title: Auxin coreceptor IAA17/AXR3 controls cell elongation in Arabidopsis thaliana root by modulation of auxin and gibberellin perception

status: Public on Apr 01 2023

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: Proper functioning of the nuclear auxin pathway is essential for regulating plant growth and development by maintaining auxin homeostasis. To understand better physiological mechanisms involved in auxin signaling pathways we investigated the localization and effect of accumulation of auxin coreceptor IAA17/AXR3 in root. We demonstrate that the accumulation of stable nuclear AXR3-1 protein interferes with auxin homeostasis, causing auxin insensitivity and increased rapid root cell elongation followed by detained growth. This growth pattern is associated with changes in phytohormone gene expression. Data from transcriptomic screen combined with reporter lines and mutant studies declare essential role of auxin homeostasis in maintaining optimal root growth rate and development. We proposed a model in which rapid cell elongation is caused by combination of AXR3-1-dependent auxin insensitivity associated with unblocked gibberellin effect on root. This study demonstrate that plants coordinate gibberellin homeostasis by the auxin signaling pathway, contributing to avoid excessive root elongation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from 2 lines inducible overexpressing stable form of auxin coreceptor AXR3-1 and from Col-0 treated with IAA (3-indoleacetic acid; Sigma-Aldrich), PEO-IAA (2-(1H-Indol-3-yl)-4-oxo-4-phenyl-butyric acid ; MedChemExpress) and mock (ethanol). Experimental material was lines expressing stable form of AXR3-1 under estradiol inducible promoter (line g1090 promoter g1090::XVE>>AXR3-1-mCherry (10.1038/nature13663)) and under heat shock promoter (line HS::AXR3-1 (10.1242/dev.00659)) in Col-0 background. Each of these lines has an appropriate control (treated in the same way as the mutant line, it means Col-0 treated with estradiol or heat shock). RNA from 50 Arabidopsis thaliana root tips (1-2 mm) were extracted, 3 biological replicas were used.

first: Monika

last: Kubalová

first: Matyáš

last: Fendrych

last: Müller


title: Satellite cell heterogeneity for proinflammatory chemokine expression

status: Public on Apr 19 2023

city: Tempe

first: Christopher

middle: L

last: Plaisier

state: Arizona

department: SBHSE

country: USA

institute: Arizona State University

type: Expression profiling by high throughput sequencing

summary: The expression of proinflammatory signals at the site of muscle injury are essential for efficient tissue repair and their dysregulation can lead to inflammatory myopathies. In these studies, we examined the contribution of satellite cells, the stem cell population of skeletal muscle, to proinflammatory signaling. Mouse satellite cells in culture express Tnfa, Ccl2, and Il6 within 2 hours of lipopolysaccharide treatment. Single-cell RNA sequencing revealed the satellite cell cultures were heterogeneous, consisting of seven clusters representing the continuum between activation and differentiation. Lipopolysaccharide treatment led to transcription of a broad profile of the C-C and C-X-C chemokines (eg. Ccl2, Ccl5, and Cxcl0) and cytokines (eg. Tgfb1, Bmp2, Il18 and Il33) associated innate immune cell recruitment and satellite cell proliferation. One cell cluster was enriched for genes in the antiviral interferon pathway that could be induced with lipopolysaccharide treatment. Activation of antiviral interferon pathway in satellite cells was also detectable at the site of cardiotoxin induced muscle injury. These data demonstrate that capability of satellite cells are responsive to inflammatory signals to secrete chemokines and cytokines. Further, we identified a novel subset of satellite cells with activated antiviral interferon pathway in the absence of injury or infection.

overall_design: Single-cell RNA-seq of muscle from B6129SF1/J that has either been treated with sham or lipopolysaccharide.

first: Alexander

middle: B

last: Andre

first: Katherina

middle: P

last: Rees

first: Samantha

last: O'Connor

first: Grant

last: Severson

first: Jason

middle: M

last: Newbern

first: Jeanne

last: Wilson-Rawls

first: Alan

last: Rawls


title: Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus

status: Public on Apr 22 2023

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: GO-CRISPR: a highly controlled workflow to improve discovery of gene essentiality

city: Ottawa

first: Pirunthan

last: Perampalam

state: ON

address: 336 Drumlsih Lane

country: Canada

summary: Genome-wide CRISPR screens aid researchers in discovering genes that function across a broad range of cellular mechanisms. Loss-of-function screens are particularly useful for identifying essential genes through loss of cell fitness measurements. However, loss-of-function screens are more challenging compared to gain-of-function screens due to the limited dynamic range of decreased sgRNA sequence detection. Here we describe Guide-Only control CRISPR (GO-CRISPR), an improved loss-of-function screening workflow, and its companion software package, Toolset for the Ranked Analysis of GO-CRISPR Screens (TRACS; https://github.com/developerpiru/TRACS). We demonstrate a typical GO-CRISPR workflow in a non-proliferative 3D spheroid model of dormant high grade serous ovarian cancer. We compare the results from our GO-CRISPR screen and demonstrate the discovery of novel pathways that were not possible using the currently established CRISPR screening method.

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design: GO-CRISPR and its accompanying software, TRACS, robustly improve the discovery of essential genes in challenging biological scenarios.

first: James

middle: I

last: McDonald

first: Frederick

middle: A

last: Dick


title: Netrin and its dependence receptors are mediators of high-grade serous ovarian cancer cell survival

summary: We previously showed that DYRK1A is essential for ovarian cancer spheroid cell survival. DYRK1A regulates transcription by assembling the DREAM repressor complex and also regulates RNA polymerase II. However, the present understanding of how DYRK1A regulates transcription in high-grade serous ovarian cancer (HGSOC) spheroid cells to promote quiescence and survival is lacking. Here we performed GO-CRISPR screens in a panel of HGSOC spheroid cells in combination with transcriptional analyses of DYRK1A deficient spheroid cells. We identified netrin signaling components as essential factors of HGSOC spheroid cell survival. Netrin is well-characterized in axon development but has recently been implicated in other cancer types. We found that knockout of netrin ligands or receptors affects viability of spheroid cells. Netrin ligands and receptors are upregulated in HGSOC cells in suspension conditions. Together, this work suggests that the netrin signaling pathway may be a potential therapeutic target to specifically eliminate spheroid cells in HGSOC and highlights it as an important area requiring further investigation in the context of ovarian cancer.

overall_design: We analyzed three ovarian cancer cell lines: iOvCa147 (GSE150246), OVCAR8, and TOV1946. Each cell line has three replicates for each condition (Adherent (Ad)or Reattached Spheroid (R)). Each condition contains data for Cas9 positive and Cas9 negative samples. The initial plasmid library and GO-CRISPR screen data for iOvCa147 can be found at GSE150246. GO-CRISPR screens for OVCAR8 and TOV1946 were analyzed using TRACS as described in GSE150246. iOvCa147 RNA-seq samples were analyzed using STAR and BEAVR.

first: Daniel

middle: T

last: Passos


title: The effect of 1-Oleoyl-lysophosphatidylethanolamine (LPE) on the RORgt activity in Th17 cells

status: Public on May 08 2023

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

country: Japan

institute: KAZUSA DNA Research Institute

summary: Th17 cells are a helper cell subset of pro-inflammatory T cells, which have diverse functions ranging from neutrophilic-inflammatory responses against pathogens to driving a number of autoimmune diseases. Accumulating evidence indicates that specific cellular lipid metabolic pathways that include fatty acid or cholesterol play an essential role in regulating the differentiation and function of Th17 cells. However, what molecular mechanisms link lipid metabolism and RORgt function during Th17-cell differentiation? By using a combination of a CRISPR- based screening system and a global lipidome analysis, we addressed this question in an effort to identify a specific lipid metabolite that is essential for RORgt-mediated Th17-cell differentiation. We found five lipid enzymes that elicit RORgt activity and constitute a core molecular signature of Th17 cells. Furthermore, although Th17 cells treated with TOFA, which is a ACC1 inhibitor, showed decreased mRNA expression of Th17 specific gene and chromatin accessibility at Th17 cell specific gene loci, we also found that extrinsic supplementation of LPE (1-18:1)  restored the phenotype of ACC1-inhibited Th17 cells. Taken together, these series of results indicated that LPE (1-18:1) synthesized from the five lipid metabolic enzymes was required for RORgt to function appropriately in Th17-cell differentiation.

overall_design:
Related to Fig 2,   RNA-seq was performed to investigate lipid synthesis genes which regulate differantiation of Th17 cells.
Related to Fig 4.   RNA-seq was performed to investigate the role of LPE (1-18:1) on the regulation of Th17 cells specific gene expression.
Related to Fig 5,   ATAC-seq was performed to investigate the role of LPE (1-18:1) on the chromatin accessibility at Th17 cell specific gene loci.

first: Yusuke

last: Endo

first: Takahiro

last: Nakajima

first: Kazutaka

last: Ikeda

first: Yoshitaka

last: Taketomi

first: Satoru

last: Yokoyama

first: Shigemi

last: Sasamoto

first: Hikari

middle: K

last: Asou

first: Keisuke

last: Miyako

first: Yoshinori

last: Hasegawa

last: Kawashima

first: Osamu

last: Ohara

first: Makoto

last: Murakami

first: Toshinori

last: Nakayama


title: Single Nuclei Transcriptomics Delineates Complex Interactions Between Immune and Renal Cells Contributing to Kidney Graft Fibrosis

status: Public on Mar 06 2023

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: Purpose: Chronic allograft dysfunction (CAD) remains a major obstacle in kidney transplantation. However, the molecular pathogenesis of human CAD is unknown. Herein, we tested the hypothesis that single nuclei transcriptomics of human kidney allograft fibrosis will reveal diverse cell types, deconvolve complex fibrosis-driving pathways, and provide deeper insights into the progression of kidney allograft dysfunction.

overall_design: A total of 9 biospies were included: 6 from CAD patients with IFTA and 3 from patients with stable graft function with normal/nonspecific histopathology served as controls. Included samples were preserved in RNAlater and sequncing quality were compared to frozen samples kidney biopsies.

first: Jennifer

last: McDaniels

middle: C

first: Cem

last: Kuscu

first: Canan

first: Elissa

last: Bardhi

first: Thomas

last: Rousselle

first: Cinthia

last: Drachenberg

first: Manish

last: Talwar

middle: D

last: Eason

first: Thangamani

last: Muthukumar

middle: G

last: Maluf

first: Valeria

middle: R

last: Mas


title: Effects of xenogeneic complement 90-minute exposure on neonatal porcine Sertoli cells (NPSC).

status: Public on Feb 15 2023

city: Lubbock

first: Jannette

last: Dufour

state: TX

department: Cell Biology and Biochemistry

institute: Texas Tech University Health Sciences Center

summary: To investigate changes in gene expression influenced by a 90-minute incubation in human serum with complement preserved.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for baseline NPSC (Control, n=3) and NPSC after 90-minute exposure to human complement (Complement, n=3).

