first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

institute: Nestle Institute Of Health Sciences

summary: Fate decisions in the embryo are controlled by a plethora of microenvironmental interactions in a three-dimensional niche. To investigate whether aspects of this microenvironmental complexity can be engineered to direct myogenic human induced pluripotent stem cell (hiPSC) differentiation, we screened cell types present in the developmental or adult stem cell niche in heterotypic suspension embryoids. We identified embryonic endothelial cells and fibroblasts as highly permissive for myogenic specification of hiPSCs. After two weeks of sequential Wnt and FGF pathway induction, these three-component embryoids (iTCEs) are enriched in Pax7 positive embryonic-like myogenic progenitors (eMPs) that can be isolated by flow cytometry. Myogenic differentiation of hiPSCs in iTCEs relies on a specialized structural microenvironment and depends on MAPK, PI3K/AKT, and Notch signaling. After transplantation in a mouse model of Duchenne muscular dystrophy, eMPs repopulate the stem cell niche, reactivate after repeated injury and, compared to adult human myoblasts, display enhanced fusion and lead to stronger muscles. Altogether, we provide a two-week protocol for efficient and scalable suspension-based 3D derivation of Pax7 positive myogenic progenitors from hiPSCs.

overall_design: QuantSeq from human induced pluripotent stem cell (hiPSC), three-component embryoids (TCEs) which comprise of murine growth arrested embryonic fibroblasts - GAeFib (Fibro), murine embryonic endothelial cells - eEC (Endo) and hiPSCs in comination and alone.

first: Omid

last: Mashinchian

first: Filippo

last: De Franceschi

first: Sina

last: Nassiri

first: Joris

last: Michaud

first: Eugenia

last: Migliavacca

first: Patrick

last: Aouad

first: Sylviane

last: Metairon

first: Solenn

last: Pruvost

first: Sonia

last: Karaz

first: Paul

last: Fabre

first: Thomas

last: Molina

first: Pascal

last: Stuelsatz

first: Nagabhooshan

last: Hegde

first: Emmeran

last: Le Moal

first: Gabriele

last: Dammone

first: Nicolas

last: Dumont

first: Matthias

last: Lutolf

middle: N

first: C

last: Bentzinger


title: uscfDNA-oriented sequencing pipeline profiling the cell-free DNA populations in plasma

status: Public on May 10 2022

city: Los Angeles

first: Jordan

last: Cheng

country: USA

institute: UCLA

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

overall_design: Refer to individual Series


title: Microarray analysis of embryonic E15 mouse gonads from control male, female and Amh; Inhbb dKO males

status: Public on May 12 2022

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Fate determination and maintenance of fetal testes in most mammals occur cell autonomously as a result of the action of key transcription factors in Sertoli cell. In the mouse testis AMH and Activin B are required for the maintenance of Sertoli  cell fate. In the absence of both AMH and Activin B initial testis differentiation (E12.5) occurs normally but, by embryonic day 15.5, Sertoli cells at the testis poles transdifferentiate into granulosa cells.

overall_design: We compared the transcriptional profile of control testis, control ovaries and dKO  (Amh-/-; Inhbb-/-) testis at embryonic day 15.5

first: Karina

middle: F

last: Rodriguez

first: Humphrey

middle: H

last: Yao


title: Microarray analysis of embryonic E12.5 mouse gonads from control male, female and Amh; Inhbb dKO males

summary: Fate determination and maintenance of fetal testes in most mammals occur cell autonomously as a result of the action of key transcription factors in Sertoli cell. In the mouse testis AMH and Activin B are required for the maintenance of Sertoli  cell fate. By E12.5, the testis of the dKO male are comparable with the conrol testis as Amh and Activin B are not required for the initial testis differentiation. By E15.5 Sertoli cells at the testis poles in the dKO transdifferentiate into granulosa cells.

