title: Gene-expression data of (WT) and knock-out (KO) bone marrow derived macrophages (BMDMs) from C57BL/7 mice

first: Nicolas

last: Fasel

summary: We provide gene expression data of wild-type (WT) and various knock-out (KO) bone marrow derived macrophages (BMDMs) from mice (C57BL/6) in different conditions of infections and treatments. We included BMDMs from WT (female and male), Ifnar-/-, IFNg-/-, iNOs-/-, Nlrx1-/- (female and male), Nox2-/- and Prx5-/- mice. BMDMs were either infected with a human protozoan parasite Leishmania guyanensis with or without its endosymbiant double-stranded RNA (dsRNA) virus, Leishmania RNA Virus 1 (LgyLRV1+ and LgyLRV1-, respectively). Alternatively BMDMs were treated with a TLR3 agonist poly I:C, a TLR2 agonist FSL1, with H2O2 or tBHQ.

overall_design: Transcriptomic analysis of WT (female and male), Nlrx1-/- (female and male), Nrf2-/- female, Prx5-/- female and Prx5+/+ (littermate) female BMDMs

first: Amel

last: Bekkar

first: Nathalie

last: Isorce

first: Filipa

last: Teixeira

first: Tiia

last: Snäkä

first: Dmitry

last: Kopelyanskiy

first: Florence

last: Prével

first: Marta

last: Reverte

first: Chantal

last: Desponds

first: Stéphanie

last: Claudinot

first: Ioannis

last: Xenarios


title: Intestinal type 2 inflammation reprograms mesenteric adipose tissue and permanently alters its resident immune cell niche [single-cell RNA-seq]

status: Public on Apr 15 2022

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

country: USA

institute: Johns Hopkins University

type: Expression profiling by high throughput sequencing

summary: In addition to adipocytes, adipose tissue (AT) is populated by mesenchymal stem cells (MSC) in stages of commitment to the adipocyte lineage, and immune cells which support homeostatic tissue function. How MSC and immune cells interact during infection is poorly understood. We found that during intestinal nematode infection, MSC in gut-associated AT (mFAT) exhibit a bias away from commitment to the adipocyte lineage towards a pluripotent progenitor state. During this time, MSC became metabolically active, and began secreting the alarmins IL-33 and TSLP, and extracellular matrix collagens. In parallel, mFAT became irreversibly populated by Th2 resident memory (Th2RM) cells, which make the tissue modulatory cytokines amphiregulin and TGFβ1. Secretion of these cytokines, and Th2RM activation and maintenance, was driven by IL-33 and TSLP and in turn MSC activation was induced by amphiregulin and TGFβ1. Our findings link Th2RM cells to reversible mFAT remodeling during intestinal infection and underscore the reciprocal dependence of stroma and resident immune cells for lasting tissue immunity.

overall_design: The stromal vascular fraction of the mesenteric adipose tissue was recovered. Single cells were sequenced using the 10X Genomics Chromium controller. One mouse per condition was used.

first: Agnieska

last: Kabat

first: Alexandra

last: Hackl

first: David

middle: E

last: Sanin

first: Patrice

last: Zeis

first: Katarzyna

last: Grzes

first: Ryan

last: Kyle

first: George

last: Caputa

first: Joy

last: Edwards-Hicks

first: Nisha

last: Rana

first: Angela

last: Castoldi

first: Matteo

last: Villa

first: Leentje

last: Dreesen

first: Jonathan

middle: D

last: Curtis

first: Joseph

middle: F

last: Urban

first: Dominic

last: Grun

first: Erika

middle: L

last: Pearce

first: Edward

middle: J


title: Global gene-regulatory targets of FOSL1, FOSL2 and BATF in human Th17 cells [RNA-seq]

status: Public on Apr 12 2022

city: Turku

first: Sini

last: Junttila

address: Tykistökatu 6 A

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

summary: The aim of this study was to investigate the transciptional mechanisms governed by FOSL1, FOSL2 and BATF for regulation of human Th17 cell-function. FOSL factors were transiently perturbed using RNAi (KD) and over-expression (OE) strategies, whereas BATF was perturbed using RNAi only. RNA-seq was then performed to determine their global transciptional targets.

overall_design: Altogether 48 RNA-seq samples [12 - BATF KD, 24 - FOSL KD, and 12 - FOSL OE] were analysed. The analysis was based on 3 biological replicates of each condition in Th17-polarized cells.

first: Ankitha

last: Shetty

first: Subhash

middle: K

last: Tripathi

first: Tanja

last: Buchacher

first: Rahul

last: Biradar

first: Santosh

last: Bhosale

first: Tapio

last: Envall

first: Asta

last: Laiho

first: Robert

last: Moulder

first: Omid

last: Rasool

first: Sanjeev

last: Galande

first: Laura

last: Elo

first: Riitta

last: Lahesmaa


title: Transcriptome Analaysis of humanized lungs in COVID-19 [scRNAseq]

status: Public on Apr 10 2022

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

summary: Mice with a human immune system (humanized mice), generated by transplantation of human hematopoietic stem and progenitor cells (HSPCs), serve as invaluable tools to study the development and function of the human immune system in vivo. MISTRG6 mouse model, engineered by a human/mouse homolog gene-replacement strategy, provides physiological factors for essentially all classes of human HSPCs to develop in mice. MISTRG6 (acronym for genes replaced) mice encode humanized M-CSF (enabling monocytes and  tissue macrophage development), GM-CSF/IL-3 (to provide lung alveolar macrophages), SIRPa (establish macrophage tolerance to human cells), ThPO (hematopoiesis and platelets), and IL-6 (better engraftment allowing study of adult human patients and improved antigen-specific antibody responses as well as human IL-6 per se), in a Rag2/Gamma common chain deleted background. By adapting recombinant adeno-associated virus (AAV)-driven gene therapy to deliver hACE2 to the lungs, which allows infection with SARS-CoV-2 of MISTRG6 mice engrafted with HPSCs, we created a humanized mouse model of COVID-19 that recapitulates the distribution and function of the human innate and adaptive immune system and is amenable to the mechanistic study of COVID-19 and its myriad of complications. We evaluated the lung transcriptional landscape and response to therapeutics in this model. First, we assessed the impact of anti-IFNAR2 and Remdesivir combined therapy and control dexamethasone therapy on the immunological transcriptome of SARS-CoV-2 infected MISTRG6-hACE2 mice by focusing on differentially regulated human genes in whole lung tissue. We treated infected MISTRG6-hACE2 mice with Remdesivir, anti-IFNAR2 antibody or a combination of the two starting 7dpi, to sequentially target viral replication and the IFN-dependent cascade downstream of infection. As a control, we also treated mice with dexamethasone, one of the few treatments that significantly reduced hospitalization and mortality in the clinic. Next, we compared the single cell transcriptomes of human immune cells from infected mice late in disease (28dpi) with their uninfected counterparts to gain a deeper understanding of transcriptional changes at the cellular level. Finally, we focused our efforts on deeper characterization of monocyte/macrophage clusters at early (4dpi) or late (14 and 28dpi) infection.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We successfully delivered AAV-hACE2 to lung tissues of immune-reconstituted MISTRG6 mice (MISTRG6-hACE2) that have been engrafted with human HSPCs. MISTRG6-hACE2 mice were then infected with SARS-CoV-2.  Mice were treated with therapeutics starting at 7dpi. For whole tissue transcriptional analysis in response to therapeutics: whole lungs, collected at 14dpi and 28dpi, were homogenized. RNA was RNA was extracted with the RNeasy mini kit (Qiagen) per the manufacturer’s protocol.For single cell transcriptional analysis: lungs from infected mice were collected and digested at 37°C for 20 min using digestion cocktail containing 1 mg/ml collagenase D (Sigma) and 30 µg/ml DNase I (Sigma-Aldrich) in RPMI. Single cell suspensions from digested lungs were stained with antibodies against human CD45 and mouse CD45. Human immune cells were sorted (humanCD45+mouseCD45-DAPI-) and stained with TotalSeq (TotalSeq™-B0251 anti-human Hashtag 1 Antibody: GTCAACTCTTTAGCG; TotalSeq™-B0252 anti-human Hashtag 2 Antibody: TGATGGCCTATTGGG) antibodies (Biolegend) prior to processing for droplet based scRNA-seq. Duplicates from each condition/time point were pooled in equal numbers to ensure 10000 cells were encapsulated into droplets using 10X Chromium GEM technology. Libraries were prepared in house using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics). scRNA-seq libraries were sequenced using Nova-Seq. Raw sequencing reads were processed with Cell Ranger 3.1.0 using a human-mouse combined reference to generate a gene cell count matrix.

first: Esen

last: Sefik

first: Richard

last: Flavell


title: Single Cell Transcriptomics of Human Native Kidney and Kidney Allografts

status: Public on Apr 19 2022

city: New York

first: Pavel

last: Morozov

state: NY

department: Tuschl Lab

institute: Rockefeller University

summary: We tested the hypothesis that single-cell RNA-sequencing (scRNA-seq, 10X) and computational analysis of human kidney allograft biopsies will reveal new cell types and cell states and yield insights to personalize the care of transplant recipients.

overall_design: 3 kidney biopsies from 3 individuals for scRNA-seq; (i) HK: native kidney biopsy from a living kidney, (ii) AK1: allograft kidney biopsy with transplant glomerulopathy, fibrosis, and worsening kidney function but with undetectable circulating anti-HLA antibodies, and (iii) AK2: allograft kidney biopsy after treatment of active antibody-mediated rejection but with persistent circulating donor-specific anti-HLA antibodies.

first: Thangamani

last: Muthukumar

first: Hemant

last: Suryawanshi


title: Transcriptome-wide mapping of dihydrouridine sites with D-seq

status: Public on Apr 16 2022

city: NEW HAVEN

first: Wendy

middle: V

last: Gilbert

address: 333 Cedar St

department: MB&B

institute: Yale University

summary: We report the development of D-Seq, a sequencing based technique for identification of dihydrouridine (D) modifications within RNA. We performed D-Seq on S. cerevisiae and find the first evidence for dihydrouridylation of endogenous mRNAs.

overall_design: RNA was treated with NaBH4 to modify D residues, which cause RT stops. The sites of DUS-dependent RT stops were used to identify D sites.

first: Austin

middle: S

last: Draycott

first: Cassandra

last: Schaening-Burgos

first: Maria

last: Rojas-Duran

first: Loren

last: Wilson

first: Leonard

last: Schärfen

first: Karla

middle: M

last: Neugebauer

first: Sigrid

last: Nachtergaele


title: Investigation of the potential mechanisms underlying nuclear F-actin organization in ovarian cancer cells by high-throughput screening in combination with deep learning

status: Public on Apr 11 2022

city: Hangzhou

first: Yiyan

last: Zheng

address: Zhiqiang Road 428

country: China

institute: Westlake Laboratory of Life Sciences and Biomedicine

summary: We sequenced a set of ovarian cancer cell lines with or without overexpression of a fluorescent nuclear F-actin probe. It is to compare different ovarian cancer cell types which have distinct nuclear F-actin patterns, and try to seek the difference behind that phenotype. Meanwhile, we also want to check whether the nuclear F-actin probe would affect the transcriptional profile of the cell line.