first: Rachel

last: Washburn

first: Dalia

last: Martinez-Marin


title: Base editor induced mutation spectrum in GFP, human ATP1a1, human TP53BP1 and murine MyoD

status: Public on Oct 30 2023

city: Zurich

first: Richard

last: Chahwan

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

summary: Analysis of  targeted genomic and epigenomic mutations within GFP, human ATP1a1, human TP53BP1 and murine MyoD induced through  state-of the art base editors

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Genomic DNA was isolated from human HEK293T cells which constiutively express GFP or murine 3T3 cells  which were transfected with the base editor and a gene-specific gRNA. Specific gene locus was amplified with barcoded primers and subjected to amplicon deep sequencing with either through PacBio Sequencing or Illumina Sequencing

first: Julian

last: Weischedel

first: Laurence

last: Higgins

first: Sally

last: Rogers


title: Persistent Inflammation of the Rectum in Perianal-Fisulizing Crohn's Disease Associates with Goblet Cell Function

status: Public on Feb 20 2023

city: Atlanta

first: Greg

last: Gibson

state: GA

address: North Ave NW

institute: Georgia Institute of Technology

summary: Perianal Fistulizing Crohn’s Disease (perianal-CD) is a debilitating form of CD typically associated with prolonged periods of morbidity. Leveraging single-cell RNA sequencing, rectal mucosal tissue was sequenced from individuals following anti-TNF biologic therapy having either active perianal-CD and inflamed rectal mucosa or healed perianal-CD but non-inflamed mucosa. Single cell transcriptomic profiles of the inflamed and non-inflamed tissue were contrasted to test for specific cellular subsets of rectal epithelial and immune cell compartments associated with inflamed perianal disease. We identified eight broad classes of epithelial, six of immune, and a small population of stromal cells in the rectal mucosa. There was an increase in colonocytes in the non-inflamed tissue compared to the inflamed tissue, and an increase of naïve b cells and plasma cells associated with inflamed tissue. The cell type proportions of immune cells, highlighted patient heterogeneity of cell type abundance and potential dysregulation of both the immune and epithelial compartment. We also note enrichment of IgG plasma cells in inflamed tissue of two donors and expansion of IgA plasma cells of non-inflamed tissue in two donors. Differential gene expression analysis of goblet cells revealed enrichment of inflammatory pathways, such as IL6 and interferon gamma signaling, in inflamed tissue. These inflammatory pathways might affect tight junctions between epithelial cells leading to increased permeability and potentially affect fistula formation. Our findings suggest dysregulation of crypt maturation during persistent inflammation and over-abundance of goblet cells and colonocyte precursors in inflamed tissue of perianal-CD.

overall_design: Single cell transcriptomic profiles of inflamed or non-inflamed rectal mucosal biopsies of individuals diagnosed with Perianal-Fistualizing Crohn's Disease. There is one non-IBD control.

first: Savannah

first: Sushma

last: Chowdary Maddipatla

first: Shanta

last: Murthy

first: Anne

last: Dodd

first: Ranjit

last: Singh Pelia

first: Vasantha

last: Kolachala

first: Duke

last: Geem

first: Jason

last: Matthews

first: Subra

last: Kugathasan


title: A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (ATAC-Seq)

city: OXFORD

first: Anil

last: Upreti

state: OH

address: 501 E High St, Oxford, OH 45056

department: Biology

institute: Miami University

summary: Lens epithelial explants consist of lens epithelial cells (P8 FVB/N mice) grown in vitro on their native basement membrane, the lens capsule. For decades, biologists have used lens epithelial explants to study lens fiber cell differentiation. However, the global change in the accessibility of the chromatin and transcriptome during the process of explanting and culture is unknown. Therefore, P8 FVB/N lens epithelial explants cultured in either unsupplemented media or media containing 50% bovine vitreous humor for one or five days were collected.  Chromatin and RNA was collected for ATAC-sequencing and RNA-sequencing respectively. Differentially accessible regions and differentially expressed genes were identified for each condition to provide a genome wide view of chromatin architecture and gene expression during fiber cell differentiation in vitro. Vitreous humor generally increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had relatively little effect on the accessibility of most of the genes highly expressed in the lens epithelium despite dramatic reductions in the transcript levels of these genes.

overall_design: Comparative genomic landscape analysis using ATAC-seq for lens epithelial explants with different treatments (Culture Media (CM) and Differentiation Media (DM)) and different time points (Immediately after the lens epithelium collection, 24 hrs in culture media (D0), after an additional day in CM (D1_CM) or DM (D1_DM),  after an additional (relative to Day 0) 5 days in CM (D5_CM) or DM (D5_ DM). Biological replicates were collected in duplicate.

first: Michael

last: Robinson

first: Jared

last: Tangeman

first: Stephanie

last: Padula


title: Transcriptome analysis of pre-implantation embryos

status: Public on Feb 24 2023

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: We produced transcriptome data from twenty two blastocysts

overall_design: All embryos were produced in vitro


title: A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants (RNA-Seq)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lens epithelial explants with different treatments (Culture Media (CM) and Differentiation Media (DM)) and different time points (Immediately after the lens epithelium collection, 24 hrs in culture media (D0), after an additional day in CM (D1_CM) or DM (D1_DM),  after an additional (relative to Day 0) 5 days in CM (D5_CM) or DM (D5_ DM). Biological replicates were collected in triplicate.


title: Targeting tumor cells toward the antigenic specificity of bystander T cells in tumor microenvironment potentiates cancer immunotherapy

status: Public on Feb 02 2023

city: Beijing

first: Ziyu

last: Li

address: 5 Summer Palace Road, Haidian District, Beijing, China

department: Biomedical Pioneering Innovation Center

country: China

institute: Peking University

summary: Tumor-specific T cells are crucial in anti-tumor immunity and act as targets for cancer immunotherapies. However, these cells are numerically scarce and functionally exhausted in tumor microenvironment (TME), leading to the inefficacious immunotherapies in most cancer patients. In contrast, emerging evidence suggested that tumor-irrelevant bystander T (TBYS) cells are abundant and preserve functional memory properties in TME. To leverage TBYS cells in TME to eradicate tumor cells, we developed an oncolytic virus-based immunotherapy that delivers TBYS cell epitopes (OV-BYTE) into tumor cells, which efficiently redirects the antigen specificity of tumor cells to preexisting TBYS cells and effectively retards tumor growth in multiple preclinical models. Remarkably, the OV-BYTE strategy curtailed tumor progression by targeting SARS-CoV-2-specific T cell memory induced by natural infection or vaccination, providing important insights into the improvement of cancer immunotherapies in a great population with a history of SARS-CoV-2 infection or COVID-19 vaccination.

overall_design: To explore the molecular features of TBYS cells and how these cells respond to OV-BYTE therapy, C57BL/6 mice receving the transfer of congenically marked P14 CD8+ and SM CD4+ T cells recognizing two distinct LCMV glycoprotein (GP) epitopes were infected with LCMV Armstrong and engrafted with MC38 cells on day 60-post infection when LCMV immune memory was established. After 5 injections of PBS or NDV-WT or NDV-GP, MC38 tumor-infiltrating bystander P14 CD8+ and SM CD4+ T cells were FACS-sorted and analyzed using scRNA-seq. As controls, conventional memory SM CD4+ T cells were harvested from the spleens of C57BL/6 mice at day 60-post infection of LCMV Armstrong. To explore the changes of TCR repertoire in tumor-reactive CD8+ T cells, LCMV Armstrong-infected mice were engrafted with MC38 tumors and then intratumorally administrated with PBS or NDV-WT or NDV-GP. Then, CD45+ immune cells and CD45- non-immune cells from PBS- or NDV-WT- or NDV-GP-treated MC38 tumors were isolated and performed with scRNA-seq/scTCR-seq library construction. Furthermore, MC38 tumor-specific p15E tetramer+ CD8+ T cells were also isolated from PBS- or NDV-WT- or NDV-GP-treated MC38 tumors and performed with TCR-seq libarary construction.

first: Xiangyu

last: Chen


title: Alternative mRNA splicing in human epidermal differentiation

status: Public on Jan 02 2023

city: Irvine

first: Bryan

last: Sun

state: California

address: 829 Medical Sciences Ct

institute: University of California Irvine

summary: To identify the changes in mRNA isoforms expressed in human epidermal differentiation, primary human keratinocytes were sequenced in progenitor and differentiation conditions.

overall_design: Comparative mRNA isoform analysis of RNA-seq data for primary human keratinocytes in progenitor and differentiated conditions.

first: Takashima

last: Shota

first: Otten

last: Auke

first: Sun

last: Wujianan

first: Cai

last: Pengfei

first: Cheng

last: Binbin

first: Bui

last: Jolina

first: Amarbayar

last: Oyumergen

first: Li

last: Zongkai

first: Qu

last: Kun

last: Bryan


title: RNAseq Profiling of Blood from Patients with Coronary Artery Disease: Signature of a T Cell Imbalance.

status: Public on Jan 03 2023

city: Washington

first: Timothy

last: McCaffrey

state: DC

address: 2300 I Street NW

department: Department of Biochemisty & Molecular Biology

institute: The George Washington University

summary: Background: Cardiovascular disease had a global prevalence of 523 million cases and 18.6 million deaths in 2019.  The current standard for diagnosing coronary artery disease (CAD) is coronary angiography either by invasive catheterization (ICA) or computed tomography (CTA).  Prior studies employed single-molecule, amplification-independent RNA sequencing of whole blood to identify an RNA signature in patients with angiographically confirmed CAD.  The present studies employed Illumina RNAseq and network co-expression analysis to identify systematic changes underlying CAD. Methods: Whole blood RNA was depleted of ribosomal RNA (rRNA) and analyzed by Illumina total RNA sequencing (RNAseq) to identify transcripts associated with CAD (iTRACs) in 177 patients presenting for elective invasive coronary catheterization.  The resulting transcript counts were compared between groups to identify differentially expressed genes (DEGs) and to identify patterns of changes through whole genome co-expression network analysis (WGCNA).  Results: The correlation between Illumina amplified RNAseq and the prior SeqLL unamplified RNAseq was quite strong (r=0.87), but there was only 9% overlap in the DEGs identified.  Consistent with the prior RNAseq, the majority (93%) of DEGs were down-regulated ~1.7-fold in patients with mild to severe CAD (>20% stenosis).  DEGs were predominantly related to T cells, consistent with known reductions in Tregs in CAD.  Network analysis did not identify pre-existing modules with a strong association with CAD, but patterns of T cell dysregulation were evident.  iTRACs were enriched for transcripts associated with ciliary and synaptic transcripts, consistent with changes in the immune synapse of developing T cells. Conclusions: These studies confirm and extend a novel mRNA signature of a Treg-like defect in CAD. The pattern of changes is consistent with stress-related changes in the maturation of T and Treg cells, possibly due to changes in the immune synapse.

