xiaochang

last: Zhang

address: 920 E 58th St, CLSC 507A

department: Human Genetics

institute: The University of Chicago

summary: In the mammalian neocortex, diverse projection neuron types are generated by the same pool of neural progenitors in sequential waves. How neuronal cell type specification is related to developmental timing remains unclear. To determine whether neural progenitor cell heterogenity correlates with neuronal type spcification, we performed single cell RNA sequencing analysis of the developing mouse neocortex (E10.5 through E18.5) by Drop-Seq. We uncovered cellular and molecular diversity among neuroepithelial cells, radial glial cells, intermediate progenitors and neuron types.

overall_design: Dorsal forebrain tissues were collected from embryonic day 10.5, 12.5, 14.5, 15.5, 16.5 and 18.5 CD-1 mice (Charles River), dissociated into single cells, captured by the Drop-Seq protocol and analyzed for cell clusters and differential gene expression.

first: Bowei

last: Kang


title: Seq data of aortas

status: Public on Feb 23 2021

city: BEIJING

first: YINGCHUN

last: HAN

state: BEIJING

address: CHAOYANG DISTRICT

institute: Anzhen Hospital

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

overall_design: Refer to individual Series


title: A cascade for zinc mediated transcriptional activation by the zinc-sensing nuclear receptor HIZR-1 on the regulator of lysosome biogenesis HLH-30 to achieve homeostasis

status: Public on May 15 2021

city: Saint Louis

first: Ciro

last: Cubillas Ramirez

state: Missouri

address: 4577 McKinley, Campus Box 8103, 3607 Cancer Research Building

department: Developmental Biology

institute: Washington University in St Louis, School of Medicine

summary: Zinc is an essential element for animals and stored in de novo synthesized lysosome related organelles called bilobed granules in Caenorhabditis elegans. Defining how zinc regulated transcription drives the observed lysosome remodeling is key to understand zinc homeostasis processes. Here we describe a positively regulated zinc network controlled by HIZR-1 and HLH-30, the zinc sensor and the master regulator of the autophagy-lysosomal pathway in Caenorhabditis elegans, respectively; essential for connecting zinc homeostasis to lysosome biogenesis. Our studies indicate that either hizr-1 and hlh-30 are necessary and sufficient to activate transcription of lysosome-genes under high dietary zinc conditions. Consistent with the hizr-1 and hlh-30 dependency for high zinc response, we found DNA enhancer elements corresponding to the high zinc activation element consistently adjacent to E-boxes in the promoter regions of lysosome-genes. We defined a regulatory network based on the contribution of each transcription factor. Since zinc cannot be degraded, the autophagy-lysosomal pathway could play a key role in removing zinc excess

overall_design: Two Caenorhabditis elegans strains, wild type and a hizr-1 loss-of-function mutant were independtly exposed to high dietary zinc conditions and compared to a non-supplemented zinc condition. Two biological samples each strain and each condition were used.

last: Cubillas

first: Adelita

last: Mendoza

first: Daniel

last: Schneider

last: Murphy

last: Herrera

last: Edwards

first: Clifford

last: Luke

first: Stephen

last: Pak

first: Gary

last: Silverman

first: Abhinav

last: Diwan

first: Kerry

last: Kornfeld


title: Genome-wide enhancer maps link disease variants to genes and cell types

city: Stanford

first: Jesse

last: Engreitz

address: 450 Serra Mall

department: Genetics

institute: Stanford University

summary: We generated ATAC-seq and H3K27ac ChIP-seq data in immortalized immune cancer cell lines to predict enhancer-gene regulation using the ABC model.

first: Joseph

last: Nasser

first: Tung

last: Nguyen

last: Ray

first: Charles

last: Epstein

first: Nir

last: Hacohen

first: Eric

last: Lander


title: RNA-seq data of aortas with atherosclerotic or medial calcification

last: HAN

summary: Vascular calcification is the ectopic deposition of calcium hydroxyapatite minerals in arterial wall. However, the underlying molecular mechanisms regulating vascular calcification remain incompletely understood. In this study, we applied RNA sequencing to explore the mechanism of vascular calcificaiton in both medial and atherosclerotic vascular calcification models.

overall_design: mRNA profiles of aortas from 2-month old wild type, 16-month old ApoE-/-(atherosclerotic calcificaiton) and chronic kidney diseased mice(medial calcification).

first: Yingchun

last: Han


title: MicroRNA-seq data of aortas from chronic kidney disease (CKD) induced vascualr calcification mouse model

summary: MicroRNAs (miRNAs) are short noncoding RNAs that impact protein expression, regulating a variety of physiological processes. To date, a few miRNAs have been implicated in the process of vascular calcification; however, our understanding of the miRNAs involved and their regulatory mechanisms remains incomplete.The analysis showed differences of microRNAs in the aortas after CKD induced vascular calcification.

overall_design: Examination of MicroRNA profiles of aortas induced by CKD induced vascualr calcification mouse model.