overall_design: Five different cell types including three biological repilcates for each cell type were sequenced.

first: Wei

last: Wu

first: Xiaoxia

last: Xing

first: Mingyang

last: Wang

first: Yinzhou

last: Feng

first: Nina

last: Wietek

first: Kay

last: Chong

first: Salma

last: El-Sahhar

first: Ahmed

middle: A

last: Ahmed

first: Rongyu

last: Zang


title: PARK7/DJ-1 promotes pyruvate dehydrogenase activity and maintains Treg homeostasis during ageing

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Pyruvate dehydrogenase (PDH) is the gatekeeper enzyme of the tricarboxylic acid (TCA) cycle. Here we show that the deglycase DJ-1 (encoded by PARK7, a key familial Parkinson's disease gene) is a pacemaker regulating PDH activity in CD4+ regulatory T cells (Treg cells). DJ-1 binds to PDHE1-β (PDHB), inhibiting phosphorylation of PDHE1-α (PDHA), thus promoting PDH activity and oxidative phosphorylation (OXPHOS). Park7 (Dj-1) deletion impairs Treg survival starting in young mice and reduces Treg homeostatic proliferation and cellularity only in aged mice. This leads to increased severity in aged mice during the remission of experimental autoimmune encephalomyelitis (EAE). Dj-1 deletion also compromises differentiation of inducible Treg cells especially in aged mice, and the impairment occurs via regulation of PDHB. These findings provide unforeseen insight into the complicated regulatory machinery of the PDH complex. As Treg homeostasis is dysregulated in many complex diseases, the DJ-1-PDHB axis represents a potential target to maintain or re-establish Treg homeostasis.

overall_design: We analyzed Tregs (CD4+CD25high) isolated from the spleen of old DJ-1 knockout (KO) mice vs. age- and gender-matched WT littermates (3 WT, 3 KO) using the Affymetrix Mouse Gene 2.0 ST Array. RNA samples of Tregs sorted from 45-weeks old DJ-1-/- mice and DJ-1+/+ littermates using BD FACSAria III, were analysed at EMBL Genomics Core Facility (Heidelberg. Germany). Array data was processed by Affymetrix Expression Console v1.4 using Exon-level analysis. No techinical replicates were performed.

first: Ni

last: Zeng

first: Christophe

last: Capelle

first: Rudi

last: Balling

first: Markus

last: Ollert

middle: Q


title: Concordance of hydrogen peroxide-induced 8-oxoguanine patterns with two cancer mutation signatures of upper GI tract tumors

city: Grand Rapids

first: Gerd

middle: P.

last: Pfeifer

state: Michigan

address: 333 Bostwick Ave. NE.

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: Oxidative DNA damage has been linked to cancer, aging, inflammation, and other pathological conditions. Although the chemical nature of the damaged bases is well understood, the precise distribution of oxidatively damaged DNA bases in the human genome is not known. Here we have used the recently developed circle-damage-sequencing method to map two types of oxidative DNA damage, oxidized guanines produced by hydrogen peroxide and oxidized thymines created by treatment of cells with potassium permanganate, at single base resolution. We show that oxidized guanines, chiefly 8-oxo-G, occur strictly dependent on the G/C sequence context and show a pronounced peak at transcription start sites (TSS). We determined the trinucleotide sequence pattern of guanine oxidation. This pattern shows high similarity to the cancer-associated single base substitution signatures SBS18 and SBS36. SBS36 is found in colorectal cancers that carry mutations in MUTYH, encoding a DNA repair enzyme that operates on 8-oxo-G mispairs. SBS18 is common in inflammation-associated upper GI tract tumors including esophageal and gastric adenocarcinomas. Oxidized thymines induced by permanganate occur with a distinct dinucleotide specificity, 5’T-A/C, and are depleted at the TSS. Collectively, our data provides a comprehensive analysis of two types of oxidized DNA bases in the human genome and suggests that two cancer mutational signatures, SBS18 and SBS36, are caused by reactive oxygen species.

overall_design: Oxidized DNA damages were mapped in genome-wide in  HDF and U2OS cells treated with 10 mM of H2O2 and KMnO4, respectively.

first: Seung-Gi

last: Jin

middle: P


title: Transcriptomic analysis of Panc10.05 cells treated with indisulam

status: Public on Apr 09 2022

city: Amsterdam

first: Rodrigo

last: Leite de Oliveira

address: De Boelelaan 1118

country: Netherlands

institute: Amsterdam UMC / location VUmc

summary: Indisulam is an abandoned drug that acts as a molecular glue, inducing degradation of splicing factor RBM39 through interaction with CRL4DCAF15. We generated spontaneoulsy indisulam-resistant Panc10.05 cells and studied their response to indisulam.

overall_design: Transcriptomic analysis of Panc10.05 cells (parental and indisulam-resistant) treated with indisulam

first: Ziva

last: Pogacar

first: Kelvin

last: Groot

first: Fleur

last: Jochems

first: Matheus

last: dosSantosDias

first: Ben

last: Morris

first: Mieke

last: Roosen

first: Leyma

last: Wardak

first: Giulia

last: DeConti

first: Arno

last: Velds

first: Cor

last: Lieftink

first: Roderick

last: Beijersbergen

first: Rene

last: Bernards

last: LeitedeOliveira


title: Mapping the cardiac vascular niche in heart failure

status: Public on Apr 14 2022

city: Aachen

first: Fabian

last: Peisker

address: Pauwelsstraße 30

country: Germany

institute: Uniklinikum RWTH Aachen

summary: Various transgenic CreER;tdTomato mouse-lines (Pdgfrb-CreER, Col1a1-CreER, Gli1-CreER, Cdh5-CreER, Myh11-CreER, Ng2-CreER) were pulsed with tamoxifen and subjected to either Sham or TAC surgery at 21 days after tamoxifen induction. Two and four weeks later, tdTomato-positive cells were isolated from hearts by FACS sorting and 10x Genomics scRNA 3'RNA sequencing pipeline was applied. We identified fibroblast, endothelial cells, mural cells and Schwann cells as major cardiac cell types in our samples. Gene expression changes between subtypes of the major cell types point towards a general upregulation of extra cellular matrix related genes, with fibroblasts being the highest producer.

overall_design: We used scRNA 3' RNA sequencing product from 10x Genomics to trace vascular and perivascular cell types of the heart in murine pressure overload induced heart failure.

first: Maurice

last: Halder

first: James

last: Nagai

first: Ronghui

last: Li

first: Julila

last: Möllmann

first: Michael

last: Lehrke

first: Rebekka

last: Schneider

first: Ivan

last: Costa

first: Rafael

last: Kramann


title: Effects of S100A8 inhalation on expression of genes in the lung microenvironment

city: Sydney

first: Sze Wing

last: Wong

state: NSW

address: PO Box 81 Randwick

country: Australia

institute: Children's Cancer Institute

summary:
Because S100A8 inhalation delayed lung tumor growth (LLC) in mice but did not directly affect tumor cell viability, we sought to determine potential changes in the lung microenviornment that contributed to its anti-tumor effects.
Effects of S100A8 treatment on the lung microenvironment were assessed using a panel of 98 genes that affect immune regulation, redox, cancer growth, metastasis, hypoxia and angiogenesis.

overall_design: We averaged expression of each gene in lungs from 4-5 independent mice per treatment group. We compared gene expression in mice treated with S100A8+LLC, HBSS+LLC, S100A8+vehicle to HBSS+vehicle (control). In total, there were 4 samples.

first: Sze

middle: W

first: Joshua

last: McCarroll

first: Kenneth

last: Hsu

first: Carolyn

last: Geczy

first: Nicodemus

last: Tedla


title: LncRNA expression-profiling to predict distant metastasis in locoregionally advanced nasopharyngeal carcinoma

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: LncRNAs can be used as prognostic biomarkers in various types of cancer. We aimed to identify a lncRNA expression pattern for individual distant metastatic risk assessment in patients with locoregionally advanced nasopharyngeal carcinoma (LA-NPC).

overall_design: Using Arraystar Human LncRNA Microarray, we profiled the lncRNA expression in tissues between 18 pairs of NPC patients and healthy controls, as well as 10 pairs of LA-NPC with or without distant metastasis after radical treatment to identify distant metastasis-related lncRNAs.

first: Y

last: Liang

first: J

first: N

last: Liu


title: Quaking regulates lineage-specific splicing patterns between early progenitor cells and is required for cardiac cell fate specification

city: Galveston

first: W.

middle: Samuel

last: Fagg

state: TX

address: 301 University Blvd, Department of Surgery, MRB5.150, L21875

department: Surgery/Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

summary: Cell type-specific alternative splicing (AS) regulates tissue homeostasis, with several examples of AS promoting stem cell self-renewal or differentiation. However, the lineage-specific patterns of AS required for early progenitor cells of each of the three germ layers and the specific RNA binding proteins (RBPs) essential for early cell fate are unknown. To approach this question, we performed parallel RNA-seq on human embryonic stem cells (hESCs), hESC-derived definitive endoderm (DE), cardiac mesoderm (CM), and ectoderm (ECT) cells. Analysis of AS patterns in these datasets show that, unlike ECT cells, DE and CM cells display distinct and non-overlapping patterns of lineage-specific splicing.

overall_design: Four independent samples analyzed: undifferentiated H9 human embryonic stem cells (UD; hESCs), definitive endoderm (DE) derived from H9 hESCs, cardiac mesoderm (CM) derived from H9 hESCs, and ectoderm (ECT) derived from H9 hESCs; 3 replicates per sample

first: W

first: Naiyou

first: Ulrich

last: Braunschweig

first: Xiaoting

last: Chen

first: Steven

middle: G

last: Widen

first: John-Paul

last: Donohue

first: Jeffrey

middle: H

last: Fair

first: Matthew

middle: T

last: Weirauch

first: Benjamin

last: Blencowe

first: Mariano

last: Garcia-Blanco


title: High efficient serum free differentiation of endothelial cells from human iPS cells without sorting

status: Public on Apr 08 2022

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

summary: Introduction: Endothelial cells (ECs) form the inner lining of all blood vessels of the body, play important roles in vascular tone regulation, hormone secretion, anticoagulation, regulation of blood cell adhesion and immune cell extravasation. Limitless ECs sources are required to further in-vitro investigations of ECs’ physiology and pathophysiology as well as for tissue engineering approaches. Ideally, the differentiation protocol avoids animal derived components such as fetal serum and yields ECs at efficiencies that make further sorting obsolete for most applications.  Method: hiPSC are cultured under serum free conditions, and induced into mesodermal progenitor cells via stimulation of Wnt signaling for 24 hours. Mesodermal progenitor cells are further differentiated into ECs by utilizing a combination of human vascular endothelial growth factor A165 (VEGF), basic fibroblast growth factor (bFGF), 8-Bromoadenosine 3′,5′-cyclic monophosphate sodium salt monohydrate (8Bro), and melatonin (Mel) for 48 hours.   Result: This combination generates hiPSC derived ECs (hiPSC-ECs) at a fraction of 90.9 ± 1.5% and is easily transferable from the two dimensional (2D) mono layer into three dimensional (3D) scalable bioreactor suspension cultures. hiPSC-ECs are positive for CD31, VE-Cadherin, von-Willebrand-factor, and CD34. Furthermore, the majority of hiPSC-ECs express the vascular endothelial marker CD184 (CXCR4).  Conclusion: The differentiation method presented here generates hiPSC-ECs in only 6 days, without addition of animal sera and at an efficiency eliminating the need for further enrichment strategies, hence providing a scalable source of hiPSC-ECs.