overall_design:
RNAseq of whole blood from patient with or without angiographically confirmed coronary artery disease.
Raw data not provided for this submission. The raw data files contain identifiable sequence data that requires IRB and HIPPAA clearance before it can be shared.


title: A Transcription Factor Atlas of Directed Differentiation [SHAREseq_210322_TFAtlas]

status: Public on Jan 05 2023

city: Cambridge

first: Julia

last: Joung

state: MA

address: 75 Ames St

institute: Broad Institute

summary: SHARE-seq single-cell RNA-seq data profiling hESCs overexpressing transcription factors

overall_design: hESCs were transduced with a library of 3,550 transcription factor ORFs and cultured for 7 days before single-cell RNA-seq

first: Feng

last: Zhang


title: A transcriptome and chromatin landscape analysis of vitreous-induced lens fiber cell differentiation in mouse lens epithelial explants

first: Anil

last: Upreti


title: Limited cross-variant immune response from SARS-CoV-2 Omicron BA.2 in naïve but not previously infected outpatients

status: Public on Dec 20 2022

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Omicron is currently the dominant SARS-CoV-2 variant and several sublineages have emerged. Questions remain about the impact of previous SARS-CoV-2 exposure on cross-variant immune responses elicited by the SARS-CoV-2 Omicron sublineage BA.2 compared to BA.1. Here we show that without previous history of COVID-19, BA.2 infection induces a reduced immune response against all variants of concern (VOC) compared to BA.1 infection. The absence of ACE2 binding in sera of previously naïve BA.1 and BA.2 patients indicates a lack of meaningful neutralization. In contrast, anti-spike antibody levels and neutralizing activity greatly increased in the BA.1 and BA.2 patients with a previous history of COVID-19. Transcriptome analyses of peripheral immune cells showed significant differences in immune response and specific antibody generation between BA.1 and BA.2 patients as well as significant differences in the expression of specific immune genes. In summary, prior infection status significantly impacts the innate and adaptive immune response against VOC following BA.2 infection.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) of COVID-19 patients infected by SARS-CoV-2 Omicron subvarients (BA.1 and BA.2).

first: Ludwig

last: Knabl


title: High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq

status: Public on Jan 04 2023

city: New Haven

first: Yang

last: Liu

state: CT

address: 300 George St., Room 8300C 8th floor

department: Pathology

institute: Yale University

summary: We present spatial-CITE-seq for high-plex protein and whole transcriptome co-mapping, which was firstly demonstrated for profiling 189 proteins and transcriptome in multiple mouse tissue types. It was then applied to human tissues to measure 273 proteins and transcriptome that revealed spatially distinct germinal center reaction in tonsil and early immune activation in skin at the COVID-19 mRNA vaccine injection site. Spatial-CITE-seq may find a range of applications in biomedical research.

overall_design: Spatial profiling of RNA and protein using microfluidic based device.

first: Rong

last: Fan


title: POLK ChIP-seq data

status: Public on Dec 16 2022

city: Riverside

first: feng

last: tang

state: CA

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Pol κ in HEK293T cells.

overall_design: Genome editing-based integration of three tandem repeats of the FLAG epitope tag (3×FLAG tag) into endogenous Pol κ was conducted. Then we crosslinked DNA and proteins in chromatin, fragmented DNA, immunoprecipitated endogenous Pol  κ and its associated genomic DNA using anti-FLAG M2 beads, and subjected the resulting DNA fragments for next-generation sequencing analysis.

last: Tang

first: Yinsheng

last: Wang


title: Integrative Analysis of the Ovarian Metabolome and Transcriptome of the Yaoshan Chicken and its Hybrids

status: Public on Dec 10 2022

city: Nanning City

first: Tian

last: Wu

address: Xixiangtang District, Nanning City, Guangxi Zhuang Autonomous Region

institute: Guangxi University

summary: Laying performance is a key factor affecting production efficiency in poultry farming, but its molecular mechanism is still unclear. In this study, Yaoshan chickens, a local breed in Guizhou, China, and commercial chickens (GYR) with higher egg yield after the three-line cross improvement hybridization of Yaoshan chickens were used as animal samples. To explore the regulatory mechanism of the differences in laying performance, RNA-seq and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC‒MS/MS) were used to portray the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens. At the transcriptional level, 288 differentially expressed genes were upregulated in Yaoshan chickens and 353 differentially expressed genes were upregulated in GYR chickens. In addition, GSEA revealed that ECM-receptor interactions and the TGF-β signalling pathway were inhibited, resulting in increased egg production in GYR chickens. Furthermore, the upregulation of thiamine and carnitine was identified by metabolomic analysis to promote the laying performance of chickens. Finally, comprehensive analyses of the transcriptome and metabolome found that thiamine and carnitine were negatively correlated with ECM-receptor interactions and the TGF-β signalling pathway, which jointly regulate the laying performance of Yaoshan chickens and GYR chickens. In conclusion, our study delineates differences in the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens during the peak egg production period and provides new hypotheses and clues for further research on poultry egg production performance and the improvement of economic benefits.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of ovaries in Yaoshan and GYR

first: Xiaomeng

last: Miao


title: Single-cell profiling of alveolar rhabdomyosarcoma reveals RAS pathway inhibitors as cell-fate hijackers with therapeutic relevance

status: Public on Dec 02 2022

city: Zürich

first: Sara

middle: Giulia

last: Danielli

state: Zürich

address: Steinwiesstrasse 75

department: Department of Oncology

institute: University Children's Hospital

summary: Rhabdomyosarcoma (RMS) is an aggressive pediatric cancer. Despite robust expression of myogenic regulatory factors, RMS cells are blocked in a proliferative state and do not terminally differentiate. The extent to which the skeletal muscle lineage is represented in RMS tumors and the mechanisms leading to developmental arrest, remain elusive. Here, we used single-cell RNA sequencing (scRNAseq) to resolve RMS subpopulations under basal conditions as well as under genetic perturbation of the fusion protein PAX3:FOXO1 (P3F1).

overall_design: Primary RMS cells were cultured for low number of passages and multiplexed according to Totalseq protocol for single-cell RNA sequencing analysis.

first: Ermelinda

last: Porpiglia

first: Andrea

middle: J

last: De Micheli

first: Natalia

last: Navarro

first: Michael

last: Zellinger

first: Ingrid

last: Bechtold

first: Samanta

last: Kisele

first: Larissa

last: Volken

first: Stephanie

last: Kasper

first: Joana

last: Marques

first: Peter

last: Bode

first: Anton

last: Henssen

first: Dennis

last: Gürgen

first: Olivier

last: Delattre

first: Didier

last: Surdez

first: Josep

last: Roma

last: Bühlmann

first: Helen

last: Blau

first: Marco

last: Wachtel

first: Beat

middle: W

last: Schäfer


title: Tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis: a model for precision nephrology

status: Public on Nov 30 2022

city: Ann Arbor

first: Matthias

last: Kretzler

state: MI

address: 1150 W. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

summary: Reporter genes for TNF activation have not been studied in nephrotic syndrome cases at the single nuclear RNA-seq level. Use of archived kidney biopsy material that was fragmented into individual nuclei and assayed for presence of genes involved in TNF activation in patients predicted to have high or low expression of these genes.

overall_design:
RNAlater-preserved, archived kidney biopsies were subjected to single nuclear RNA-sequencing
Raw data not provided due to patient privacy concerns

first: Phillip

last: McCown

first: Sean

last: Eddy

first: Laura

last: Mariani

first: Edgar

last: Otto


title: Tubulointerstitium RNAseq Voom Transformed Transcriptome from the Neptune Cohort

status: Public on Dec 09 2022

address: 1150 West Medical Center Drive

overall_design:
Raw data (fastq) files are available upon approved ancillary study request from the NEPTUNE consortium (please see https://www.neptune-study.org/ancillary-studies, email contact: NEPTUNE-STUDY@umich.edu).

This dataset shares samples with other NEPTUNE transcriptomic datasets including those deposited into GEO (Accession IDs: GSE182380, GSE200818, GSE133288, GSE108112, GSE108113) and does not represent an independent set of samples from the NEPTUNE consortium.

first: Viji

last: Nair

first: Felix

last: Eichinger

first: Brad

last: Godfrey


title: The developmental transcriptome and epigenome of Owenia fusiformis reveal the development and evolution of mitraria larvae [dataset2]

status: Public on Nov 16 2022

city: London

first: Yan

last: Liang

state: London

address: mile end road

department: SBBS

country: United Kingdom

institute: Queen Mary Univerisity of London

summary: Owenia fusiformis has a unique mitraria larvae form which is different to other marine spiralians. we utilize RNA-seq and ATAC-seq to profile the gene expression and chromatin accessibility dynamics to understand their development and evolution.

overall_design:
We collected the fresh competent larvae and juvenile for RNA sequencing. We collected the fresh samples from gastrula, elongation, mitraria larvae to competent larvae to perform the ATAC expriments and profiling the chromatin accessibility.

Please note that the 'ofu_RNAseq_gene_expression.txt' contains the processed data for the RNA-seq samples in both GSE184126 and GSE202283.


title: YWHAB over-expression inhibits migration and invasion of breast cancer MDA-MB-231 cells

status: Public on Nov 26 2022

city: 淮北市

first: Zou

last: Deng

state: 安徽

address: 相山区

institute: Huaibei Normal University

summary: To investigate the function of YWHAB gene, we established MDA-MB-231 cell line overexpressing YWHAB gene.

overall_design:
Then, we performed gene expression profiling using RNA-seq data from two different cells of overexpression and control.
Comparative gene expression profiling of RNA-seq data from MDA-MB-231 cells overexpressing YWHAB.

first: Geng

last: Xuexia

first: Xu

last: Wenjie


title: Identifying candidate circulating RNA markers for coronary artery disease by deep RNA-Sequencing in human plasma

status: Public on Nov 02 2022

city: Christchurch

first: Anna

last: Pilbrow

address: 2 Riccarton Avenue

country: New Zealand

institute: University of Otago, Christchurch

summary: This study aimed to develop a short-read RNA-Seq protocol to detect mRNAs, lncRNAs and circRNAs (including putative novel lncRNAs) in human plasma. This protocol was applied to plasma from patients with established stable CAD (samples collected ~4 months after an acute coronary event) and healthy controls to screen for candidate mRNA, lncRNA and circRNA biomarkers associated with the presence of coronary artery disease and the progression from CAD to HF. We hypothesised that circulating levels of non-coding RNAs in patients with stable CAD may relect progression of atherosclerotic disease or adverse myocardial remodeling, and may help identify patients at risk of future cardiovascular events. Here we demonstrate that mRNAs, lncRNAs and circRNAs can be reliably detected in human plasma by deep RNA-Seq and report novel candidate biomarkers for the presence of CAD.

overall_design: Circulating cell-free RNA from 59 patients with stable CAD (half of whom developed HF within 3 years) and 30 controls was sequenced to a median depth of 108 paired reads per sample on an Illumina NovaSeq 6000 S1 flowcell.