overall_design: We compared the transcriptional profile of control testis, control ovaries and dKO testis (Amh-/-; Inhbb-/-) testis at E12.5


title: SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination

status: Public on May 11 2022

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

summary: The shieldin (SHLD) complex, composed of SHLD1, SHLD2, SHLD3 and MAD2L2/REV7, acts downstream of 53BP1 to counteract DNA double-strand break (DSB) end-resection and promote non-homologous end-joining (NHEJ). While 53BP1 is essential for immunoglobulin heavy chain class switch recombination (CSR), long-range V(D)J recombination and for repair of RAG-induced DSBs in XLF-deficient cells, the role of SHLD in these activities remains elusive. Here, we report that contrary to 53BP1, SHLD1 is dispensable for lymphocyte development and V(D)J recombination, even in the sensitized XLF-deficient background or for the joining of distant V(D)J segments. By contrast, SHLD1 restricts resection at AID-induced DSB ends in both NHEJ-proficient and NHEJ-deficient B cells, providing an end-protection mechanism that permits productive CSR. Finally, we show that this end-protection function is required for orientation-specific joining of AID-initiated DSBs. We propose that 53BP1 promotes V(D)J recombination and CSR through two distinct mechanisms; the synapsis of V(D)J segments and switch regions within chromatin independently of SHLD and the protection of AID-DSB ends against resection mediated by SHLD.

overall_design: The gDNA was extracted from the mouse splenic B cells with different genotypes. Then gDNA was used for CSR-HTGTS to analyze the CSR profilings and the CSR junction features.

first: Xuefei

last: Zhang

first: Frederick

middle: W

last: Alt

first: Estelle

last: Vincendeau

first: Chloé

last: Lescale


title: Human cytomegalovirus IE2 both activates and represses initiation and modulates elongation in a context-dependent manner

city: Iowa City

first: David

last: Price

state: IA

address: 431 Newton Road

department: Department of Biochemistry and Molecular Biology

institute: University of Iowa

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Using PRO-Seq, which profiles nascent transcripts, and a recently developed DFF-ChIP approach that informs on local chromatin environment, we show that IE2 controls viral gene transcription in three distinct capacities during late HCMV infection and reveal mechanisms involving direct binding of IE2 to viral DNA. IE2 represses a subset of viral promoters by binding within the target core promoter region, blocking the assembly preinitiation complexes (PICs). Remarkably, IE2 forms a repressive complex at the major immediate-early promoter region involving direct association of IE2 with nucleosomes and TBP. IE2 activates transcription by binding proximal to, but not within, core promoter regions. In addition, evidence is provided that IE2 functions as a direct roadblock to transcription elongation. At one locus, this function of IE2 is demonstrated to be important for the synthesis of a spliced RNA. Consistent with the minimal observed effects of IE2 depletion on host gene transcription, IE2 only sparingly engages the host genome.

overall_design: HCMV IE2-FKBP TB40/E and Towne strain viruses were developed as described in our previous study. Both raw and processed PRO-Seq data generated from that study are available under GEO accession number GSE139114. For RNA-Seq data generation, HFF were infected for 96 h with Towne IE2-FKBP virus and treated for the last 6 h of infection with DMSO or the last 6 or 12 h of infection with dTAG. Total RNA was isolated, processed for library generation, and sequenced as described in the manuscript. For this study, a TB40/E IE2-GFP virus was developed using GalK recombination, as described in the methods. HFF were infected for 48 h with TB40/E IE2-GFP virus. Infected cells were harvested for utilized for standard ChIP-Seq or DFF-ChIP using GFP nanobody conjugated agarose as described in the manuscript. Sequencing data were processed as described. Raw and processed data files are provided here.

first: Christopher

middle: B

last: Ball

first: Ming

last: Li

first: Mrutyunjaya

last: Parida

first: Jeffery

middle: L

last: Meier


title: Aldh2 dependent formaldehyde metabolism fuels purine demands in melanocyte stem cells

status: Public on May 09 2022

city: Edinburgh

first: Eleanor

middle: Elizabeth

last: Patton

address: MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road

country: United Kingdom

institute: MRC Human Genetics Unit, Institute of Genes and Cancer, University of Edinburgh

summary: In the McSC lineage in zebrafish, Aldh2 activity is an important source of formate through its metabolism of its substrate formaldehyde. This formate is required as input into the folate cycle, in particular de novo purine biosynthesis. This scRNA-seq experiment was conducted to investigate the global effects of Aldh2 inhibition on the transcriptomes of isolated McSCs.