overall_design: Human induced pluripotent stem cels (hiPSC) were differentiated ad under serum free conditions into mesodermal progenitor cells via stimulation of Wnt signaling for 24 hours. Mesodermal progenitor cells were further differentiated into endothelial-like cells  (ECs) by utilizing a combination of human vascular endothelial growth factor A165 (VEGF), basic fibroblast growth factor (bFGF), 8-Bromoadenosine 3′,5′-cyclic monophosphate sodium salt monohydrate (8Bro), and melatonin (Mel) for 48 hours.

first: Kurt

last: Pfannkuche


title: Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo

city: Farmington

first: Anthony

last: Vella

state: Connecticut

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

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

overall_design: Refer to individual Series


title: Antidepressants fluoxetine mediates endoplasmic reticulum stress and autophagy of Non-small cell lung cancer cells through ATF4-AKT-mTOR signaling pathway

city: shanghai

first: shali

last: shao

address: longhang road

institute: jinshan hospital of fudan university

summary: In order to investigate the specific mechanism of fluoxetine, we chose H460 cells that were more sensitive to the drug

overall_design: RNA sequencing (RNA-seq) was used to study the transcriptome of cells treated with fluoxetine and analyze the difference with control treatment

first: Shali

last: Shao

first: Xibing

last: Zhuang

first: Tiankui

last: Qiao

first: lin

last: zhang


title: Interleukin-4 receptor signaling modulates neuronal network activity

status: Public on Apr 13 2022

city: Mainz

first: Samantha

last: Schmaul

address: Langenbeckstr 1

department: Neurology

institute: University Medical Centre Mainz

summary: Neuroimmune interaction influences essential CNS processes. Hanuscheck et al. report expression of interleukin-4 receptor alpha at presynaptic terminals in mouse and human brain. Modulation of neuronal IL-R signaling alters the neuronal transcriptome, impacts synaptic transmission and causes anxiety-related behavior.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human iPSC derived neurons

first: Nicholas

last: Hanuscheck

first: Carine

last: Thalman

first: Micaela

last: Domingues

first: Muthuraman

last: Muthuraman

first: Mohammadsaleh

last: Oshaghi

first: Christina

middle: F

last: Vogelaar

first: Frauke

last: Zipp


title: Clostridioides difficile WalRK

city: Iowa City

first: Craig

last: Ellermeier

state: IA

address: 431 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

summary: Effect on gene transcript levels upon up- or down-regulation of two component system WalRK (Wal-ON and Wal-OFF)

overall_design: Wal-ON: overexpress the regulator walR from a single copy integrated on the chromosome under xylose inducible control; produce either the wildtype WalR, or a WalR-D54E mutant that is expected to mimic phosphorylated WalR and thus be constitutively active. Wal-OFF: CRISPR interference (CRISPRi) machinery integrated into the chromosome under xylose induction. sgRNA is either a negative control that does not target anywhere on the C. difficile chromosome, or targets the first gene in the wal operon, cd630_17810. Growth under no xylose conditions relies on leaky expression, growth with low xylose induces the CRISPRi machinery further.

first: Ute

last: Müh

middle: D

first: David

last: Weiss


title: Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [Costimulated CD8]

first: Anthony

last: Vella

summary: Here, we provide RNA-seq from mouse antigen-specific CD8+ T cells in naïve, antigen-primed, and antigen-primed plus costimulated states. This was used to compare levels of RNA Binding Protein transcript expression.

overall_design: 3 groups: Naïve CD8+ T cells from OT-I transgenic mice, adoptively transferred antigen-primed CD8+ T cells, adoptively transferred antigen-primed & costimulated CD8+ T cells

first: Timofey

last: Karginov

first: Antoine

last: Ménoret


title: Transcriptomic expression of A549 cells treated with indisulam and sphinx 31

first: Rodrigo

last: Leite de Oliveira

summary: Indisulam is an abandoned drug that acts as a molecular glue, inducing degradation of splicing factor RBM39 through interaction with CRL4DCAF15. We combined indisulam with sphinx 31 (a splicing factor inhibitor) and evaluated their combined activity in inducing splicing errors.

overall_design: Transcriptomic analysis of A549 cells treated with indisulam and sphinx 31. The experiment was performed in technical duplicates.

first: Ziva

last: Pogacar

first: Kelvin

last: Groot

first: Fleur

last: Jochems

first: Matheus

last: dosSantosDias

first: Ben

last: Morris

first: Mieke

last: Roosen

first: Leyma

last: Wardak

first: Giulia

last: DeConti

first: Arno

last: Velds

first: Cor

last: Lieftink

first: Roderick

last: Beijersbergen

first: Rene

last: Bernards

last: LeitedeOliveira


title: Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control

status: Public on Apr 07 2022

city: Cambridge

first: Constantine

middle: Nicholas

last: Tzouanas

state: MA

address: 45 Carleton St

department: Harvard-MIT Health Sciences and Technology

institute: Massachusetts Institute of Technology

summary: We used longitudinal scRNA-seq, PET-CT, and bacterial burden assays to understand the cellular features underlying granuloma timing and burden/resolution.

overall_design: Granulomas in Cynomolgus macaque were dissociated for scRNA-seq

middle: N

first: Travis

last: Hughes

first: Alex

last: Shalek


title: Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Developmental gene expression is often controlled by distal regulatory DNA elements called enhancers. Distant enhancer action is restricted to structural chromosomal domains that are flanked by CTCF-associated boundaries and formed through cohesin chromatin loop extrusion. To better understand how enhancers, genes and CTCF boundaries together form structural domains and control expression, we used a bottom-up approach, building series of active regulatory landscapes in inactive chromatin. We demonstrate here that gene transcription levels and activity over time reduce with increased enhancer distance. The enhancer recruits cohesin to stimulate domain formation and engage flanking CTCF sites in loop formation. It requires cohesin exclusively for the activation of distant genes, not of proximal genes, with nearby CTCF boundaries supporting efficient long-range enhancer action. Our work supports a dual activity model for enhancers: its classic role to stimulate transcription initiation and elongation from target gene promoters and a role to recruit cohesin for the creation of chromosomal domains, the engagement of CTCF sites in chromatin looping, and the activation of distal target genes.

overall_design: 146 4C-contact profiles of genetically modified or drug treated or gene knocked down (KD) K562 cells. Every condition had at least 2 technical replicates. CRISPRi KDs of indicated genes in indicated clones were compared to control KDs.

first: Niels

middle: J

last: Rinzema

first: Konstantinos

last: Sofiadis

first: Sjoerd

last: Tjalsma

first: Marjon

last: Verstegen

first: Yuva

last: Oz

first: Christian

last: Valdes-Quezada

first: Anna-Karina

last: Felder

first: Teodora

last: Filipovska

first: Stefan

last: van der Elst

first: Zaria

last: de Andrade dos Ramos

first: Ruiqi

last: Han

first: Wouter

last: de Laat


title: The purinergic P2Y14 receptor links hepatocyte death to hepatic stellate cell activation and fibrogenesis in the liver

city: NEW YORK

first: Robert

last: Schwabe

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

summary: Characterization of hepatic stellate cells (HSC) genes in the normal liver or diverse liver fibrotic models by single cell RNA sequencing.

overall_design: scRNAseq of whole injured liver (n=1), isolated HSC from normal (n=1) or fibrotic liver from CCl4 after one or several injections (n=3).

first: Aveline

last: Filliol

first: Ingmar

last: Mederacke

first: Silvia

last: Affo

first: Francesco

last: Brundu

first: Ajay

last: Nair


title: SPARTA-related RNA and DNA

status: Public on Apr 04 2022

city: Wageningen

first: Daan

middle: C.

last: Swarts

address: Stippeneng 4

department: Laboratory of Biochemistry

institute: Wageningen University

type: Non-coding RNA profiling by high throughput sequencing

summary: SPARTA-related small RNA, long RNA, and DNA

overall_design: Total and small RNAseq data of total RNA from cells expressing SPARTA or co-purified with SPARTA complexes expressed in E. coli BL21(DE3)

middle: C

first: Balwina

last: Koopal


title: Comparative analysis of mesenchymal stem cells cultivated in serum free media

status: Public on Apr 05 2022

city: Seoul

first: Min Hee

last: Kang

state: Gangnam-gu

address: Dong won Building, 333

country: South Korea

institute: Xcell Therapeutics

summary: Differential expression analysis of mRNAs and proteins showed that the expression of genes related with apoptosis, immune response, and inflammatory response were significantly up-regulated in ADSCs cultivated in FBS containing media.

overall_design: Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed using Agilent 2100 bioanalyzer with the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, Netherlands). RNA was quantified using ND-2000 spectrophotometer (Thermo Fisher Scientific). An RNA sequencing library was constructed from the control and test RNAs using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. Briefly, each 500ng of total RNA was prepared, an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library was purified from PCR components. High-throughput sequencing was performed as single-end 75-bp sequencing using NextSeq 500 (Illumina, Inc., USA). QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 [25]. Bowtie2 indices were either generated from the genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome. The alignment file was used for assembling transcripts, estimating their abundances and determining the differential expression of genes. Differentially expressed genes (DEGs) were determined based on counts from unique and multiple alignments using BEDtools [26]. The read count data were processed based on quantile normalization method using EdgeR within R (R development Core Team, 2016) using Bioconductor (Gentleman et al.,2004). Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).

first: Joo

middle: Y

last: Lee

first: Min

first: Ji

middle: E

last: Jang

first: Jeong

first: Yuyeong

last: Yang

last: Choi

first: Hong

middle: S

first: Uiil

last: Choung

first: Sang

last: Park


title: RNA-Seq of intraductal breast cancer PDX hormonally treated

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

summary: Using a large variety of methods we demostrate that PGR can be a driver of tumor proliferation even in absence of high E2. In this specific experiment we treat breast cancer cells intraductally xenografted into the ductal tree of a mouse mammary gland, with estrogen (E2), progesterone (P4) and the combination of the two (E2+P4).

overall_design: PDX cells were grown intraductally for around 2 months then hormone-releasing pellets were implanted subcutaneously where they were left for 60 days.

first: Valentina

last: Scabia


title: RNA-Seq of CTRL and PGR overexpressing MCF7 intraductal xenografts

summary: Using a large variety of methods we demostrate that PGR can be a driver of tumor proliferation even in absence of extensive E2. In this specific experiment we overexpress PGR in MCF7 cells intraductally xenografted into the ductal tree of a mouse mammary gland, which provides post-menopausal levels of E2. Despite these conditions the cells thrive and with the PGR overexpression the growth rate is double the control cells. PGR overexpressing cells exhibit consistently more invasive and metastatic properties.