first: Zoe

last: Ward

first: Aaron

last: Jeffs

first: Sebastian

last: Schmeier

first: John

last: Pearson

first: Vicky

last: Cameron

first: Chris

last: Frampton

first: Richard

last: Troughton

first: Rob

middle: N

last: Doughty

first: A

last: Richards


title: Bulk tissue RNA sequencing from human donors with and without lung fibrosis

city: Melbourne

first: Katherine

last: Monaghan

state: Victoria

address: 30 Flemington Rd, Parkville

department: Research and Development

country: Australia

institute: CSL Limited

summary: Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung condition with an unpredictable disease course. The pathology of IPF starts in the lung bases such that a patient’s lung apices are comparatively less fibrotic at the time of transplantation. We hypothesized that RNA sequencing of the lung apices and bases may identify differentially expressed genes that better reflect disease progression in IPF. Samples were derived from both right and left lungs when available and RNA Seq was performed on a total of 139 samples.

overall_design: High-quality mRNA was collected from resected lung tissue from 20 patients with IPF, 14 non-diseased control donors whose lungs were deemed unsuitable for transplantation, and 9 patients with end-stage interstitial lung disease other than IPF (non-IPF ILD).

first: Jade

last: Jaffar

first: Mae

last: Wong

first: Monther

last: Alhamdoosh

first: Milica

last: Ng

first: Nick

last: Wilson

first: Glen

last: Westall

first: Laura

last: McMillan

first: Cristina

last: Gamell-Fulla

first: Karen

last: Symons

first: Ian

last: Glaspole

first: Gregory

last: Fishbein


title: Targeted regulation of cytokines expression with a portable smart light-controllable device for tumor immunotherapy

status: Public on Oct 07 2022

city: shenzhen

first: chen

last: rui

address: 1088 Xueyuan Avenue, Shenzhen 518055, P.R. China

institute: sustech

summary: As the first type of tumor immunotherapy drugs, cytokines have attracted sustained attention due to their multi-functional cellular response in immunotherapy. However, the application of cytokines for tumor immunotherapy was still limited to their short half-time, narrow therapeutic window, and undesired side effects. Here, we constructed a portable smart light-controllable (PSLC) device to address this issue. By combining the PSLC device and light-switchable gene modules, it is theoretically possible to regulate the cytokines expressed within target tumors by optical remote control. Then, cytokine interferon-γ (IFN-γ) and chemokine CXCL10, two essential immune regulatory molecules that play crucial roles in immunotherapy, are selected to test this system.

overall_design: To investigate whether light-induced cytokines may affect the tumor microenvironment, we established three animal tumor models, including single-tumor bearing DBA/2 mice with engineered P815-IFNγ cells or P815-M cells (control), and double-tumor bearing DBA/2 mice with engineered P815-IFNγ cells and P815-M cells (control). Each animal model is divided into two groups (3 mice/group), the dark group (as control ) and the light group. After illumination, all the tumor samples were resected from animals and quickly frozen with liquid nitrogen for RNA-seq, to compare the gene expression profile between the cytokines release group and the normal group.

first: Huirong

last: Wang

first: Yi

last: Zhang

first: Yuejian

last: Mo

first: Zhan

first: Rui

last: Chen

first: Wei

last: Huang


title: Asymmetric Segregation of the Nucleosome Remodeling and Deacetylase Complex during Asymmetric Cell Divisions

status: Public on Dec 30 2022

first: Guangshuo

last: Ou

address: Tsinghua University Haidian District

department: School of Life Science

institute: Tsinghua university

summary: Asymmetric cell divisions (ACDs) generate two daughter cells with identical genetic information but distinct cell fates. Epigenetic mechanisms are crucial for cell fate specification, and it remains unclear how epigenetic information is inherited. Here, we report asymmetric segregation of the nucleosome remodeling and deacetylase complex (NuRD) during ACDs in Caenorhabditis elegans. NuRD is enriched to chromosomes of the future surviving but not apoptotic daughter cell, whereas NuRD evenly distributes to two viable siblings. Disruption of ACDs causes symmetric NuRD inheritance, and an ectopic gain of NuRD in apoptotic daughters allows cell survival and differentiation. Lack of NuRD upregulates the expression of the vital cell death-inducing gene egl-1 by increasing H3K27 acetylation on the egl-1 locus, which activates the EGL-1-CED-9-CED-4-CED-3 pathway to promote apoptosis. We propose that biased NuRD segregation during ACDs provides a previously unrecognized yet common mechanism for asymmetrically partitioning epigenetic information that contributes to binary cell fate decisions.

overall_design: 1.The embryonic SPLiT-seq of wild-type worms expressing Pegl-1::NLS::gfp;2.Embryonic mRNA profiles of  wild type and hda-1/lin-53 RNAi worms;3. Examination of H3K27ac modifications in wild type and hda-1/lin-53 RNAi worms.

first: Zhongyun

last: Xie

first: Yongping

last: Chai

first: Ming

last: Li


title: Single Cell Spatial Transcriptomics Redefines the Borderzone induced by Myocardial Infarction and Mechanical Injury

status: Public on Oct 03 2022

city: La Jolla

first: Kevin

last: King

address: 9500 Gilman Dr. MC 0412

department: Medicine and Bioengineering

institute: UC San Diego

summary: The ischemic borderzone (BZ) is a geographically complex and biologically enigmatic interface separating poorly perfused infarct zones (IZ) from comparatively healthy remote zones (RZ).  BZ cellular and molecular mechanisms are not well understood because efforts to dissect it inevitably include RZ and IZ in uncontrolled proportions. Here, we use single-cell/nuclei RNA-sequencing, spatial transcriptomics, and multiplexed RNA fluorescence in situ hybridization (mFISH) to identify BZ cardiomyocytes (CMs) subsets. BZ1 (Nppa+Xirp2-) forms a hundreds-of-microns-thick transitional layer adjacent to RZ, while BZ2 (Nppa+Xirp2+) forms a tens-of-microns-thick layer that the IZ edge. BZ2 CMs have reduced CM cell contact; colocalize with matricellular-protein-expressing myofibroblasts; and upregulate focal adhesion-, sarcomere-, and cytoskeletal-genes.  Surprisingly, the transcriptional BZ emerges within an hour of injury and is inducible by non-ischemic fine-needle-trauma. We suggest that mechanical instability and “loss of neighbor” at the BZ edge are the dominant inducers of the BZ transcriptional response.

overall_design:
Gene expression profiling of 10x Genomic Chromium single nuclei RNA-Seq or Visium spatial transcriptomics from the left ventricular myocardium or short axis sections of healthy and injured adult male C57BL6 mouse hearts (8-12 weeks). Injuries include MI (permanent ligation of the LAD coronary artery), I/R-30 (30 minutes of ischemia followed by reperfusion), transaortic constriction, isoproterenol injection, and traumatic needle injection.

Please note that the processed data files for GSM6613081, GSM6613087, GSM6613090 have been replaced on May 18, 2023 as the previous files were incomplete (missing spatial data folder and .h5 matrix file).

first: D

last: Calcagno

first: N

last: Taghdiri

first: V

last: Ninh

first: J

last: Mesfin

first: A

last: Toomu

first: R

last: Sehgal

last: Lee

first: Y

last: Liang

last: Duran

first: E

last: Adler

first: K

middle: L

last: Christman

first: F

last: Sheikh


title: Estrogen receptor alpha mutations regulate gene expression and cell growth in breast cancer through microRNAs (RNA-Seq)

status: Public on Oct 05 2022

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

summary: Estrogen receptor α (ER) mutations occur in up to 30% of metastatic ER-positive breast cancers. Recent data has shown that ER mutations impact the expression of thousands of genes not typically regulated by wildtype ER. While the majority of these altered genes can be explained by constant activity of mutant ER or genomic changes such as altered ER binding and chromatin accessibility, as much as 33% remain unexplained, indicating the potential for post-transcriptional effects. Here we explored the role of microRNAs in mutant ER-driven gene regulation and identified several microRNAs that are dysregulated in ER mutant cells. These differentially regulated microRNAs target a significant portion of mutant-specific genes involved in key cellular processes. When the activity of microRNAs is altered using mimics or inhibitors, significant changes are observed in gene expression and cellular proliferation related to mutant ER. An in-depth evaluation of miR-301b led us to discover an important role for PRKD3 in the proliferation of ER mutant cells. Our findings show that microRNAs contribute to mutant ER gene regulation and cellular effects in breast cancer cells.

overall_design: Comparitive gene expression analysis of RNA-seq data from T-47D Y537S or D538G mutant ER cell line models after treatment with a miRNA mimic/inhibitor for hsa-miR-301b-3p, hsa-miR-181c-5p, hsa-miR-331-3p, or hsa-let-7f-5p.

first: Spencer

last: Arnesen


title: Microarray analysis of naïve bone marrow derived mast cells (BMMCs) and BMMCs 4hr post ionomycin activation

status: Public on Sep 27 2022

city: Durham

first: Soman

last: Abraham

state: North Carolina

address: 207 Research Drive

institute: Duke University

summary: Gene expression profile of BMMCs four hours post activation with ionomycin compared to naive BMMCs.

overall_design: We sought to determine the gene expression changes that occur in BMMCs 4 hours post degranulation using ionomycin.  This time point was selected to identy genes that may get upregulated beyond the initial set of genes involved in degranulation which occurs within minutes of activation. To do this, BMMCs were washed into Tyrode's buffer and then activated using 1 μg/ml  ionomycin for 1 hour. Cells were then washed three times with Tyrode's buffer and resuspended in cell media for three hours. RNA was extracted from these cells and compared to RNA extracted from control BMMCs.

last: Iskarpatyoti

last: Shi

first: M

middle: P

last: Rathore

last: Miao

first: S


title: Effect of edeine B1 in gene expression of Fusarium graminearum

status: Public on Oct 02 2022

city: Daejeon

first: bomin

last: Kim

state: Yuseong

address: 141, Gajeong-ro

country: South Korea

institute: Korea reserch institute of chemical technology

summary: To investigate the inhibition metabolism of EB1 in Fusarium graminearum, F.graminearum wild type grown in YPD broth. Then harvested F.graminearum hyphae reacted with EB1 during 1, 2, 4h.

overall_design: Comparative gene expression profiling analysis of EB1 time-dependent treatment for F.graminearum.