overall_design: Tg(mitfa:GFP;crestin:mCherry) zebrafish embryos express GFP and mCherry in regenerating McSCs. Embryos were treated with an Aldh2 inhibitor (CVT-10216), or DMSO (vehicle control) from 24hpf onwards. Embryonic melanocytes were ablated by co-treating with MoTP from 24hpf, and McSC melanocyte regeneration stimulated by washing MoTP out at 64hpf. After 8 hours of melanocyte regeneration, the trunk region of embryos was dissected from the head, and crestin:mCherry+, mitfa:GFP+ or double+ cells isolated by FACs. These cells were then processed for 10x

first: Hannah

last: Brunsdon

first: E

middle: E


title: Genome-wide maps and functional peak analysis of ultrashort single-stranded cell-free DNA (uscfDNA) and mononucleosomal cell-free DNA (mncfDNA) in human plasma

first: Jordan

summary: We report the application of an uscfDNA-oriented sequencing pipeline profiling the cell-free DNA populations in plasma. The uscfDNA sequencing pipeline include two uscfDNA-optimized extraction methods (QiaM and SPRI) and one control extraction method (QiaC).  Final libraries are made with a single-stranded library prepartion kit. We generate genome-wide maps revealing the presence of an uscfDNA population (25-99bp) in addition to the mncfDNA (100-250bp).

overall_design: Whole-genome sequencing of single-stranded libraries made from extracted cfDNA extracted with QiaC, QiaM, and SPRI methods.

first: Marco

last: Morselli


title: mRNA expression profiles analysis of crocin mitigated triptolide-induced toxicity in mouse  liver tissues

status: Public on May 06 2022

city: Zhengzhou

first: Min

last: Yan

state: Henan

address: East Jinshui Road No.156

country: China

institute: Henan University of Chinese Medicine

summary: Clinical use of triptolide (TP) is restricted due to severe toxicity. This study assessed the protective effect of crocin (CR) as a natural antioxidant against TP-induced toxicity. Mouse Liver tissues were selected from the Control, MTP, and MTP+CR groups for transcriptome studies.

overall_design: The mice were randomly placed in the following 3 groups (n=4): A. Normal saline (NC); B. 300μg/kg Moderate-dose TP (MTP); C. 300μg/kg Moderate-dose TP + 100 mg/kg CR (MTP+CR);  The mice were administrated the treatments daily via oral gavage for 7 days at a volume of 0.2 ml/10 g per dose.

first: Yinyin

first: Junwei

last: Zhao

first: Xiangxiang

last: Wu

first: Huahui

last: Zeng


title: Inhibition of DYRK1A promotes cardiomyocyte proliferation and heart repair after myocardial infarction [RNA-Seq]

city: Chongqing

first: Cong

last: Lan

state: Chognqing

address: 10 Changjiangzhilu Road

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University

summary: To explore effect of DYRK1A silencing on gene expression of primary cultured cardiomyocytes isolated from 1-day-old SD rats

overall_design: Neonatal cardiomyocytes in primary culture were transfected with siRNA against DYRK1A (si-DYRK1A) or scramble siRNA (si-NC) and cultured for 48 h to prepare sample (three biological replicates for each group), and RNA-sequencing (RNA-Seq) were performed using mRNA extracted from these samples.

first: Caiyu

last: Chen

first: Shuang

last: Qu

first: Nian

last: Cao

first: Hao

last: Luo

first: Cheng

last: Yu

last: Wang

first: Yuanzheng

last: Xue

first: Xuewei

last: Xia

first: Chao

last: Fan

first: Hongmei

last: Ren

first: Pedro

middle: A

last: Jose

first: Zaicheng

last: Xu

first: Gengze

first: Chunyu


title: Mitochondrial RNA modifications shape metabolic plasticity in metastasis

status: Public on May 05 2022

city: Heidelberg

first: Sylvain

last: Delaunay

address: Im Neuenheimer Feld 280

department: Tumor BIology

country: Germany

institute: German Cancer Research Center (DKFZ)

type: Methylation profiling by high throughput sequencing

summary: To investigate the implication of methylation and formylation of mitochondrial tRNAs on cancer development, we performed an untargeted and targeted (mt-tRNAMET) BS-seq and fCABseq.

overall_design: Comparative m5C and f5C profiling analysis of BS-seq and fCABseq data for human derived keratynocytes (NHEK) and FaDu human cell line.