overall_design: MCF7 CTRL and PGR overexpressing cells were grown intraductally for 45 days. The mammary glands collected at endpoint were snap-frozen, RNA extracted and sequenced.


title: Studying the effects of endogenous and exogenous histidine supplementation on Pichia pastoris cultured in YPA

status: Public on Apr 06 2022

city: Bangalore

first: Aditi

last: Gupta

state: Karnataka

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

country: India

institute: Indian Institute of Science

summary: A histidine prototrophic strain achieves A600 three-four fold higher than a histidine auxotroph when cultured in nutrient rich media YPA, which is abundant in amino acids. This retaded growth of histidine auxotroph in YPA can also be rescued by supplementing media with exogenous histidine. Here, we aim to study the transcriptomic changes associated with culturing of histidine auxotroph and prototroph in YPA and also the effects of histidine addition to the culture medium of histidine auxotroph.

overall_design: Wild type cells were cultured in nutrient rich medium containing yeast extract, peptone and acetate as a carbon source (YPA), alone or supplemented with 650 uM histidiene. Cells were harvested after 24 hours followed by RNA preparation using QIAGEN RNEASY Mini Kit which was then subjected to RNA-SEQ.

first: P

last: Rangarajan


title: Systematic Evaluation of Parameters in RNA Cytosine Methylation Analysis

city: Blacksburg

first: Zachary

last: Johnson

state: VA

address: 1015 Life Science Cir

department: FLSI

institute: Virginia Tech

summary: Here we systematically analysis bisulfite-treated RNA sequencing data (RNA BS-seq) for the purpose of identifying m5C methylation data from mouse neural stem cells. We isolated mitochondrial fractions to better understand the m5C characteristics of RNAs found in these cellular compartments. Throughout the analysis, we identify key parameters to be used in RNA m5C methylation analysis, and identify downstream effects of artifact detection on RNA m5C levels. In addition, we utilized Unique Molecular Identifiers (UMIs) in conjunction with ERCC (External RNA Controls Consortium) as RNA controls to identify rates of m5C artifcats generated by RNA duplication and PCR amplification error rates. Using various preparation parameters, we identify ideal preparation methods for RNA BS-seq.

overall_design:
Analysis of RNA BS-seq data across various RNA BS-seq preparation methods of mitochondrial isolates.
Please note that processed data file generated from multiple samples is linked to the corresponding rep1 sample -or- to the Series records.

first: Xiguang

last: Xu

first: Hehuang

last: Xie


title: Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [CRISPR]

first: Anthony

last: Vella

summary: Here we provide a dataset of deep RNA sequencing from mouse CD8+ T cell CRISPR-mediated knockout of RBP Tardbp after adoptive transfer and antigen+costimulatory stimulus (in mice) which we show is critical for optimal CD8+ T effector function.

overall_design: 2 groups: adoptively transferred Control gRNA CRISPR CD8+ T cells, adoptively transferred Tardbp gRNA CRISPR CD8+ T cells ; both groups received antigen (SIINFEKL) + costimulation (anti-OX40, anti-41BB)

first: Timofey

last: Karginov

first: Antoine

last: Ménoret


title: Differential Metabolic Requirement Governed by Transcription Factor c-Maf Dictates Innate γδT17 Effector Functionality in Mice and Humans

city: Shanghai

first: Xu

last: Chen

address: Zhizaoju Road No.639

institute: Shanghai Jiao Tong University School of Medicine

summary: To investigate the human γδT17 cells from oral cancers, we performed sc-RNAseq of two pairs of oral cancers with normal tissues.

overall_design: 2 cases of oral cancer tissues with paired 2 cases of adjacent normal tissues

first: Fuxiang

first: Jun

last: Yan


title: Dihydroartemisinin  Exerts Antifibrotic and Anti-inflammatory Effects in Graves’ Ophthalmopathy by Targeting Orbital Fibroblasts

city: guangzhou

first: Shenglan

state: guangdong

address: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 South Xianlie Road, Guangzhou , People’s Republic of China

institute: zhongshan ophthalmic center

summary: Graves’ ophthalmopathy (GO) is a common orbital disease that threatens visual function and appearance. Orbital fibroblasts (OFs) are considered key target and effector cells in GO. In addition, hyaluronan (HA) production, inflammation, and orbital fibrosis are intimately linked to the pathogenesis of GO. In this study, we explored the therapeutic effects of dihydroartemisinin (DHA), an antimalarial drug, on GO-derived, primary OFs. RNA sequencing was conducted to identify differentially expressed genes (DEGs) in DHA-treated OFs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs was performed to explore potential mechanisms mediating the antifibrotic effect of DHA on GO-derived OFs. Results showed that DHA dose-dependently inhibited OF proliferation and downregulated, at the mRNA and protein levels, TGF-β1-induced expression of fibrosis markers, including alpha smooth muscle actin (α-SMA) and connective tissue growth factor (CTGF). Furthermore, DHA inhibited TGF-β1 induced phosphorylation of extracellular signal-regulated protein kinase 1/2 (ERK1/2) and signal transducer and activator of transcription 3 (STAT3), which suggested that DHA exerted antifibrotic effects via suppression of the ERK and STAT3 signaling pathways.In conclusion, our study provides first-time evidence that DHA may significantly alleviate pathogenic manifestations of GO by inhibiting proliferation, fibrosis- and inflammation-related gene expression, and HA production in OFs. These data suggest that DHA may be a promising candidate drug for treatment of GO.

overall_design: GO-derived orbital fibroblasts were treated with DHA (0, 20 μM) with or without TGF-β1 (10 ng/mL) (n=3 cultures/treatment) for 48 h. Examinations were taken in this three groups.


title: Deciphering in vivo reprogramming using single cell RNA sequencing in the pancreas

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

summary: The manipulation of cell fates through reprogramming is one of the most exciting advances in recent years. The most striking breakthrough in the field occurred when Yamanaka first illustrated the possibility to convert differentiated cells into pluripotent stem cells by the ectopic expression of four transcription factors, Oct4, Sox2, Klf4 and c-Myc or OSKM. Our laboratory has demonstrated that transient expression of these four Yamanaka factors leads to teratoma formation in mice indicative of in vivo reprogramming. We were interested in deciphering the intermediate events of de-differentiation induced by OSKM in vivo before reaching pluripotency. For this purpose, we focused on the pancreas which we found to be the organ with the highest reprogramming efficiency in vivo. To gain an insight into the cellular heterogeneity generated by OSKM activation in vivo, we performed single cell RNA sequencing of partially reprogrammed pancreas. We found that in vivo reprogramming leads to the loss of pancreatic acinar identity and the acquisition of an atypical tubular morphology different from normal pancreatic ducts or from the metaplastic ducts produced by pancreatitis. We were able to capture cells that have lost their acinar identity and they have acquired alternative cell fates. This analysis provide us with a list of markers characteristic of the intermediate stages of OSKM reprogramming.

overall_design: Single cell RNAseq of reprogrammed pancreas (i4F) compared to WT and cerulein-induced damaged pancreas

first: Dafni

last: Chondronasiou

last: Martínez de Villarreal

first: Elena

last: Meléndez

first: Francisco

last: Real

first: Manuel

last: Serrano


title: Dot1L recruits OGT target chromatin to regulate histones O-GlcNAcylation

city: Wuhan

first: Bo

address: East Lake South Road

department: College of Life Sciences

institute: Wuhan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: OGT (O-GlcNAc transferase) is the distinctive enzyme responsible for catalyzing O-GlcNAc to the serine or threonine residues of thousands of cytoplasm and nuclear proteins that are involved in DNA damage, RNA splicing, and transcription preinitiation and initiation complex assembly. However, the molecular mechanism by OGT regulating gene transcription remains elusive. Using proximity labeling based mass spectrometry, we searched for functional partners of OGT and found that Dot1L, the conserved and unique histone methyltransferase mediated histone H3 lys79 methylation required for gene transcription, DNA damage repair, cell proliferation, and embryo development, interacts with OGT. Although this specific interaction does not regulate the enzymatic activity of Dot1L, it facilitates OGT-dependent histones O-GlcNAcylation. Moreover, OGT associates with Dot1L at transcription start sites, and depleting Dot1L decreased OGT associated with chromatin globally. Notably, downregulation of Dot1L reduces the levels of histone H2B S112 O-GlcNAcylation and histone H2B K120 ubiquitination in vivo, which are associated with gene transcription regulation. Taken together, these results reveal a Dot1L-dependent O-GlcNAcylation of chromatin.

overall_design: Cut&Tag dataset of OGT and Dot1L in HEK293T cells. Cut&Tag dataset of OGT in HEK293T cells treated with or without siRNA targeted Dot1L.Study the roles of DOT1L in histones O-GlcNAcyaltion regulation

first: Can

last: Zhang

first: Ao

last: Jiang

first: Xianhong

first: Fenfei

last: Liang

first: Xueqing

last: Wang

first: Danni

last: Li

first: Chenglong

last: Liu

first: Xiaomei

first: Jing

last: Xia

first: Yang

first: Yirong

first: Zelan

last: Yang

first: Jia

first: Yu

last: Zhou

first: Liang

first: Hui

last: Sun


title: RNA-Seq of MCF7 intraductal xenografts hormonally treated

first: Giovanna

last: Ambrosini

summary: Using a large variety of methods we demostrate that PGR can be a driver of tumor proliferation even in absence of extensive E2. In this specific experiment we treat MCF7 cells intraductally xenografted into the ductal tree of a mouse mammary gland, with estrogen (E2), progesterone (P4) and the combination of the two (E2+P4).

overall_design: MCF7 cells were grown intraductally for 45 days. 7 days after injection hormone pellets were implanted subcutaneously.

first: Valentina

last: Scabia


title: High-throughput sequencing Transcriptomes Analysis of WT and Kcnj2 KO mouse BMDMs treated with LPS or kir2.1 inhibitor

city: HangZhou

first: Di

state: ZheJiang

address: No.866, Yuhangtang Road, Xihu District, Hangzhou

institute: ZheJiang university

summary:
Purpose:Mouse BMDM is the universal cell type of studying innate immunity.This study was to analyze LPS induced innate immune response and the relationship between the inward rectifier potassium channel Kir2.1 and  LPS induced innate immune respone
Methods: WT and Kcnj2 KO BMDM cells were treated with or without LPS for 6 hours in the presence of kir2.1 inhibitor ML133 or not. Then mRNA profiles of these samles were generated by High-throughput sequencing analysis, in triplicate, using illumina HiSeq 2000. And the differential mRNA profiles were analyzed.
Results: mRNA profiles of more than 20000 genes were analyzed, and differential expression profiles were compared .
Conclusions: Our study represents the first detailed analysis of transcriptomes of WT and Kcnj2 KO mouse BMDM treated with LPS or kir2.1 inhibitor, with biologic replicates, generated by RNA-seq technology. This data was useful to analyze the relationship between Kir2.1 and  LPS induced innate immune respone

overall_design: mRNA profiles of mouse BMDM treated with LPS and phgdh inhibitor were generated by High-throughput sequencing, in triplicate, using HiSeq 2000.