first: Hun

first: Bomin


title: Mst1-mediated phosphorylation of FoxO1 and C/EBP-β Stimulates Cell-protective Mechanisms in Cardiomyocytes

status: Public on Sep 12 2022

city: Stanford

first: Siavash

last: Moghadami

address: 299 Campus Drive, Fairchild Science Building, Room D236

department: Neurobiology

institute: Stanford University

summary: The molecular mechanisms by which FoxO transcription factors mediate diametrically  opposite cellular responses, namely death and survival, remain unknown. Mst1  phosphorylates FoxO1 Ser209/Ser215/Ser218/Thr228/Ser232/Ser243, thereby inducing  nuclear translocation of FoxO1 in cardiomyocytes. Mst1 inhibits the FoxO1-mediated  transcription of proapoptotic genes but promotes that of prosurvival genes. Mst1 increases  FoxO1-C/EBP-β interaction and phosphorylates C/EBP-β at Thr299, thereby promoting transcription of prosurvival genes. Myocardial ischemia/reperfusion (I/R) injury was larger in cardiac-specific FoxO1 knockout (c-FoxO1–/–) mice than in control mice. However, the concurrent presence of C/EBP-β T299E phospho-mimetic mutation reduced infarct size in c-FoxO–/– mice. The C/EBP-β phospho-mimetic mutant exhibited a higher binding to the promoter of prosurvival genes compared to wild-type C/EBP-β. In conclusion,  phosphorylation of FoxO1 by Mst1 inhibits the binding of FoxO1 to pro-apoptotic gene promoters but enhances its binding to C/EBP-β, phosphorylation of C/EBP-β, and transcription of prosurvival genes, which stimulate protective mechanisms in the heart.

overall_design: ChIP-seq

first: Junichi

last: Sadoshima

first: Yasuhiro

last: Maejima

first: Jihoon

last: Nah

first: Zahra

last: Aryan

first: Peiyong

last: Zhai


title: RT2 Profiler PCR array of FoxO1 related genes in mice cardiomyocytes

summary: mRNA levels of the known 91 FoxO1 target genes were evaluated with RT2 Profiler PCR array in cardiomyocytes transduced with LacZ, Mst1, FoxO1, FoxO1+Mst1, or FoxO1+DN-Mst1 genes were evaluated with RT2 Profiler PCR arrays.

overall_design: Cardiomyocytes transduced with LacZ were considered control while, cardiomyocytes transduced with FoxO1, Mst1, FoxO1+Mst1, and FoxO1+DN-Mst1 were considered as experimental groups.


title: RNA-sequencing for the characterization of the transcriptome of SUM 159 parental and Paclitaxel (PTX) resistant breast cancer cells.

status: Public on Sep 20 2022

city: Ioannina

first: Angeliki

last: Magklara

address: Panepistimioupoli Ioanninon

department: Department of Medicine/Department of Biomedical Research (Ioannina) Foundation for Research & Technology-Hellas

country: Greece

institute: University of Ioannina/nstitute of Molecular Biology & Biotechnology

summary: RNA-sequencing was performed in SUM 159 parental and PTX resistant breast cancer cells in an effort to identify novel regulators of chemoresistance that could potentially be targeted in Triple Negative Breast Cancer (TNBC). The bioinformatic analysis identified numerous differentially expressed genes including several known chemoresistance markers, as well as novel genes that may play an important role in breast cancer chemoresistant cells.

overall_design: Examination of the transcriptome of SUM 159 parental and PTX resistant breast cancer cells and comparison of their gene expression profiles. The experiment was performed in biological duplicates.

first: Dimitris

last: Kordias

first: Styliani

last: Papadaki

first: John

last: Verigos


title: Plasma TNFSF10B levels associated with acamprosate treatment response in patients with alcohol use disorder

status: Public on Sep 21 2022

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

summary: Acamprosate is an anti-craving drug used in alcohol use disorder (AUD) pharmacotherapy. However, only a subset of patients achieves optimal treatment outcomes. The identification of predictive biomarkers of acamprosate treatment response in patients with AUD would be a substantial advance in addiction medicine. We designed this study to use proteomics data as a quantitative biological trait as a step toward identifying inflammatory modulators that might be associated with acamprosate treatment outcomes. The NIAAA-funded Mayo Clinic Center for the Individualized Treatment of Alcoholism study had previously recruited 442 AUD patients who received three months of acamprosate treatment. However, only 267 subjects returned for the 3-month follow-up visit and, as a result, had treatment outcome information available. Baseline alcohol craving intensity was the most significant predictor of acamprosate treatment outcomes. Baseline plasma TNFSF10 concentration was associated with alcohol craving intensity and variation in acamprosate treatment outcomes among AUD patients. We also performed RNA sequencing using baseline peripheral blood mononuclear cells from AUD patients with known acamprosate treatment outcomes which revealed that inflammation-related pathways were highly associated with relapse to alcohol use during the three months of acamprosate treatment. These observations represent an important step toward advancing our understanding of the pathophysiology of AUD and molecular mechanisms associated with acamprosate treatment response. In conclusion, applying omics-based approaches may be a practical approach for identifying biologic markers that could potentially predict alcohol craving intensity and acamprosate treatment response.

overall_design: Peripheral blood mononuclear cells (PBMCs) samples were isolated from 15 ml of whole blood before acamprosate treatment using Ficoll density gradient centrifugation. We lysed the cells in Trizol and extracted total RNA using the RNeasy mini kit (Qiagen, Valencia, CA, USA). The RNA integrity numbers (RIN) were between 8.5-9.2 for the PBMC samples (relapse: n=27, non-relapse: n=26). RNA-seq experiments were conducted by GENEWIZ using an Illumina HiSeq 4000 with eight samples in each lane using 100bp paired end index reads. Fastq files containing paired RNA-Seq reads were aligned with STAR (23) against the UCSC human reference genome (hg19). We performed RNA-seq differential expression analysis using the DESeq2 package with default parameters.

first: Ming-Fen

last: Ho

first: Richard

last: Weinshilboum


title: Self-Renewing Presomitic Mesoderm Progenitor Lines Reprogrammed from human urine cells [Reprogramming bulk RNA-seq]

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

summary: Vertebrate formation is the defining feature of all vertebrates1,2. Yet, each vertebrate species appears to have a unique timing mechanism for forming somites along the vertebral column3-5. Human vertebrate formation remains poorly studied due to technical and ethical limitations. Here we report the generation of self-renewing stem cells with characteristic presomitic mesoderm (PSM) features by reprogramming epithelial cells isolated from human urine. These induced expandable presomitic mesoderm progenitor cells (UiPSM) proliferated extensively for more than 30 passages in chemically defined conditions, robustly producing 1040 UiPSM cells. UiPSM established presomitic mesodermal transcription profile, not detected pluripotency, ectoderm and endoderm related genes. UiPSM developed into presomitic mesodermal lineage cells, such as skeletal muscle cells(skm), osteoblast and chrondroblast cells in vivo and vitro, when transplanted UiPSM derived human skm cells in muscle injury model, the skm cells can survive in vivo and contribute to muscle regeneration up to one month. Thus, UiPSM is a powerful system to study human somite development and provide strategies for regenerative medicine in musculoskeletal system.

overall_design: Building library and sequencing process of producing UiPSM


title: Sea anemone single cell tissue profiling [scRNA-seq]

status: Public on Sep 09 2022

city: Vienna

first: Alison

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

summary: Sub-adult tissue pieces were processed into single cell RNA sequencing libraries in order to catalog spatial information and cell type distribution

overall_design: Sub-adult Nematostella vectensis were dissected into four tissue pieces and dissociated into single cell suspensions that were loaded into a 10x Genomics Chromium Single Cell Controller

first: Ulrich

last: Technau

first: Julia

last: Steger


title: Transcriptomic profiling of sea anemone tissues

status: Public on Sep 14 2022

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

overall_design: Refer to individual Series


title: Clonal expansion and epigenetic inheritance shape long-lasting NK cell memory [scRNA ex vivo]

status: Public on Sep 05 2022

city: Berlin

first: Timo

last: Rückert

address: Charitéplatz 1

department: Innate Immunity

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: We report profiling of single cell chromatin accessbility and gene expression of human NK cells from CMV-seropositive and -negative healthy blood donors ex vivo, as well as chromatin remodeling after in vitro stimulation via NKG2C and/or IL-12+IL-18.

overall_design: scRNA-seq with detection of surface proteins (CITE-seq) of ex vivo isolated human Natural Killer cells

first: Chiara

last: Romagnani


title: Clonal expansion and epigenetic inheritance shape long-lasting NK cell memory [scATAC in vitro]

overall_design: scATACseq with detection of surface proteins (ASAP-seq) of in vitro stimulated (via NKG2C and/or IL-12+IL-18) human Natural Killer cells


title: Clonal expansion and epigenetic inheritance shape long-lasting NK cell memory


title: Monocyte/macrophage heterogeneity during skin wound healing in mice

status: Public on Sep 08 2022

city: Chicago

first: Timothy

middle: Jon

last: Koh

state: IL

address: 1919 W Taylor Room 650

institute: University of Illinois at Chicago

summary: Monocytes and macrophages isolated from skin wounds on male C57BL6/J mice on day 3, 6, and 10 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per time point. Fresh cells with viability over 70% processed using the 10x Chromium platform. Libraries sequenced on HiSeq with paired-end reads. Fastq files were generated and demultiplexed into single cells using Cell Ranger software

overall_design: Single cell RNA-seq data from 10X Chromium. Three samples: WT_D3, WT_D6, and WT_D10

first: Jingbo

last: Pang

first: Mark

last: Maienschein-Cline


title: Clonal expansion and epigenetic inheritance shape long-lasting NK cell memory [scATAC ex vivo]

overall_design: scATACseq with detection of surface proteins and mitochondrial DNA (ASAP-seq/mtscATAC-seq) of ex vivo isolated human Natural Killer cells


title: Self-Renewing Presomitic Mesoderm Progenitor Lines Reprogrammed from human urine cells [Reprogramming scRNA-seq]

status: Public on Sep 01 2022

summary: Vertebrae formation is the defining feature of all vertebrates1,2. Yet, each vertebrate species appears to have a unique timing mechanism for forming somites along the vertebral column3-5. Human vertebrate formation remains poorly studied due to technical and ethical limitations. Here we report the generation of self-renewing stem cells with characteristic presomitic mesoderm (PSM) features by reprogramming epithelial cells isolated from human urine. These induced expandable presomitic mesoderm progenitor cells (UiPSM) proliferated extensively for more than 30 passages in chemically defined conditions, robustly producing 1040 UiPSM cells. UiPSM established presomitic mesodermal transcription profile, not detected pluripotency, ectoderm and endoderm related genes. UiPSM developed into presomitic mesodermal lineage cells, such as skeletal muscle cells(skm), osteoblast and chrondroblast cells in vivo and vitro, when transplanted UiPSM derived human skm cells in muscle injury model, the skm cells can survive in vivo and contribute to muscle regeneration up to one month. Thus, UiPSM is a powerful system to study human somite development and provide strategies for regenerative medicine in musculoskeletal system

overall_design: Sequencing the collected the cell samples in the reprogramming proocess including Day0,Day3,Day6


title: Tension sensing by FAK governs nuclear mechanotransduction, trancriptome and fate  endothelial transcriptome and fate

status: Public on Aug 28 2022

first: Md Zahid

last: Akhter

address: 835 S Wolcott Ave

department: Pharmacology & Regenerative Medicine

summary: Endothelial cell (EC) attachment to the matrix and adjacent cells generates a mechanical environment that maintains a restrictive barrier against the uncontrolled influx of circulating protein and immune cells. Mechanisms that mediate the transition from restrictive to leaky endothelium, a hallmark of tissue injury exemplified by acute lung injury (ALI), remain elusive. Here, we show that FAK sensing and transmission of mechanical tension to the EC nucleus governs cell fate. In FAK-deleted EC, increased EC tension activated DNMT3a, which induced methylation of the KLF2 promoter leading to impaired synthesis of KLF2 and restrictive EC transcriptome, including S1PR1. FAK suppressed DNMT3a activity by restricting the tyrosine phosphorylation of nuclear envelope protein, emerin at Y74/Y95, and its localization in a nuclear cap. Inhibiting emerin phosphorylation or DNMT3a activity in damaged lungs enabled KLF2 transcription of S1PR1, rescuing the restrictive EC phenotype. Our works reveal a paradigm whereby FAK sensing of tension transmission to the nucleus maintains restrictive EC transcriptome and lung homeostasis.