first: Michaela

last: Frye

first: Sabine

last: Dietmann

first: Agnes

last: Hotz-Wagenblatt


title: Inhibition of DYRK1A promotes cardiomyocyte proliferation and heart repair after myocardial infarction

first: Cong

last: Lan


title: WGBS and RNA-seq of Danio rerio in HSPC generation

city: Tianjin

first: chao

last: tang

state: Tianjin

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

summary: In this study, we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First, we generated a comprehensive DNA methylation landscape of EHT, which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1-deficient embryos, we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically, we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling, thus contributing to defects in the EHT in dnmt1-deficient embryos. Herein, we identified that DNA methylation, as epigenetic regulator, participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish.

overall_design: WGBS and RNA-seq of Danio rerio in EC,HE and HSPC.

first: Lu

first: Ping

last: Zhu


title: In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

city: Berlin

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

institute: Max Delbrück Center for Molecular Medicine (MDC)


title: The genetic profile of  murine primary cells cultured from tumors (MPC)

city: Suita

first: Shotaro

last: Tatekawa

state: Osaka

address: 2-2(D10), Yamadaoka, Suita-city

department: Departments of Radiation Oncology,

country: Japan

institute: The University of Osaka Graduate School of Medicine

summary: We established cell lines (fibroblasts) from pancreatic tumors in a mouse model of pancreatic carcinogenesis overexpressing METTL3 and performed RNAseq to examine changes in the gene profile of fibroblasts upon METTL3 overexpression. For the present study, we used the database of murine embryonal fibroblast (MEF) as the experimental control (GSE133753; GSM3926647, GSM3926648, GSM3926649 and GSE193354; GSM5795876, GSM5795877, GSM5795878).

overall_design: Total RNA was extracted from nine clones of cell lines, and RNA- sequencing was performed.

first: S

first: M

last: Konno

first: H

last: Ihii


title: RNA-seq profiling in Arabidopsis thaliana wild-type and hrlp-2

city: Singapore

first: Yu

last: Zhang

state: Singapore

address: 1 Research Link national university of singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: To investigate the function of RNA-binding protein HRLP in flowering time control, we created hrlp-2 mutant and collected 9-day-old seedlings to perform RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 9-day-old wild-type Col and hrlp-2 seedlings. Each sample has three biological replicates.

first: Hao

last: Yu

first: Lisha

last: Shen


title: Digestion treatment of uscfDNA extracted by SPRI Method

first: Jordan

last: Cheng

overall_design: Testing various DNA digestions and library preparation of extracted uscfDNA

first: Marco

last: Morselli


title: Peripheral blood transcriptomic profiles of rejection and polyomavirus-associated nephropathy after kidney transplantation

city: Leuven

first: Maarten

last: Naesens

address: Herestraat 49

department: Department of Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven

summary: Kidney transplant injury processes are associated with molecular changes in renal tissue, primarily related to immune cell activation and infiltration. How these processes are reflected by molecular alterations in circulating immune cells is poorly understood. We performed RNA-sequencing on 384 biobanked blood samples from four transplant centers, taken at time of a kidney allograft biopsy, selected for their phenotype (acute T cell- and antibody-mediated rejection, polyomavirus-associated nephropathy, and control). We performed differential expression analysis and pathway analysis per phenotype.   In peripheral blood, differentially expressed genes in rejection vs. no rejection samples demonstrated upregulation of glucocorticoid receptor and NOD-like receptor signaling pathways. Pathways enriched in antibody-mediated rejection were strongly immune-specific, whereas pathways enriched in T cell-mediated rejection were less immune related. Differentially expressed genes in polyoma viremia and polyomavirus-associated nephropathy were similar and demonstrated upregulation of mitochondrial dysfunction and interferon signaling pathways.   Our results highlight the immune activation pathways in peripheral blood leukocytes at time of antibody-mediated rejection and polyomavirus nephropathy and provide a framework for future therapeutic interventions.

overall_design: RNAsequencing of 384 biobanked blood samples from four transplant centers, taken at time of a kidney allograft biopsy, selected for their phenotype (acute T cell- and antibody-mediated rejection, polyomavirus-associated nephropathy, and control).