first: Weiwei

last: Yu


title: High-throughput sequencing Analysis of Transcriptomes of depolarized  mouse BMDM cell

summary:
Purpose:Mouse BMDM is the universal cell type of studying innate immunity.This study was to analyze LPS induced innate immune respone and the relationship between the membrane potential and  LPS induced innate immune respone
Methods: WT  BMDM cells were treated with or without LPS for 6 hours in the pressence of membranepotential depolarization stimuli. Then mRNA profiles of these samles were generated by High-throughput sequencing analysis, in triplicate, using Illumina HiSeq /Novaseq or MGI2000. And the differencial mRNA profiles were analyzed.
Results: mRNA profiles of more than 20000 genes were analyzed, and differencial expression profiles were compared .
Conclusions: Our study represents the first detailed analysis of transcriptomes of WT and membrane potential depolarized macrophages, with biologic replicates, generated by RNA-seq technology. This data was useful to analyze the relationship between membrane potential and  LPS induced innate immune respone

overall_design: mRNA profiles of mouse BMDM treated with LPS and KCl or Gramicidin  were generated by High-throughput sequencing, in triplicate, using Illumina HiSeq /Novaseq or MGI2000.


title: Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [splicing]

city: Farmington

first: Anthony

last: Vella

address: 263 Farmington Ave

institute: UConn Health

summary: Here, we provide deep RNA-seq from mouse antigen-specific CD8+ T cells in naïve, antigen-primed, and antigen-primed plus costimulated states. This was used to measure splicing changes between groups.

overall_design: 3 groups: Naïve CD8+ T cells from OT-I transgenic mice, adoptively transferred antigen-primed CD8+ T cells, adoptively transferred antigen-primed & costimulated CD8+ T cells

first: Timofey

last: Karginov

first: Antoine

last: Ménoret


title: Acute ethanol challenge differentially regulates expression of Growth Factors and miRNA expression profile of whole tissue of the dorsal hippocampus

status: Public on Apr 03 2022

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Acute ethanol exposure produces rapid alterations in neuroimmune gene expression that are both time- and cytokine-dependent. Interestingly, adolescent rats, who often consume binge-like quantities of alcohol, displayed reduced neuroimmune responses to acute ethanol challenge. However, it is not known whether growth factors, a related group of signaling factors, respond to ethanol similarly in adults and adolescents. To test this, adolescent and adult Sprague Dawley rats of both sexes were injected with either ethanol or saline, and brains were harvested 3 hr post-injection for assessment of growth factor, cytokine, or miRNA expression. RNASeq revealed a rapid suppression of 12 miRNA species. Of the miRNA affected by ethanol, the majority were related to inflammation or cell survival and proliferation factors, including FGF2, MAPK, NFκB, and VEGF.

overall_design: Adult male Sprague Dawley rats (n=8 per group, N= 16) were injected with ethanol (4 g/kg) in early adulthood (P70-80) and euthanized 3 hr later. Brain tissue sections were submitted to RNAseq including enrichment for miRNA in the sample similar to that used previously (Ignacio, Mooney, & Middleton, 2014). For each rat, 1 μg of total RNA was purified using the TruSeq Small RNA Sample Prep kit (Illumina, San Diego, CA, USA) and subsequent gel purification for small (20-30 nt) RNA species. Libraries were indexed and multiplexed in sets of 8 (6 sets total) prior to sequencing (single-end, 37 cycles) using Reagent Kit v3 reagents on a MiSeq Benchtop Sequencer (Illumina, San Diego, CA, USA).

first: Thaddeus

last: Barney

first: Terrence

last: Deak


title: Mitochondrial mutations alter endurance exercise response and determinants in mice

status: Public on Apr 01 2022

city: Philadelphia

first: Patrick

middle: Michael

last: Schaefer

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: RNA Sequencing of skeletal muscle and heart of mice with distinct mitochondrial mutations revealed a differential transcriptomic response to endurance exercise training and altered determinants of exercise capacity and response.

overall_design: We studied five mouse strains with distinct mitochondrial mutations on the C57BL/6Eij (Nnt+/+) background. Control B6 mice, ND5 mice (ND5 m.12352C>T, ND5S204F), ND6 mice (ND6 m.13997G>A, ND6P25L), CO1 mice (CO1m.6589T>C , CO1V421A) and ANT1 mice (ANT1, Slc25a4-/-). Mice were exercise trained (50% of maximal running capacity, every 2nd day, 45min, for a total of 8 weeks) or non-exercised, exercise capacity was tested prior and following that time period and mice were sacrificed (cervical dislocation) 6 days after the last training session. The soleus muscle and heart were flash frozen and RNASeq was performed. Differential gene expression and GSEA between strains and between exercised and non-exercised for each strain was performed. In addition, expression data of every mouse were correlated to the exercise capacity (running time and VO2max) and exercise response ( delta running time and delta VO2max). For heart, RNASeq was correlated to ejection fraction of every mouse measured by echocardiography.

middle: M

first: Komal

last: Rathi

first: Arrienne

last: Butic

first: Wendy

last: Tan

first: Katherine

last: Mitchell

first: Douglas

last: Wallace


title: Antigen-specific CD8+ T cell transcriptome and splicing changes after costimulation in vivo [Costimulation CD8 Repeat]

summary: Here, we provide a dataset from a repeat RNA-seq from mouse antigen-specific CD8+ T cells in naïve, antigen-primed, and antigen-primed plus costimulated states. These were used to measure splicing changes between groups and compare levels of RNA Binding Protein transcript expression.


title: Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia

city: Davis

first: Alex

last: Nord

state: CA

address: 1544 Newton Court

department: Neurobiology, Physiology, & Behavior

institute: University of California, Davis

summary: Enhancers integrate transcription factor signaling pathways that drive cell fate specification in the developing brain. We paired enhancer labeling and single-cell RNA-sequencing (scRNA-seq) to delineate and distinguish specification of neuronal lineages in mouse medial, lateral, and caudal ganglionic eminences (MGE, LGE, and CGE) at embryonic day (E)11.5. We show that scRNA-seq clustering using transcription factors improves resolution of regional and developmental populations, and that enhancer activities identify specific and overlapping GE-derived neuronal populations. First, we mapped the activities of seven evolutionarily conserved brain enhancers at single-cell resolution in vivo, finding that the selected enhancers had diverse activities in specific progenitor and neuronal populations across the GEs. We then applied enhancer-based labeling, scRNA-seq, and analysis of in situ hybridization data to distinguish transcriptionally distinct and spatially defined subtypes of MGE-derived GABAergic and cholinergic projection neurons and interneurons. Our results map developmental origins and specification paths underlying neurogenesis in the embryonic basal ganglia and showcase the power of scRNA-seq combined with enhancer-based labeling to resolve the complex paths of neuronal specification underlying mouse brain development.

overall_design:
Single-cell RNA-sequencing of ganglionic eminences in E11.5 mouse brain.

The file GSE199352_LMOlist.csv.gz at the foot of this record contains the sample barcodes and associated enhancer information.

first: Linda

last: Su-Feher

first: Anna

last: Rubin

first: Shanni

last: Silberberg

first: Rinaldo

last: Catta-Preta

first: Kenneth

last: Lim

first: Athena

middle: R

last: Ypsilanti

first: Iva

last: Zdilar

first: Christopher

last: McGinnis

first: Gabriel

middle: L

last: McKinsey

first: Thomas

last: Rubino

first: Michael

last: Hawrylycz

first: Carol

last: Thompson

first: Zev

last: Gartner

first: Luis

last: Puelles

first: Hongkui

last: Zeng

first: John

last: Rubenstein


title: Single-cell profiling of histone modifications and transcription in developmental systems with EpiDamID [mouse EB]

first: Jop

last: Kind

summary: We developed EpiDamID, an adaptation of existing DamID protocols that extends their applicability to histone PTMs.

overall_design: Profiling H3K27me3 and Ring1B in single-cells of Embryonic Bodies at day 7, 10 and 14 days post aggregation with scDam&T-seq.

first: Franka

last: Rang

first: Kim

last: de Luca

first: Sandra

last: de Vries

first: Ellen

last: Boele

first: Christian

last: Valdes-Quezada

first: Phong

last: Nguyen

first: Isabel

last: Guerreiro

first: Yuko

last: Sato

first: Hiroshi

last: Kimura

first: Jeroen

last: Bakkers


title: Single-cell profiling of histone modifications and transcription in developmental systems with EpiDamID [zebrafish]

overall_design: Profiling H3K9me3 in zebrafish 15-somite embryos with scDam&T-seq.


title: Single-cell profiling of histone modifications and transcription in developmental systems with EpiDamID [RPE1]

overall_design: Profiling diverse histone post-translational modifications in RPE1 cells using EpiDamID.


title: Serotonin limits generation of chromaffin cells during adrenal organ development

city: Vienna

first: Irina

last: Poverennaya

state: Österreich

address: Spitalgasse 4 / Medizinishe Universitat Wien, Zentrum fur Hirnforschung

department: Neuroimmunology

country: Austria

institute: Medical University of Vienna

summary: Adrenal glands are the major organs releasing catecholamines and regulating our stress response. The mechanisms balancing generation of adrenergic chromaffin cells and protecting against neuroblastoma tumors are still enigmatic. Here we revealed that serotonin (5HT) controls the numbers of chromaffin cells by acting upon their immediate progenitor “bridge” cells via 5-hydroxytryptamine receptor 3A (HTR3A), and the aggressive HTR3Ahigh human neuroblastoma cell lines reduce proliferation in response to HTR3A-specific agonists. In embryos (in vivo), the physiological increase of 5HT caused a prolongation of the cell cycle in “bridge” progenitors leading to a smaller chromaffin population and changing the balance of hormones and behavioral patterns in adulthood. These behavioral effects and smaller adrenals were mirrored in the progeny of pregnant female mice subjected to experimental stress, suggesting a novel maternal-fetal link that controls developmental adaptations. Finally, these results corresponded to a size-distribution of adrenals found in wild rodents with different coping strategies.

overall_design: We isolated individual cells from AGM region or from the dissected intact adrenal glands with surrounding tissue from human embryos at post-conception weeks 5, 6, and 7 and subjected them to single-cell transcriptomics sequencing using 10x Chromium approach.

first: Polina

last: Kameneva

first: Victoria

middle: I

last: Melnikova

first: Maria

last: Kastriti

first: Anastasia

last: Kurtova

first: Emil

last: Kryukov

first: Aliia

last: Murtazina

first: Louis

last: Faure

first: Artem

middle: V

last: Artemov

first: Tatiana

last: Kalinina

first: Nikita

last: Kudryashov

first: Michael

last: Bader

first: Jan

last: Skoda

first: Petr

last: Chlapek

first: Lucie

last: Curylova

first: Lukas

last: Sourada

first: Jakub

last: Neradil

first: Marketa

last: Tesarova

first: Massimo

last: Pasqualetti

first: Patricia

last: Gaspar

first: Vasily

last: Yakushov

first: Boris

last: Sheftel

first: Tomas

last: Zikmund

first: Jozef

last: Kaiser

first: Erik

last: Sundström

first: Kaj

last: Fried

first: Natalia

last: Alenina

first: Elena

last: Voronezhskaya

first: Igor

last: Adameyko


title: Single-cell profiling of histone modifications and transcription in developmental systems with EpiDamID [mouse ESC]