overall_design: 6 samples (RNA-seq)

first: Md

middle: Z

first: Pascal

last: Yazbeck

first: Mohammad

last: Tauseef

first: Mumtaz

last: Anwar

first: Sayanti

last: Datta

first: Vigneshwaran

last: Vellingiri

first: Jagdish

last: Joshi

first: Nityanand

last: Srivastava

first: Stephen

last: Lenzini

first: Guangjin

last: Zhou

first: James

last: Lee

first: Mukesh

last: Jain

first: Jae-Won

last: Shin

first: Dolly

last: Mehta


title: A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma

status: Public on Aug 18 2022

city: Boston

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

summary: Novel single cell technologies have paved the way for the characterization and improved biological understanding of clear cell renal cell carcinoma (ccRCC) where the focus has been mostly on the immunological compartments of the tumor microenvironment (TME). However, the identification of metastatic tumor cell clones, and the stromal compartments of TME of untreated ccRCC patients still remains to be elucidated. Here we perform single-cell RNA-sequencing on treatment naive ccRCC and adjacent normal kidney tissue.

overall_design: Human kideny tissue were disaggregated and profiled using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) .


title: Self-Renewing Presomitic Mesoderm Progenitor Lines Reprogrammed from human urine cells [UiPSC and UiPSM scRNA-seq]

first: Xingnan

last: Huang

overall_design: Building library and sequencing process of producing teratoma cells of UiPSC and UiPSM


title: Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling

city: New York

first: Dana

last: Pe'er

state: NY

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: In many cancers, treatment failure is linked to changes in tumor cell state or lineage, and often involves the reactivation of stem-like or developmental transcriptional programs. How this plasticity unfolds at a molecular level and whether it plays a causal role in drug resistance remains unclear. Here, we model the origin and dynamics of lineage plasticity in prostate cancer and its relationship to antiandrogen-based therapeutic resistance. In time course experiments utilizing genetically engineered mouse models and murine organoid cultures of prostate cancer, we find that plasticity initiates in an epithelial population defined by mixed luminal and basal lineage gene expression, and that it depends on elevated JAK and FGFR kinase activity. Organoid cultures from patients with late-stage castration-resistant disease harboring mixed-lineage cells reproduce the dependency we observe in mice, by upregulating luminal gene expression upon JAK and FGFR kinase inhibitor treatment. Single-cell analysis of human tumor samples confirms the presence of mixed lineage cells with elevated JAK/STAT and FGFR signaling in a subset of patients with metastatic disease, with implications for stratifying patients for clinical trials.

overall_design: Here, we model the origin and dynamics of lineage plasticity in prostate cancer and its relationship to antiandrogen-based therapeutic resistance. In time course experiments utilizing genetically engineered mouse models and murine organoid cultures of prostate cancer.

first: Joseph

middle: M

last: Chan

first: Samir

last: Zaidi

first: Wouter

last: Karthaus

first: Charles

last: Sawyers


title: Self-Renewing Presomitic Mesoderm Progenitor Lines Reprogrammed from human urine cells [Passage bulk RNA-seq]

summary: Vertebrate formation is the defining feature of all vertebrates1,2. Yet, each vertebrate species appears to have a unique timing mechanism for forming somites along the vertebral column3-5. Human vertebrate formation remains poorly studied due to technical and ethical limitations. Here we report the generation of self-renewing stem cells with characteristic presomitic mesoderm (PSM) features by reprogramming epithelial cells isolated from human urine. These induced expandable presomitic mesoderm progenitor cells (UiPSM) proliferated extensively for more than 30 passages in chemically defined conditions, robustly producing 1040 UiPSM cells. UiPSM established presomitic mesodermal transcription profile, not detected pluripotency, ectoderm and endoderm related genes. UiPSM developed into presomitic mesodermal lineage cells, such as skeletal muscle cells(skm), osteoblast and chrondroblast cells in vivo and vitro, when transplanted UiPSM derived human skm cells in muscle injury model, the skm cells can survive in vivo and contribute to muscle regeneration up to one month. Thus, UiPSM is a powerful system to study human somite development and provide strategies for regenerative medicine in musculoskeletal system

overall_design: Building library and sequencing different passages of UiPSM


title: Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys [sc3seq_mouse]

status: Public on Aug 01 2022

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: In vitro oogenesis is key to elucidating the mechanism of human female germ-cell development and its anomalies. Accordingly, pluripotent stem cells have been induced into primordial germ cell-like cells and into oogonia with epigenetic reprogramming, yet further reconstitutions remain a challenge. Here, we demonstrate ex vivo reconstitution of fetal oocyte development in both humans and cynomolgus monkeys (Macaca fascicularis). With an optimized culture of fetal ovary reaggregates over three months, human and monkey oogonia enter and complete the first meiotic prophase to differentiate into diplotene oocytes that form primordial follicles, the source for oogenesis in adults. The cytological and transcriptomic progressions of fetal oocyte development in vitro closely recapitulate those in vivo. A comparison of single-cell transcriptomes among humans, monkeys, and mice unravels primate-specific and conserved programs driving fetal oocyte development, the former including a distinct transcriptomic transformation upon oogonia-to-oocyte transition and the latter including two active X chromosomes with little X-chromosome upregulation. Our study provides a critical step forward for realizing human in vitro oogenesis and uncovers salient characteristics of fetal oocyte development in primates.

overall_design: Transcriptome analysis of mouse fetal gonadal cells using bulk 3' RNA-seq.

first: Ken

last: Mizuta

first: Yoshitaka

last: Katou

first: Baku

last: Nakakita

first: Aoi

last: Kishine

first: Yoshiaki

last: Nosaka

first: Saki

last: Saito

first: Chizuru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Ikuo

last: Kawamoto

first: Masataka

last: Nakaya

first: Tomoyuki

last: Tsukiyama

first: Masahiro

last: Nagano

first: Yoji

last: Kojima

first: Tomonori

last: Nakamura

first: Akihito

last: Horie

first: Masaki

last: Mandai

first: Hiroshi

last: Ohta

first: Mitinori

last: Saitou


title: Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys [sc3seq_macfas]

first: Yukihiro

last: Yabuta

overall_design: Single cell transcriptome analysis of cynomolgus monkey germ cells using SC3-seq technology.

first: Ken

last: Mizuta

first: Yoshitaka

last: Katou


title: Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys [sc3seq_human]

overall_design: Single cell transcriptome analysis of human germ cells using SC3-seq technology.

first: Baku

last: Nakakita

first: Aoi

last: Kishine

first: Yoshiaki

last: Nosaka


title: Gene count level transcriptomic data of high grade serous ovarian cancer

status: Public on Aug 02 2022

first: Dale

last: Garsed

state: VIC

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

summary: Transcriptomic profiling was done on 81 primary tumours, 1 relapse tumour, 5 autopsy tumours (whole tissue sections or macrodissected to enrich for tumour), 29 ascites and 7 normal fallopian tube samples. 1 of the primary tumours is a low grade serous ovarian cancer sample.

overall_design:
Between 500 ng and 2 μg of total RNA (RNA integrity number >7, except for autopsy samples) was used for library preparation using the TruSeq RNA Sample Preparation v2 kit (Illumina) as per the manufacturer’s instructions using the Low-Throughput protocol. All libraries were sequenced as paired-end 100-bp on a HiSeq2000 instrument (Illumina).
**Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession code EGAD00001000877**

first: Liz

last: Christie

first: Ahwan

last: Pandey

first: David

last: Bowtell


title: Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys [10x_macfas]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Single cell transcriptome analysis for monkey female  germ cell development using 10X genetics scRNA-seq.

last: Kato

first: Saki

last: Saito

first: Chizuru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Masataka

last: Nakaya

first: Tomoyuki

last: Tsukiyama

first: Takuya

last: Yamamoto


title: Self-Renewing Presomitic Mesoderm Progenitor Lines Reprogrammed from human urine cells

first: Xingnan

last: Huang


title: Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys [10x_human]

first: Yukihiro

last: Yabuta

overall_design: Single cell transcriptome analysis for human female  germ cell development using 10X genetics scRNA-seq.

last: Mizuta

first: Tomonori

last: Nakamura

first: Akihito

last: Horie

first: Masaki

last: Mandai

first: Hiroshi

last: Ohta

first: Mitinori

last: Saitou


title: Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: PRMT6-CDC20 facilitates glioblastoma progression via the degradation of CDKN1B

status: Public on Mar 31 2023

city: suzhou

first: Ji

last: Wang

address: 1055 Sanxiang Road, Gusu District

institute: Soochow University

summary: PRMT6, a type I arginine methyltransferase, di-methylates the arginine residues of both histones and non-histones asymmetrically. Increasing evidence indicates that PRMT6 plays a tumor mediator involved in human malignancies. Here, we aim to uncover the essential role and underlying mechanisms of PRMT6 in promoting glioblastoma (GBM) proliferation. Investigation of PRMT6 expression in glioma tissues demonstrated that PRMT6 is overexpressed, and elevated expression of PRMT6 is negatively correlated with poor prognosis in glioma/GBM patients. Silencing PRMT6 inhibited GBM cell proliferation and induced cell cycle arrest at the G0/G1 phase, while overexpressing PRMT6 had opposite results. Further, we found that PRMT6 attenuates the protein stability of CDKN1B by promoting its degradation. Subsequent mechanistic investigations showed that PRMT6 maintains the transcription of CDC20 by activating histone methylation mark (H3R2me2a), and CDC20 interacts with and destabilizes CDKN1B. Rescue experimental results confirmed that PRMT6 promotes the ubiquitinated degradation of CDKN1B and cell proliferation via CDC20. We also verified that the PRMT6 inhibitor (EPZ020411) could attenuate the proliferative effect of GBM cells. Our findings illustrate that PRMT6, an epigenetic mediator, promotes CDC20 transcription via H3R2me2a to mediate the degradation of CDKN1B to facilitate GBM progression. Targeting PRMT6-CDC20-CDKN1B axis might be a promising therapeutic strategy for GBM.