first: Elisabet

last: Van Loon

first: Henriette

last: de Loor

first: Amaryllis

last: Van Craenenbroeck

first: Jasper

last: Callemeyn

first: Claire

last: Tinel

first: Baptiste

last: Lamarthée

first: Priyanka

last: Koshy

first: Ben

last: Sprangers

first: Dirk

last: Kuypers

first: Wilfried

last: Gwinner

first: Dany

last: Anglicheau

first: Pierre

last: Marquet


title: Digestion treatment of uscfDNA extracted by QiaM Method


title: KDM5A inhibits anti-tumor immune response through downregulation of antigen presentation pathway in ovarian cancer [CUT&RUN]

status: Public on May 02 2022

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The infiltration of effector CD8+ T cells into tumors is one of the major predictors of clinical outcome for epithelial ovarian cancer (EOC) patients. Immune cell infiltration is a complex process that could be affected by the epigenetic makeup of the tumor. Here, we demonstrate that a lysine 4 histone H3 (H3K4) demethylase KDM5A impairs immune cell infiltration and inhibits anti-tumor immune response. Mechanistically, KDM5A silences genes involved in antigen processing and presentation pathway. Antigen processing and presentation is a critical step that is required for CD8+ T cells infiltration and activation of CD8+ T cell mediated anti-tumor immune response. KDM5A inhibition restores the expression of antigen presentation pathway in vitro and promotes anti-tumor immune response mediated by CD8+ T cells in vivo in a syngeneic EOC mouse model. Notably, a negative correlation between expression of KDM5A and genes involved in antigen processing and presentation pathway such as HLA-A and HLA-B is observed in the majority of cancer types. In summary, our results establish KDM5A as a regulator of CD8+ T cells tumor infiltration and demonstrate that KDM5A inhibition is a novel therapeutic strategy aiming to boost anti-tumor immune response.

overall_design: CUT&RUN of KDM5A and H3K4me3 in WT cells.

first: Rugang

last: Zhang

first: Heng

last: Liu


title: The genetic profile of METTLs-KD and the inhibition of PLK1

status: Public on May 04 2022

first: Shotaro

last: Tatekawa

summary: We identified PLK1 as a key gene methylated by METTL3 in MeRIP-sq using the sh-METTL3 cell line of MIAPaCa-2. In the present study, we evaluated the changes in gene expression paterns induced by PLK1 inhibition and METTL3-KD

overall_design: Total RNA was extracted from three cell types, MIAPaCa-2 sh-CTL, MIAPaCa-2 sh-METTL3, as well as MIAPaCa-2 sh-CTL treated with PLK1i (NMS-P937 for 24hr at 80 nM), and RNA- sequencing was performed.

first: S

first: M

last: Konno

first: H

last: Ihii


title: KDM5A inhibits anti-tumor immune response through downregulation of antigen presentation pathway in ovarian cancer [RNA-seq]

overall_design: RNA-seq of KDM5A WT and KO cells.


title: Transcriptomics of retinal endothelial cells isolated from mice at Postnatal day 6.

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

summary: Transcriptome of endothelial cells (ECs) isolated from mouse retinas at Postnatal (P) day 6.

overall_design: Isolation of ECs from retinas of P6 pups.

first: Yu

middle: T

last: Ong

first: Marco

last: Castro

first: Jorge

last: Andrade

first: Stefan

last: Gunther

middle: R

first: Michael

last: Potente


title: Transcriptome analyses of Pst DC3000-inoculated Arabidopsis thaliana Col-0 and 35S::CBP60g plants at normal and elevated temperature

city: Durham

first: Jonghum

last: Kim

address: 124 Science Dr

department: Biology

institute: Duke university

summary: We performed RNA sequencing of Pseudomonas syringae pv. tomato (Pst) DC3000-infected A. thaliana Col-0 and 35S::CBP60g plants at normal (23C) and elevated (28C) temperatures. 4-week-old plants were pre-incubated at 23C and 28C for 48h and then leaves were syringe-infiltrated with DC3000 bacterial inoculum. Plants were incubated at their respective temperatures (23C or 28C) for another 24h post-inoculation before tissue collection for RNA extraction. RNA samples for submitted for RNA sequencing and we found different clusters of DC3000-regulated genes that were similarly or differentially regulated between Col-0 and 35S::CBP60g at elevated temperature. Temperature-downregulated DC3000-induced genes in Col-0 plants that were restored in 35S::CBP60g plants were enriched for immunity/defense-related genes, including those essential for host salicylic acid (defense hormone) biosynthesis and accumulation.

overall_design: 4 treatments were used: (1) 23C DC3000 Col-0; (2) 23C DC3000 35S::CBP60g; (3) 28C DC3000 Col-0; and (4) 28C DC3000 35S::CBP60g. For each treatment, three individual plants (independent biological replicates) were sampled.