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

institute: Hubrecht Institute

overall_design: Profiling H3K27me3 and H4K20me1 in single mouse embryonic stem cells with scDam&T-seq.

first: Franka

last: Rang

first: Kim

last: de Luca

first: Sandra

last: de Vries

first: Ellen

last: Boele

first: Christian

last: Valdes-Quezada

first: Phong

last: Nguyen

first: Isabel

last: Guerreiro

first: Yuko

last: Sato

first: Hiroshi

last: Kimura

first: Jeroen

last: Bakkers


title: Role and diagnostic performance of host epigenome in respiratory morbidity after RSV infection: the EPIRESVi study

city: Santiago de Compostela

first: Sara

last: Pischedda

state: A Coruña

address: Avenida da Choupana s/n

department: Instituto de Investigación Sanitaria de Santiago de Compostela

institute: Hospital Clinico Universitario de Santiago de Compostela

type: Methylation profiling by genome tiling array

summary: Infinium MethylationEPIC was used to analyze the DNA methylation changes related to the development of wheezing and / or asthma induced after RSV infection.

overall_design: DNA was extracted from whole blood collected from 77 participants. The treated DNA was hybridized to the Illumina Infinium MethylationEPIC BeadChip.

first: Irene

last: Rivero-Calle

first: Alberto

last: Gómez-Carballa

first: Miriam

last: Cebey-López

first: Ruth

last: Barrel-Arca

first: Jose

last: Gómez-Rial

first: Jacobo

last: Pardo-Seco

first: María

last: Curras-Tuala

last: Viz-Lasheras

first: Xabi

last: Bello

first: Ana

middle: B

last: Crujeiras

first: Ángel

last: Díaz-Lagares

first: Maria

middle: T

last: González-López

first: Federico

last: Martinon-Torrez

first: Antonio

last: Salas


title: Single-cell profiling of histone modifications and transcription in developmental systems with EpiDamID [bulk ChIP-seq]

first: Jop

last: Kind

overall_design: Profiling diverse histone post-translational modifications in mouse embryonic stem cells and RPE1 cells with ChIP-seq.

first: Franka

last: Rang

first: Kim

last: de Luca

first: Sandra

last: de Vries

first: Ellen

last: Boele

first: Christian

last: Valdes-Quezada

first: Phong

middle: D

last: Nguyen

first: Isabel

last: Guerreiro

first: Yuko

last: Sato

last: Kimura


title: The Arabidopsis F-box protein FBW2 degrades AGO1 to avoid spurious loading of illegitimate small RNA [PARE-seq]

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

summary: RNA silencing is a conserved mechanism in eukaryotes and is involved in development, heterochromatin maintenance and defense against viruses. In plants, ARGONAUTE1 (AGO1) protein plays a central role in both microRNA (miRNA) and small interfering RNA (siRNA)-directed silencing and its expression is regulated at multiple levels. Here we report that the F-box protein FBW2 targets proteolysis of AGO1 by a CDC48-mediated autophagy mechanism. We found that FBW2 assembles an SCF complex that recognizes the MID-PIWI domain of AGO1 and requires its C-terminal domain containing a GW motif for AGO1 turnover. We show that FBW2 has a preference for unloaded AGO1 and also for some mutated forms of the protein. FBW2 loss of function increases RNA silencing activity, but does not lead to strong growth or developmental defects. However, under conditions in which small RNA production or accumulation is affected, the failure to degrade AGO1 in fbw2 mutants becomes more deleterious for the plant. Hence, we show that the non-degradable AGO1 protein assembles high molecular complexes and binds illegitimate small RNAs.

overall_design: PARE seq profiling of five different Arabidopsis mutants and the corresponding wildtype (Col0) with 3 biological replicates each from Total RNA.

last: Baldrich

first: Thibaut

last: Hacquard

first: Marion

last: Clavel

first: Esther

last: Lechner

first: Imma

last: Pérez-Salamó

first: Mikhail

last: Schepetilnikov

first: Benoît

last: Derrien

first: Marieke

last: Dubois

first: Nicolas

last: Baumberger

first: Hervé

last: Vaucheret

first: Blake

last: Meyers

first: Pascal

last: Genschik


title: KLF15 and PPARδ cooperativity in the orchestration of lipid metabolism

status: Public on Mar 31 2022

city: Pittsburgh

first: Erica

middle: Kai Yan

last: Fan

state: Pennsylvania

address: 3471 Fifth Ave

institute: University of Pittsburgh

summary: We characterize the KLF15 cistrome in vivo in skeletal muscle and find that the majority of KLF15 binding is localized to distal intergenic regions and associated with genes related to circadian rhythmicity and lipid metabolism. We identify critical interdependence between KLF15 and the nuclear receptor PPARδ in the regulation of lipid metabolic gene programs. We further demonstrate that KLF15 and PPARδ co-localize genome-wide, interact, and are dependent on one another to exert their transcriptional effects on target genes.

overall_design: Examination of transcription factor cooperativity in genome-wide regulation of lipid metabolism in skeletal muscle

first: Liyan

first: David

last: Sweet

middle: K

first: Domenick

last: Prosdocimo

first: Annmarie

last: Madera

first: Zhen

last: Jiang

first: Roshan

last: Padmanabhan

first: Saptarsi

last: Haldar

first: Vinesh

last: Vinayachandran

first: Mukesh

last: Jain


title: Single-cell profiling of histone modifications and transcription in developmental systems with EpiDamID

first: Jop

last: Kind

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

sample_organism:
Danio rerio
Homo sapiens
Mus musculus

platform_organism:
Danio rerio
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The effect of early life social stress on mouse Ventral Tegmental Area transcriptomic profile

city: Rome

first: Daniela

last: Palacios

address: Largo Francesco Vito 1

country: Italy

institute: Università Cattolica del Sacro Cuore

summary: This study investigated the impact of  psychosocial stress experienced during adolescence on the development of the brain dopaminergic system. The experiment was designed to evaluate the transcriptomic changes in the ventral tegmental area of mouse brain after one week of repeated exposure to a threatening mouse during preadolescence (P14-P21).

overall_design: We performed comparison between the ventral tegmental area mRNA profiles of P21 Social Stressed (SS) mice (n=5)  and P21 unhandled control (CTR) (n=5)  mice - two experimental groups.

first: Clarissa

last: Catale

first: Constantin

last: Heil

first: Luisa

last: Lo Iacono

first: Valeria

last: Carola


title: The Arabidopsis F-box protein FBW2 degrades AGO1 to avoid spurious loading of illegitimate small RNA [ncRNA-Seq]

first: Patricia

last: Baldrich Gonzalez

overall_design: small RNA seq profiling of five different Arabidopsis mutants and the corresponding wildtype (Col0) with 3 biological replicates each and two conditions, Total RNA and AGO1-IP RNA.

last: Baldrich

first: Thibaut

last: Hacquard

first: Marion

last: Clavel

first: Esther

last: Lechner

first: Imma

last: Pérez-Salamó

first: Mikhail

last: Schepetilnikov

first: Benoît

last: Derrien

first: Marieke

last: Dubois

first: Nicolas

last: Baumberger

first: Hervé

last: Vaucheret

first: Blake

last: Meyers

first: Pascal


title: Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate [Iso-seq]

city: St Paul

first: Shaun J

middle: J

last: Curtin

email: shaun.curtin@usda.gov, curti242@umn.edu

state: MN

address: 1991 Upper Buford Circle, 411 Borlaug Hall

department: Agronomy and Plant Genetics

institute: USDA-ARS-PSRU

summary: RNA-seq and Iso-seq reads used used for gene charaterization. Pacbio amplicon sequencing reads used for mutant characterization

overall_design: RNA-seq of 6 tissues of Medicago sativa

first: Susan

last: Miller

first: Melinda

last: Dornbusch

first: Andrew

last: Farmer

first: Raúl

last: Huertas

first: Juan

last: Gutierrez-Gonzalez

first: Nevin

last: Young

first: Deborah

last: Samac

first: Shaun


title: Interferons limit autoantigen-specific CD8+ T-cell expansion in the non-obese diabetic mouse

city: Nedlands

first: Nicola

last: Principe

state: WA

address: 6 Verdun St

institute: University of Western Australia

summary:
Interferon gamma (IFNg) is a proinflammatory cytokine implicated in autoimmune diseases. However, deficiency or neutralization of IFNg have been disappointing in reducing disease.
We characterised islet antigen-specific T cells in non-obese diabetic (NOD) mice lacking all three IFN receptor genes. Diabetes was minimally affected, however, at 125 days of age antigen-specific CD8+ T cells, quantified using major histocompatibility complex class I tetramers, were present in 10-fold greater numbers in Ifngr mutant NOD mice.
T cells from Ifngr mutant mice had increased proliferative responses to interleukin 2 (IL-2). They also had reduced phosphorylated STAT1 and its target gene, suppressor of cytokine signalling 1 (SOCS-1).
IFN-g controls the expansion of antigen-specific CD8+ T cells by mechanisms that include increased SOCS-1 expression that regulates IL-2 signaling. The expanded CD8+ T cells are likely to contribute to normal diabetes progression despite reduced inflammation in Ifngr mutant mice.

overall_design: Bulk TCRβseq of IGRP-tetramer positive CD8 T cells and non-tetramer CD8+CD44+ T cells sorted from peripheral lymphoid organs (PLO) of 4 wild-type NOD mice and 4 Ifngr1-mutant NOD mice at 125 days of age. Each sample represents an individual biological replicate (i.e. no duplicate samples from the same mouse).

first: Jonathan

last: Chee


title: Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate [RNA-seq]

overall_design: Iso-seq of 6 tissues of Medicago sativa


title: The Arabidopsis F-box protein FBW2 degrades AGO1 to avoid spurious loading of illegitimate small RNA

first: Patricia

last: Baldrich Gonzalez


title: Deciphering responses of the fetal suprachiasmatic nuclei to the rhythmic maternal signals using omics approach

city: Prague 4

first: Martin

last: Sládek

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology of the Czech Academy of Sciences

summary: We report circadian (time series, circadian time 0, 3, 6, 9, 12, 18, 21h) transcriptomic analysis of mouse fetal (embryonic day 17) suprachiasmatic nuclei (SCN) from either sham operarated ad libitum fed mothers (group A) or from SCN-lesioned mothers on resctricted feeding regime. The analysis revealed low amplitude rhythms in the fetal SCN driven by maternal SCN and/or maternal feeding behavior.

overall_design: Examination of fetal SCN tissue from two groups of mothers on different feeding regime with intact or destroyed cental pacemaker, by RNAseq in a time series

first: Philipp

last: Greiner

first: Pavel

last: Houdek

first: Alena

last: Sumová


title: Macrophage-produced VEGFC is induced by efferocytosis to resolve inflammation and  improve ventricular function after myocardial infarction (RNA-Seq)

city: Chicago

first: Connor

last: Lantz

state: IL

address: 303 E. Chicago Ave. Ward 4-075

institute: Northwestern University

summary: Recent reports have suggested a protective role for vascular endothelial growth factor C (VEGFC) during acute cardiac lymphangiogenesis post MI. Glinton et al. report that defective efferocytosis by macrophages after experimental MI leads to a reduction in cardiac lymphangiogenesis and Vegfc expression.