overall_design: To test the effect of suppression of PRMT6 on the gene expression, U87 cells were transfected with PRMT6 Scramble shRNA (NC) or PRMT6 shRNA. PRMT6-knockdown U87 cells were compared to control cells.

first: Zongyu

last: Xiao

first: Qing

last: Lan

first: Yezhong


title: Transcriptomic  analysis of HCC1954 Parental(Pa),  synchronous (S-BM), latent residual (Lat) or metachronous (M-BM) brain metastases cells

status: Public on Jul 27 2022

city: DALLAS

first: Srinivas

last: Malladi

state: Texas

address: NB7218, DEPARTMENT OF PATHOLOGY, UT SOUTHWESTERN MEDICAL CENTER

department: PATHOLOGY

institute: UT Southwestern Medical Center

summary: We did the transcriptomic profiling of HCC1954 Parental(Pa),  synchronous (S-BM), latent residual (Lat) or metachronous (M-BM) brain metastases cells

overall_design: Examination of gene expression in HCC1954 Parental(Pa),  synchronous (S-BM), latent residual (Lat) or metachronous (M-BM) brain metastases cells

first: Parida

last: Pravat Kumar

first: Malladi

last: Srinivas


title: Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells

status: Public on Jul 20 2022

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: "Sapienza" University of Rome

summary:
We have developed a novel in vitro protocol for the derivation of bona fide Pharyngeal Endoderm (PE) cells from hESCs. We demonstrated that our PE cells robustly express Pharyngeal Endoderm markers, they are transcriptionally similar to PE cells isolated from in vivo mouse development and represent a transcriptionally homogeneous population. Importantly, we elucidated the contribution of Retinoic Acid in promoting a transcriptional and epigenetic rewiring of PE cells. In addition, we defined the epigenetic landscape of PE cells by combining ATAC-Seq and ChIP-Seq of histone marks.

This SuperSeries is composed of the SubSeries listed below.

first: Andrea

last: Cipriano

first: Alessandro

last: Calicchio

first: Jonathan

last: Fiorentino

first: Danielle

last: Gomes

first: Mahdi

last: Moqri

first: Alexander

last: Parker

first: Sajede

last: Rasouli

first: Matthew

last: Caldwell

first: Francesca

last: Briganti

first: Maria

last: Roncarolo

first: Antonio

last: Baldini

first: Katja

last: Weinacht

first: Gian

last: Tartaglia

first: Vittorio

last: Sebastiano


title: Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (Single-cell RNA-Seq)

summary: We have developed a novel in vitro protocol for the derivation of bona fide Pharyngeal Endoderm (PE) cells from hESCs. We demonstrated that our PE cells robustly express Pharyngeal Endoderm markers, they are transcriptionally similar to PE cells isolated from in vivo mouse development and represent a transcriptionally homogeneous population. Importantly, we elucidated the contribution of Retinoic Acid in promoting a transcriptional and epigenetic rewiring of PE cells. In addition, we defined the epigenetic landscape of PE cells by combining ATAC-Seq and ChIP-Seq of histone marks.

overall_design: We performed a scRNA-Seq analysis of Definitive Endoderm and Pharyngeal Endoderm cells.


title: Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (Histone Modification ChIP-Seq)

overall_design: We performed ChIP-seq experiments for the histone modifications H4K4me3, H3K4me1, H3K27me3, and H3K27ac on Definitive Endoderm and Pharyngeal endoderm cells (two independent replicates per ChIP experiment) and identified the chromatin states produced by these marks in the two cell types.


title: Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (Bulk RNA-Seq)

overall_design: We performed a comparative gene expression profiling analysis of bulk RNA-seq data from human Embryonic Stem Cells, Definitive Endoderm, Anterior Foregut Endoderm, and Pharyngeal Endoderm cells (three biological replicates for each condition)


title: Molecular and Anatomical Characterization of Parabrachial Neurons and Their Axonal Projections

status: Public on Jul 15 2022

city: Seattle

first: Richard

last: Palmiter

state: WA

address: 1959 NE Pacific St

institute: UW/HHMI

summary: We characterize the transcriptional profiles of neuronal subpopulations in the mouse parabrachial nucleus.

overall_design: High-throughput single-cell RNA sequencing of the mouse parabrachial nucleus using 10X Genomics 3' v2 chemistry.

first: Jane

middle: Y

last: Chen

first: Marcus

last: Basiri

first: Garret

last: Stuber


title: Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (ATAC-Seq)

first: Alessio

last: Colantoni

overall_design: We performed ATAC-seq experiments on Definitive Endoderm, Anterior Foregut Endoderm and Pharyngeal Endoderm cells (two independent replicates for each condition) and identified the open chromatin regions in the three conditions.

first: Andrea

last: Cipriano


title: Single-Cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in a Mouse Cerebral Aneurysm Model

status: Public on Jul 12 2022

city: New Orleans

first: Alejandra

last: Martinez Lege

state: United States

address: 1430 Tulane Ave

department: Neurosurgery

institute: Tulane University

summary: Cerebral aneurysms were induced in adult male mice using an elastase model. Single-cell RNA sequencing was then performed on circle of Willis samples obtained at 14 days post-aneurysm induction.

overall_design: Single-cell suspension from surgically isolated circle of Willis arteries from sham, animals that formed cerebral aneurysms and animals that had ruptured aneurysms were subjected to scRNA-seq.

first: A

last: Martinez

first: G

last: Tortelote

last: Dumont


title: TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner.

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute


title: TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner [RNA-Seq]

summary: TET proteins mediate DNA demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and other oxidative derivatives. We have previously demonstrated a dynamic enrichment of 5hmC during T and invariant natural killer T cell lineage specification. Here, we investigate shared signatures in gene expression of Tet2/3 DKO CD4 single positive (SP) and iNKT cells in the thymus. We discover that TET proteins exert a fundamental role in regulating the expression of the lineage specifying factor Th-POK, which is encoded by Zbtb7b. We demonstrate that TET proteins mediate DNA demethylation - surrounding a proximal enhancer, critical for the intensity of Th-POK expression. In addition, TET proteins drive the DNA demethylation of site A at the Zbtb7b locus to facilitate GATA3 binding. GATA3 induces Th-POK expression in CD4 SP cells. Finally, by introducing a novel mouse model that lacks TET3 and expresses full length, catalytically inactive TET2, we establish a causal link between TET2 catalytic activity and lineage specification of both conventional and unconventional T cells.

overall_design: We compared gene expression (by bulk RNA-seq) in thymic CD4 SP cells isolated from control (wild type, WT) and Tet2/3 DKO mice

first: Ageliki

last: Tsagaratou


title: TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner [CUT&RUN]

overall_design: We compared the binding of the transcription factor GATA-3 across CD4 SP cells isolated from 3 control (wild type) and 2 Tet2-/-Tet3flx/flxCD4cre (DKO) mice by using CUT&RUN assay.


title: FAK is required for suppressing aberrant nuclear mechanotransduction and DNA methylation to prevent vascular injury

status: Public on Jul 11 2022

first: Md Zahid

last: Akhter

summary: Mechanical forces generated through adhesive interaction of endothelial cells (EC) influence nuclear envelope and thereby gene transcription. Alteration in EC mechanical forces may trigger aberrant gene transcription leading to lethal vascular diseases including acute lung injury (ALI). The intrinsic pathways that instruct EC nuclear-mechanotransduction and thereby maintains vascular homeostasis remain elusive. We have identified focal adhesion kinase (FAK)-mediated mechanotransduction at the nuclear envelope in instructing transcription of EC-barrier protective genes. We show that loss of EC-FAK increases intracellular tension, which in turn activates nuclear envelop protein emerin, and DNA methyltransferase 3a (DNMT3a). Methylation of transcription factor KLF2 promoter by DNMT3a impaired KLF2 synthesis and transcription of the crucial barrier-maintaining gene, S1PR1. Restoring KLF2 or S1PR1 expression or impairing emerin or DNMT3a activity rescued vascular homeostasis in lungs with FAK-deficient or           WT-damaged endothelium. Thus, FAK protects against tension-induced aberrant DNA methylation in EC and is a promising target to prevent ALI.

overall_design: 2 samples (ATAC-seq)

first: Md

first: Pascal

last: Yazbeck

first: Mohammad

last: Tauseef

first: Mumtaz

last: Anwar

first: Sayanti

last: Datta

first: Vigneshwaran

last: Vellingiri

first: Jagdish

last: Joshi

first: Nityanand

last: Srivastava

first: Stephen

last: Lenzini

first: Guangjin

last: Zhou

first: James

last: Lee

first: Mukesh

middle: K

last: Jain

first: Jae-Won

last: Shin

first: Dolly

last: Mehta


title: Gut bacterial-derived 12,13-diHOME promotes M1-like inflammatory macrophage polarization and trained immunity targeting interferon responses [h-Mf-RNA-seq]

status: Public on Jul 08 2022

city: San Francisco

first: Din

last: Lin

state: California

address: 513 Parnassus Ave.

institute: University of California, San Francisco

summary: Elevated infant fecal concentrations of bacterial-derived lipid 12,13-diHOME increases risk for atopy and asthma development in childhood, mechanistically how this lipid may contribute to disease susceptibility is unknown. Here we demonstrate macrophages exposed to 12,13-diHOME exhibit inflammatory IL-1highCD206low M1-like polarization, reduce bacterial phagocytic capacity. In co-culture assays, antigens in the presence of 12,13-diHOME further amplifies M1-like frequency, promotes CD20+CD38-IgD-CD27+ memory B cells expansion and IgE production. Epigenetic analyses indicates 12,13-diHOME exposure promotes DNA methylation, chromatin compaction, specifically diminishing access to interferon-stimulated response elements and transcription factor binding sites. In vivo, in murine airway allergic sensitization model, gut bacterial-derived 12,13-diHOME exacerbated both airway allergic inflammation and IL-1, IL-7, one-carbon metabolism and Toll-like receptor signaling. Our data suggests that 12,13-diHOME reprograms macrophage effector function, B-cell interactions and epigenetic modifications promoting phenotypes plausibly play a role in shaping early life microbiome development and innate immune dysfunction related to allergic sensitization in childhood.

overall_design: To understand how 12,13-diHOME promoted M1-like macrophage polarization, we performed bulk RNA-sequencing (RNA-seq) on monocyte-derived human macrophages from two donors exposed to either vehicle (DMSO), 12,13-diHOME or a combination of 12,13-diHOME and peanut flour (Pnut). We focused our RNA-Seq analyses on 4, 8, and 24 hours post exposure.

first: Kevin

last: Magnaye

first: Cara

middle: E

last: Porsche

first: Elze

last: Rackaityte

first: Susan

middle: V

last: Lynch


title: Gut bacterial-derived 12,13-diHOME promotes M1-like inflammatory macrophage polarization and trained immunity targeting interferon