overall_design: Bulk mRNA sequencing 9 days post injury of cardiac extracts of Vegfcfl/fl versus Vegfcfl/fl;LysMCre mice subjected to coronary artery occlusion

first: Kristofor

last: Glinton

first: Edward

last: Thorp


title: Histone functions as a cell-surface receptor for AGEs

city: Bunkyo-ku

first: Masanori

last: Itakura

state: Tokyo

address: 1-1-1 Yayoi

country: Japan

institute: The University of Tokyo

summary: Reducing sugars can covalently react with proteins to generate a heterogeneous and complex group of compounds called advanced glycation end products (AGEs). AGEs are generally considered as pathogenic molecules, mediating a pro-inflammatory response and contributing to the development of a number of human diseases. However, the intrinsic function of AGEs remains to be elucidated. We now provide multiple lines of evidence showing that AGEs can specifically bind a cell-surface protein and regulate its functions. To identify cellular binding partners for AGEs, we used dehydroascorbic acid (DHA)-modified serum albumins as one of the AGEs to screen for binding proteins in the lipid raft fraction prepared from mouse splenocytes and identified histone localized on the cell-surface as an AGE-binding protein. Histone ubiquitously recognized AGEs, including proteins modified with glucose and its metabolites. AGEs inhibited the binding of plasminogen to the histone component H2B which functions as a cell-surface plasminogen receptor on monocytes/macrophages. Moreover, AGEs regulated the recruitment of monocytes/macrophage to the site of inflammation. Our discovery of histone as a cell-surface receptor for AGEs suggests that, beside our common concept of AGEs as danger-associated molecular patterns mediating a pro-inflammatory response, they may also be involved in the homeostatic response via binding to histone.

overall_design: We evaluated transcripts in peritoneal macrophages derived from mice treated with BSA or AGEs by RNA-seq.

first: Koji

last: Uchida


title: Group IVE Cytosolic Phospholipase A2 Limits Psoriatic Inflammation by Mobilizing the Anti-inflammatory Lipid N-Acylethanolamine

city: Tokyo

first: Tetsuya

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

summary: Psoriasis is an inflammatory disorder characterized by keratinocyte hyper-proliferation and Th17-type immune responses. However, the roles of bioactive lipids and the regulation of their biosynthesis in this chronic skin disease are not fully understood. Herein, we show that group IVE cytosolic phospholipase A2 (cPLA2epsilon/PLA2G4E) plays a counterregulatory role against psoriatic inflammation by producing the non-canonical anti-inflammatory lipid N-acylethanolamine (NAE). Lipidomics analysis of mouse skin revealed that NAE species and their precursors (N-acyl-phosphatidylethanolamine and glycerophospho-N-acylethanolamine) were robustly increased in parallel with the ongoing process of imiquimod (IMQ)-induced psoriasis, accompanied by a marked upregulation of cPLA2epsilon in epidermal keratinocytes. Genetic deletion of cPLA2epsilon/Pla2g4e exacerbated IMQ-induced ear swelling and psoriatic marker expression, with a dramatic reduction of NAE-related lipids in IMQ-treated, and even normal, skin. Stimulation of cultured human keratinocytes with psoriatic cytokines concomitantly increased PLA2G4E expression and NAE production, and supplementation with NAEs significantly attenuated the cytokine-induced upregulation of the psoriatic marker S100A9. Increased expression of cPLA2epsilon was also evident in the epidermis of psoriatic patients. These findings reveal for the first time the in vivo role of cPLA2epsilon, which is highly induced in the keratinocytes of the psoriatic skin, promotes the biosynthesis of NAE-related lipids, and contributes to limiting psoriatic inflammation.

overall_design: We compared gene expression in Pla2g4e-/- (knockout) skin at P0 with Pla2g4e+/+ (wild type) controls. Individual array samples were generated by pooling equal amounts of total RNA derived from skin of 5 animals.

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: RNA sequence data from liver-specific Pten/Traf3 knockout mice [HepG2 RNA-seq]

city: Suita

first: Takahiro

last: Kodama

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka university, Graduate School of Medicine

summary:
Intrahepatic cholangiocarcinoma (ICC) is known to have a poor prognosis among primary liver cancers.
We created a vitro model of cholangiocarcinogenesis using HepG2 with specifically knockdown of Pten and Traf3.
RNA sequence was performed with RNA extracted from the liver of mice lacking liver-specific Pten and Traf3.

overall_design: RNA sequence data from Pten/Traf3 knockdown HepG2 cells

first: Yuto

last: Shiode

first: Tetsuo

last: Takehara

first: Daisuke

last: Motooka


title: A Novel platform for single-cell RNA-sequencing and its application in genome medicine [bulk]

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: we describe the utility of this novel platform in the field of genome medicine using a full-length approach to evaluate the relationship between transcriptional and mutational heterogeneity on single cells in dermal fibroblasts derived from patients with Hutchinson-Gilford progeria syndrome (HGPS)

overall_design: Bulk RNA sequencing in order to detrmnie the dynamic range of the assay

first: Maren

last: Sitte

first: Orr

last: Shomroni


title: Arp2/3 complex activity is necessary for mouse ESC differentiation, times formative pluripotency, and enables lineage specification

city: San Francisco

first: Diane

last: Barber

address: 513 Parnassus Ave HSW618

department: Department of Cell & Tissue Biology

institute: University of California San Francisco

summary: Mouse embryonic stem cells (mESCs), a model for differentiation into primed epiblast-like cells (EpiLCs), have revealed transcriptional and epigenetic control of early embryonic development. The control and significance of morphological changes, however, remain less defined. We show marked changes in morphology and actin architectures during differentiation that depend on Arp2/3 complex but not formin activity. Inhibiting Arp2/3 complex activity pharmacologically or genetically does not block exit from naive pluripotency but attenuates increases in EpiLC markers. We find that inhibiting Arp2/3 complex activity delays formative pluripotency and causes globally defective lineage specification as indicated by RNA-sequencing, with significant effects on TBX3-depedendent transcriptional programs. We also identify two previously unreported indicators of mESC differentiation; MRTF and FHL2, which have inverse Arp2/3 complex-dependent nuclear translocation. Our findings on Arp2/3 complex activity in differentiation and the established role of formins in EMT indicate that these two actin nucleators regulate distinct modes of epithelial plasticity

overall_design: A total of 9 RNA libraries were prepared with three paired biological replicates for each condition including control +LIF2i, control 72h -LIF2i, and CK666 72h -LIF2i.

first: Francesca

last: Aloisio


title: Macrophage-produced VEGFC is induced by efferocytosis to resolve inflammation and  improve ventricular function after myocardial infarction

first: Connor

last: Lantz


title: A Novel platform for single-cell RNA-sequencing and its application in genome medicine [cellenone]

overall_design:
CellenONE/ICELL8 novel platform for scRNA-Seq
Additional information in cellenone_demultiplexed.txt


title: Macrophage-produced VEGFC is induced by efferocytosis to resolve inflammation and  improve ventricular function after myocardial infarction (ChIP-Seq)

overall_design: H3K27Ac ChIP-sequencing  of C57BL6J bone marrow derived macrophages after incubation with UV-treated apoptotic Jurkat cells for 6 hours

first: Kristofor

last: Glinton


title: Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate

first: Shaun J

last: Curtin


title: Gene expression analysis of murine endometrial cancer cell lines and murine normal endometrium

city: Kyoto

first: mise

last: yuka

address: 54 Kawahara-cho, Shogoin, Sakyo-ku,

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

summary: Endometrium-specific Cre-Lox deletion of both Pten and Tp53 via regulation of the progesterone receptor promoter is known to generate a spontaneous carcinogenic mouse model of endometrial cancer.  A mouse endometrial cancer cell line, mECC, was established from the uterine carcinoma tumor tissue of its pure strain model generated by backcrossing in C57BL/6 mice. A high-grade endometrial cancer cell line (Highly Progressive mECC: HPmECC) was established by further introducing c-Myc in mECCs. RNA sequencing analysis was performed using cultured HPmECCs and mECCs, as well as primary cultured C57BL/6 normal endometrial cells for assessing the genetic characteristics of HPmECCs.

overall_design: RNA-Seq in murine endometrial cancer cell-lines from C57BL/6 mice with or without overexpressed Myc and normal C57BL/6 mice endometrium.

first: Yuka

last: Mise

first: Tsukasa

last: Baba


title: Transcriptomic profiling of diabetic rats treated with peripherical focused ultrasound (pFUS)

city: Niskayuna

first: John

last: Graf

state: New York

address: One Research Circle

institute: GE Global Research

summary: To better characterize the systemic response of diabetic rats to daily hepatoportal pFUS stimulation, we conducted transcriptomic profiling of different metabolic tissues by RNAseq. For this purpose, we included samples from liver, intestines, kidney, adipose, muscle, pancreas, hypothalamus and blood in the Zucker diabetic fatty (ZDF) and diet induced obese (DIO) rodent models. ZDF rats spontaneously develop type 2 diabetes (T2D) as a result of a missense mutation (fatty, fa) in the leptin receptor gene and develop moderate hyperglycemia spontaneously as a result of the insulin resistance and pancreatic insufficiency.   DIO model uses a high fat/high carbohydrate diet to induce obesity and insulin resistance.  Following development of obesity low dose streptozotocin (STZ) is used to induce a moderate level of pancreatic beta cell death which impairs insulin secretion similar to that seen in later stage T2D. Tissue samples were processed and analyzed after 3 days, 4 weeks, and 7 weeks of 3 minute per day pFUS treatments. All procedures performed were done in accordance with the National Institutes of Health (NIH) Guidelines under protocols approved by the Institutional Animal Care and Use Committee (IACUC) of GE Global Research.

overall_design: Transcriptomic profiles of liver, intestines, kidney, adipose, muscle, pancreas, hypothalamus and blood of ZDF and DIO rats treated with 3 days, 4 weeks, and 7 weeks of 3 minute per day pFUS treatments.

first: Victoria

last: Cotero

first: Chris

last: Puleo


title: Impact of Diet and aPD1 on CD8 metabolism

city: Bethesda, MD

first: Kylynda

middle: C

last: Bauer

state: Maryland

address: Building 10, NIH

institute: NIH-NCI

summary: Only a small fraction of patients with HCC benefit from immune checkpoint inhibitor (ICI) therapy. Recently published studies suggest that HCC in patients with NASH does not respond the ICI therapy. Indeed, we demonstrate that anti-PD1 therapy is not working in several murine NASH models. CD8+ T cells were identified as the effector of anti-PD1 therapy. We observed a proinflammatory phenotype if hepatic CD8+ T cells that does not explain the inefficacy of anti-PD1 therapy in NASH. However, our study revealed an impairment of intratumoral CD8+ T cells movement abilities in NASH. Additionally, a broad reduction of metabolic fitness was observed in hepatic CD8+ T cells NASH. This was restored by metformin treatment. The combination treatment of anti-PD1 and metformin reduced intrahepatic tumor burden in NASH, a finding with important implications for NASH patients. This GEO submission contains raw files for the CD8 nsolver microarray analyses.

overall_design: 12 samples: 3 REG Control (diet = standard mouse chow, no treatment), 3 REG aPD1 (regular diet, aPD1 treated), 3 MCD control (methionine/choline-deficient diet, no treatment), 3 MCD aPD1 (MCD diet, aPD1 treatment)

first: Simon

last: Wabitsch

first: Tim

middle: F

last: Greten


title: A Novel platform for single-cell RNA-sequencing and its application in genome medicine [icell8]

first: Gabriela

last: Salinas

overall_design:
scRNA Seq ICELL8 full length approach
Additional information in icell8_demultiplexed.txt


title: Single cell RNA sequence data from liver-specific Pten/Traf3 knockout mice

first: Takahiro

last: Kodama

summary:
Intrahepatic cholangiocarcinoma (ICC) is known to have a poor prognosis among primary liver cancers.
We created a mouse model of cholangiocarcinogenesis by specifically deleting Pten and Traf3 in the liver.
single cell RNA sequence was performed with RNA extracted from the liver of mice lacking liver-specific Pten and Traf3.

overall_design: single cell RNA sequence data from liver-specific Pten/Traf3 knockout mice

first: Yuto

last: Shiode

first: Tetsuo

last: Takehara

first: Daisuke

last: Motooka


title: Massive expression of cysteine-containing proteins is cytotoxic, manifesting as abnormal morphology in yeast cells

city: okayama

first: Shotaro

last: Namba

state: okayama

address: 3-1-1 tsusimanaka

department: Graduate school of environment and life science

institute: Okayama University

summary: The enhanced green fluorescent protein (EGFP) is considered to be a harmless protein because the critical expression level that causes growth defects is higher than that of other proteins. Here we found that overexpression of EGFP, but not a glycolytic protein Gpm1, triggered the cell elongation phenotype in the budding yeast Saccharomyces cerevisiae. By the morphological analysis of the cell overexpressing each of five fluorescent proteins harboring different properties, we revealed that cysteine content was associated with the cell elongation phenotype. We further confirmed this finding by mutational analysis of an EGFP with additional cysteines, a cysteine-containing glycolytic enzyme Tpi1, and a cysteine-less glycolytic enzyme Gpm1. The abnormal cell morphology triggered by overexpression of EGFP was also observed in the fission yeast Schizosaccharomyces pombe. Overexpression of cysteine-containing protein was toxic, especially at high-temperature, while the toxicity could be modulated by additional protein characteristics. The morphological abnormality seemed to be triggered by the S-S bond-triggered protein aggregation, and by the interaction with a chaperone Ssa1 and the heat shock transcription factor Hsf1. Evolutionary analysis of duplicated genes showed that cysteine toxicity may be an evolutionary bias to exclude cysteine from highly expressed proteins. The overexpression of cysteine-less moxGFP, the least toxic protein revealed in this study, would be a good model system to understand the physiological state of protein burden triggered by ultimate overexpression of harmless proteins.

overall_design: A multicopy plasmid, pTOW40836, was trasnsformed into diploid yeast cells BY4743. The eGFP and moxGFP on the plasmid are expressed from the THD3 promoter. The cells transfected with the empty vector were used as a control and compared with the transcriptome of cells in which eGFP and moxGFP are expressed cells.

first: Hisaaki

last: Kato

first: Shuji

last: Shigenobu

first: Takashi

last: Makino

first: Hisao

last: Moriya


title: RNA sequence data from liver-specific Pten/Traf3 knockout mice

summary:
Intrahepatic cholangiocarcinoma (ICC) is known to have a poor prognosis among primary liver cancers.
We created a mouse model of cholangiocarcinogenesis by specifically deleting Pten and Traf3 in the liver.
RNA sequence was performed with RNA extracted from the liver of mice lacking liver-specific Pten and Traf3.


title: Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer (RRBS)

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

type: Methylation profiling by high throughput sequencing

summary:
Colorectal cancer (CRC) remains the third most common cancer in the US, with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1. DNA methylation and transcriptome analysis was performed to evaluate the rhesus macaque as a model organism to study carcinogenesis, develop immunotherapies and vaccines, and implement chemoprevention approaches pertinent to sporadic MSI-H and LS CRC in humans.

NIH grant(s):

Grant ID: 5 P30 CA016672-44
Grant title: Cancer Center Support Grant
Affiliation: The University of Texas MD Anderson Cancer Center
Grantor: NCI

overall_design: We performed reduced representation bisulfite sequencing (RRBS) in fourteen colorectal tumors and fourteen matched normal mucosa samples

last: Deng


title: Gene expression profiles of ears infected with Staphylococcus aureus at ZT4

city: Setagaya-ku

first: Kosuke

last: Tanegashima

address: 2-1-6 Kamikitazawa

summary:
We analysed the gene expression profiles after infection of Staphylococcus aureus at ZT4 in CXCL14-KO mice. The group of genes categolized as GO defense response (GO: 006952) were upregulated upon a response to Staphylococcus aureus infection.
The expression of IL1b, Cxcl2, and Ccl3 were significantly suppressed in infected ear of Cxcl14-KO compared to that of WT.

overall_design: PBS with or without 10^7 CFUs of S. aureus were injected intradermally into the pinnae of each ear of WT-C57BL/6 or Cxcl14-KO mice using a 30G insulin syringe at ZT4. Their ears were subjected to microarray andlysis after 3 hours post injection.

first: Kojiro

last: Tsujihana

first: Yasumasa

last: Nishito

first: Hitoshi

last: Okamura

first: Takahiko

last: Hara


title: BPTF is essential for murine neocortical development

city: Ottawa

first: Dave

last: Picketts

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

country: Canada

institute: OHRI

summary: Chromatin remodeling complexes modulate DNA accessibility permitting neuronal progenitor cells to proliferate and differentiate to form the mammalian neocortex. In the case of BPTF, the major subunit of a chromatin remodelling complex called NURF, mutations leading to its haploinsufficiency have been linked to cause a recently annotated human neurodevelopmental disorder called NEDDFL (Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies). Patients with this syndrome are mainly characterized with microcephaly and intellectual disability. We conditionally knockout (cKO) the Bptf gene during neocortical neurogenesis to analyze its role during embryonic and postnatal brain development. The Bptf cKO animals reveal significant forebrain hypoplasia. During cortical neurogenesis, the cKOs show a reduction in intermediate neuronal progenitor (INP) cells, an increase in apoptosis as well as a prolonged cell cycle of proliferating progenitors. Similarly, the cKOs have decreased proportions of pyramidal neurons expressing Ctip2 and Foxp1. Lastly, our RNA-seq analysis delineates gene pathways deregulated by Bptf’s removal, which are involved in neurogenesis and neuronal differentiation. Our results indicate that Bptf is critical for murine telencephalon neurogenesis. The hypoplasia demonstrated in the mouse model can resemble the microcephaly displayed by the human NEDFFL patients, highlighting the relevance of chromatin remodelling complexes during intricate neural developmental processes.

overall_design: BPTF Emx1-Cre P0 forebrain mRNA stranded sequenced libraries

first: Gerardo

last: Zapata

first: David


title: Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer

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

NIH grant(s):

Grant ID: 5 P30 CA016672-44
Grant title: Cancer Center Support Grant
Affiliation: The University of Texas MD Anderson Cancer Center
Grantor: NCI

overall_design: Refer to individual Series


title: A genome-wide CRISPR activation screen identifies PRRX2 as a regulator of enzalutamide resistance in prostate cancer [RNA-seq]

status: Public on Mar 30 2022

first: Sarki

last: Abdulkadir

address: 303 E Superior St

summary: We report that PRRX2 mediates enzalutamide resistance by activating the anti-apoptotic BCL2 and theE2F/RB1 cell cycle pathways.

overall_design: We used LNCaP cells to over-express the transcription factor PRRX2 using CRISPR activation. Negative Control (LNCaP-sgNC) and PRRX2 over-expressing cells (LNCaP-sgPRRX2) were treated with the AR inhibitor enzalutamide (5uM) for 7 days. We then studied gene expression changes in both cell lines treated with enzalutamide or DMSO.

first: Yara

last: Rodriguez


title: Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer (RNA-Seq)

summary:
Colorectal cancer (CRC) remains the third most common cancer in the US, with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1. DNA methylation and transcriptome analysis was used to evaluate the rhesus macaque as a model organism to study carcinogenesis, develop immunotherapies and vaccines, and implement chemoprevention approaches pertinent to sporadic MSI-H and LS CRC in humans.

NIH grant(s):

Grant ID: 5 P30 CA016672-44
Grant title: Cancer Center Support Grant
Affiliation: The University of Texas MD Anderson Cancer Center
Grantor: NCI

overall_design: We performed RNA-Seq in 21 colorectal tumors and twenty matched normal mucosa samples


title: MCTR3 reprograms arthritic monocytes to upregulate Arginase-1 and exert pro-resolving and tissue-protective functions in experimental arthritis

city: London

first: Esteban

middle: Alberto

last: Gomez Cifuentes

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary University of London

summary: We aim to demonstrate that pro-resolving mediator maresin conjugate in tissue regeneration 3 (MCTR3) potently regulates join arthritic inflammation as well as bone and cartilage repair.

overall_design: K/BxN serum was administered to C57BL/6 to induce prolong inflammatory arthritis. Mice were treated with monocytes isolated from arthritic mice that were previously incubated with vehicle (n controls = 4) or 1nM MCTR3 (n treatment = 4) . Cells were isolated from paw joints, sorted for CD45+ cells and single cell RNA sequencing was performed.

first: Kimberly

last: Pistorius

first: Lucy

last: Ly

first: Patricia

last: Sousa

last: Gomez

first: Duco

last: Koenis

first: Anna

last: Rodrigues

first: Julie

last: Foster

first: Jane

last: Sosabowski

first: Mark

last: Hopkinson

first: Vinthini

last: Rajeeve

first: Pedro

last: Cutillas

first: Bernd

last: Spurr

first: Andrew

last: Pitsillides

first: Constanino

last: Pitzalis

first: Jesmond

last: Dalli


title: Gas6 improves plaque burden, yet worsens behavior and induces microglial inflammation in the APP/PS1 model of Alzheimer’s disease

city: Rochester

first: O'Banion

last: Kerry

state: United States of America

address: 601 Elmwood Ave

country: USA

institute: University of Rochester

summary: We sought to determine the effects of Gas6 on Alzheimer’s disease pathology through overexpression of Gas6 using an adeno-associated viral vector in the APP/PS1 model of Alzheimer’s disease. 9 month old male and female APP/PS1 and nontransgenic littermates received bilateral stereotactic hippocampal injections of AAV-Gas6 or AAV-control, an attenuated Gas6 protein that does not bind the Axl receptor. One month after injections, mice performed a battery of behavioral tasks and brains were processed for immunohistochemistry, transcriptional analyses, and flow cytometry.

overall_design: Microglia (CD45int CD11b+) were sorted from isolated hippocampi and processed for RNAseq.

first: Laura

last: Owlett

first: Berke

last: Karaahmet

first: John

last: Olschowka

first: M

last: O’Banion