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


title: Hippocampal cells multiplex positive and negative engrams

status: Public on Jul 13 2022

city: CAMBRIDGE

first: Shawn

last: Liu

state: MA

address: 455 MAIN STREET

institute: Whitehead Institute for Biomedical Research

summary: The hippocampus is involved in processing a variety of mnemonic computations including the spatiotemporal components, as well as the corresponding emotional dimensions, of contextual memory.1-3 Recent studies have demonstrated vast structural and functional heterogeneity along the dorsal-ventral axis1,5 of the hippocampus, and while much is known about how the dorsal hippocampus processes spatial-temporal content, much less is known about whether or not the ventral hippocampus (vHPC) partitions positive and negative experiences into distinct sets of cells.4-9  Here, we combine transgenic and all-virus based activity-dependent tagging strategies to visualize multiple valence-specific engrams in the vHPC and demonstrate two partially segregated cell populations and projections that respond to positive and negative experiences. Next, using an RNA sequencing approach, we find that vHPC positive and negative engram cells display distinct transcriptional programs compared to a neutral engram population. Additionally, while optogenetic manipulation of tagged cell bodies in vHPC is not sufficient to drive preference or avoidance, stimulation of tagged vHPC terminals projecting to the amygdala and nucleus accumbens (NAc), but not the prefrontal cortex (PFC), drives preference and avoidance. These terminals also can undergo a “switch” or “reset” in their capacity to drive either, thereby demonstrating their flexible contributions to behavior. We conclude that the vHPC contains genetically, cellularly, and behaviorally distinct populations of cells processing positive and negative memory engrams. Together, our findings provide a novel means by which to visualize multiple engrams within the same brain and point to their unique genetic signatures as reference maps for the future development of new therapeutic strategies.

overall_design: The hippocampus contains neurons that correspond to positive and negative engrams, which are segregated by their molecular, cellular, and projection-specific features

first: Bingbing

last: Yuan


title: Gut bacterial-derived 12,13-diHOME promotes M1-like inflammatory macrophage polarization and trained immunity targeting interferon responses [m-lung-RNA-seq]

summary: Elevated infant fecal concentrations of bacterial-derived lipid 12,13-diHOME increases risk for atopy and asthma development in childhood, mechanistically how this lipid may contribute to disease susceptibility is unknown. Here we demonstrate macrophages exposed to 12,13-diHOME exhibit inflammatory IL-1bhighCD206low M1-like polarization, reduce bacterial phagocytic capacity. In co-culture assays, antigens in the presence of 12,13-diHOME further amplifies M1-like frequency, promotes CD20+CD38-IgD-CD27+ memory B cells expansion and IgE production. Epigenetic analyses indicates 12,13-diHOME exposure promotes DNA methylation, chromatin compaction, specifically diminishing access to interferon-stimulated response elements and transcription factor binding sites. In vivo, in murine airway allergic sensitization model, gut bacterial-derived 12,13-diHOME exacerbated both airway allergic inflammation and IL-1, IL-7, one-carbon metabolism and Toll-like receptor signaling. Our data suggests that 12,13-diHOME reprograms macrophage effector function, B-cell interactions and epigenetic modifications promoting phenotypes plausibly play a role in shaping early life microbiome development and innate immune dysfunction related to allergic sensitization in childhood.

overall_design: To understand the effect of 12,13-diHOME to lung tisse in vivo in an airway allergen challenged model, we performed bulk RNA-sequencing (RNA-seq) on lung of mice exposed to either a combination of 12,13-diHOME and CRA (cockroach alleregen), CRA alone, 12,13-diHOME alone, or vehicle.


title: Gut bacterial-derived 12,13-diHOME promotes M1-like inflammatory macrophage polarization and trained immunity targeting interferon responses [h-Mf-ATAC-seq]

overall_design: To understand how 12,13-diHOME promoted M1-like macrophage polarization, we performed ATAC-seq human macrophages from four donors exposed to either vehicle (DMSO) or 12,13-diHOME or LPS.


title: The STING pathway does not contribute to the onset of cell senescence and SASP induction in the intervertebral disc

status: Public on Jul 06 2022

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1025 Walnut Street

department: Orthopaedic Surgery

institute: Thomas Jefferson University

summary:
Transcriptional analysis of 6-month-old primary nucleus pulposus (NP) and annulus fibrosus (AF) mouse disc tissues from wild-type (WT) and N153S mice, which harbor a mutation wich constiuitively activates Sting. Mouse details available here: https://www.jax.org/strain/033543
The cGAS-STING pathway promotes the senescence-associated secretory phenotype (SASP), which is associated with intervertebral disc degeneration, and has had implications in inflammatory musculoskeletal disorders. We examined the role of STING in the disc by examining the transcriptomic profiles of nucleus pulposus and annulus fibrosus cells in WT and N153S mice using microarray.

overall_design: Tissues from the nucleus pulposus (NP) and annulus fibrosus (AF) were harvested from the intervertebral discs of four WT and four N153S mice at 6 months of age. NP and AF tissues were collected from lumbar and caudal discs in each animal for RNA extraction and hybridization using Affymetrix microarray.

first: Olivia

last: Ottone


title: Epidermal basal domains organization highlights skin robustness to environmental exposure [scRNA-seq]

status: Public on Jul 05 2022

city: ITHACA

first: Sangeeta

last: Ghuwalewala

state: New York

address: 107 Biotechology Building 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

summary:
Purpose: To  unravel the molecular heterogeneity and characterise cell states of LRC/Non-LRC domains in interfollicular epidermis in vivo
Methods: We performed 10x genomics single-cell RNA sequencing (scRNA-seq) of FACS purified basal (Sca1+/alpha6-integrin+) IFE cells as H2BGFP LRCs, mid-LRCs, and non-LRCs from K5-tTA x pTRE-H2BGFP mice. Single-cell suspension from back (2-week chase) and tail skin (3-week chase) was processed for the barcoded single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3. The final libraries were quantified using Agilent Bioanalyzer high sensitivity DNA chip and sequenced using an Illumina NextSeq-500. The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-3.0.0) using the 10x Genomics Cell Ranger pipeline (v3.1.0).  The raw scRNA-seq data was processed using Cell Ranger from the 10x platform to generate an expression matrix that was further analyzed in R using the Seurat package version 3.1. Only high-quality cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained.
Results: We obtained a total of 13484 and 14884 high quality cells from two different skin types after combining two datasets each from LRCs/mid-LRCs/Non-LRCs for further analysis by Seurat workflow
Conclusions: Obtained high quality single cell transcriptomic data to dissect molecular and proliferative heterogeneity of interfollicular epidermis (IFE)

overall_design: Single cell RNA-seq profiles of sorted IFE LRC/Non-LRC domains from back and tail skin of wild type (WT) mice

first: Tumbar

last: Tudorita

first: Ghuwalewala

last: Sangeeta


title: Prior vaccination exceeds prior infection in eliciting innate and humoral immune responses in Omicron infected outpatients

status: Public on Jun 11 2022

city: Bethesda

first: Hye Kyung

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Antibody response following Omicron infection is reported to be less robust than that to other variants. Here we investigated how prior vaccination and/or prior infection modulates that response. Disease severity, antibody responses and immune transcriptomes were characterized in four groups of Omicron-infected outpatients (n=83): unvaccinated/no prior infection, vaccinated/no prior infection, unvaccinated/prior infection and vaccinated/prior infection. The percentage of patients with asymptomatic or mild disease was highest in the vaccinated/no prior infection group (87%) and lowest in the unvaccinated/no prior infection group (47%). Significant anti-Omicron spike antibody levels and neutralizing activity were detected in the vaccinated group immediately after infection but were not present in the unvaccinated/no prior infection group. Within two weeks, antibody levels against Omicron, increased. Omicron neutralizing activity in the vaccinated group exceeded that of the prior infection group. No increase in neutralizing activity in the unvaccinated/no prior infection group was seen. The unvaccinated/prior infection group showed an intermediate response. We then investigated the early transcriptomic response following Omicron infection in these outpatient populations and compared it to that found in unvaccinated hospitalized patients with Alpha infection. Omicron infected patients showed a gradient of transcriptional response dependent upon whether or not they were previously vaccinated or infected. Vaccinated patients showed a significantly blunted interferon response as compared to both unvaccinated Omicron infected outpatients and unvaccinated Alpha infected hospitalized patients typified by the response of specific gene classes such as OAS and IFIT that control anti-viral responses and IFI27, a predictor of disease outcome.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) of COVID-19 patients infected by SARS-CoV-2 Omicron varient.

first: Hye-Kyung

first: Ludwig

last: Knabl


title: Gene expression profiling of Calca neurons in the parabrachial nucleus (PBN)

status: Public on Jul 02 2022

city: Bellaterra

first: Elisenda

last: Sanz

state: Barcelona

address: M1/113 Facultat de Medicina

department: Institut de Neurociencies

country: Spain

institute: Universitat Autonoma de Barcelona

summary: Calca-expressing neurons in the parabrachial nucleus (PBN) play a major role in regulating appetite and transmitting real or potential threat signals. Here, we reveal transcripts specific or highly enriched in this neuronal population by using mouse genetics and a conditional viral ribosome-tagging approach to phenotype these neurons.

overall_design: Punches containing the parabrachial nucleus (PBN) of Calca-Cre mice injected with the RiboTag viral vector (AAV-DIO-Rpl22·HA) were homogenized and incubated with anti-hemagglutin (HA) antibodies and protein A/G magnetic beads to isolate the polysome-associated mRNAs of Calca neurons in the PBN. To identify differentially expressed transcripts, RNA from the inputs and immunoprecipitates was extracted, amplified, labelled, and hybridized to MouseRef-8 v2 expression beadchips.

first: G

middle: S

last: McKnight


title: Epidermal basal domains organization highlights skin robustness to environmental exposure.

overall_design: Refer to individual Series


title: Epidermal basal domains organization highlights skin robustness to environmental exposure [bulk RNA-seq]

summary:
Purpose: To  unravel the molecular heterogeneity of distinct epidermal populations in interfollicular epidermis (IFE) in vivo
Methods: We performed bulk RNA sequencing of FACS purified basal (Sca1+/alpha6-integrin+) IFE cells enriched in Slc1a3/Dlx1/Aspm CreER marked lineages. We used >10000 tdTomato+/Sca1+/α6-int+ (basal) cells from both back and tail skin at 2-weeks post TM induction from each of four CreER mouse lines and normalized them to Sca1+/α6-int+ sorted from the same mouse. Extracted RNA of high quality and low input was processed for library preparation followed by Illumina seq on HiSeq4000. The raw sample-specific FASTQ files were trimmed and mapped to the reference genome/transcriptome (mouse/mm10) and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Slc1a3/Dlx1/Aspm basal lineages in IFE