first: Jong

first: Christian

middle: M

last: Castroverde

first: Sheng

middle: Y

last: He


title: Transcriptional regulation by YAP/TAZ in human endothelial cells

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The genetic profiles based single cell level in a murine model of pancreatic carcinogenesis

summary: We tested how elevated METTL3 expression affects pancreatic cancer in a mouse model. We performed single-cell RNA-sequencing of pancreatic cancer tissue from control (EL1) and METTL3-overexpressing (WTg).

overall_design: FVB/N-EL1-Luc/EL1-TAg mice (Common Name, EL1-Luc/EL1-TAg, abbreviated as EL1) were used to transgenic mice experiments. Briefly, for co-injection to make EL1-Luc/EL1-TAg, two cDNA was used: the oncogenic cDNAs were prepared from 2.7-kb SV40 Large T-antigen, whereas the reporter cDNAs were prepared from Firefly Luciferase cDNA pGL3-Basic Vector. Each cDNA was fused with rodent pancreatic Elastase I promoter. For the construct of Mettl3 overexpressed transgenic mice, three 6-week-old female BL/6 mice were bled with two 6-week-old male BL/6 mice, and fertilized eggs were taken to perform cDNA injection in vitro to make transgenic animals. For the cDNA injection, the open-reading-flame of Mettl3 was cloned from C57BL/6J mice by PCR, of which sequence were verified; Mettl3 cDNA was fused with chimeric CAG promoter, a composite of the cytomegalovirus (CMV) enhancer with the chicken beta actin promoter (CBA). The Mettl3 overexpressing mice were crossed with EL1 mice to make the double transgenic mice (WTg). Mice were confirmed as expected genotype, by PCR. The WTg mice formed abdominal tumors, which were apparent after 6 weeks; the luminous imaging followed to administration of vivoGlo Luciferin as 150 microgram/mouse(g) confirmed the presence of tumor(s) in pancreatic region under the IVIS imaging system (SPI), whereas the opened observation of abdomen indicated around 2-cm tumor(s), and tumors were processed for the preparation of single cells. Single cell suspensions from pancreatic tumor tissues were processed with the 10x Genomics Chromium Controller according to the protocol described in the Chromium Single Cell 3' Reagent Kits User Guide Chromium Next GEM Single Cell 3' Kit v3.1 (Cat# PN-1000269), Chromium Next GEM Chip G Single Cell Kit (Cat# PN-1000127), and Dual Index Kit TT Set A (Cat# PN-1000215) were applied during processing.


title: Analysis of HOIL1-dependent gene expression in the murine small intestine

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

summary: The goal of this study was to examine the role of HOIL1 in regulating gene expression in the small intestine. Using histological and qRT-PCR analyses, we had identified type 2 inflammation, including excessive expression of Il13, Il5 and IL-4 mRNAs, in the ileum of HOIL1-deficient mice. To determine the mechanism by which HOIL1 regulates type 2 inflammation, we performed RNA-seq to identify additional transcriptional changes. Since IL-13/IL-4 signaling in intestinal epithelial cells (IECs) triggers extensive changes in the cell-type composition and expression in the epithelial layer that further promotes type 2 inflammation, we deleted the IL-4Ralpha on IECs by crossing Hoil1 mutant mice to Il4ra-floxed and Vil1cre transgenic mice to block feed-forward signaling and epithelial changes. We FACS-sorted CD45-positive and CD45-negative cells from the ileum of these mice to increase the sensitivity of detection of mRNA changes in each of these populations. In the preliminary analyses of these data, we filtered the data to identify transcriptional changes that were dependent on HOIL1, but independent of IL4Ralpha signaling on IECs. Six transcripts, in addition to Rbck1 (official gene name for Hoil1), were identified as differentially expressed (DE) in the CD45-positive population. All six genes have been previously associated with group 2 innate lymphoid cells and/or Th2 cells. Only Rbck1 was identified as DE in the CD45-negative population under these criteria.

overall_design: mRNA profiles of CD45-positive and CD45-negative cells isolated from the small intestine of Hoil1+/+Il4raflox/flox, Hoil1+/+Il4raflox/flox+Vil1cre, Hoil1-/-Il4raflox/flox, and Hoil1-/-Il4raflox/flox+Vil1cre mice (Peyer's patches removed).

first: Donna

last: MacDuff

first: Matthew

last: Wood


title: Transcriptome analyses of mock- and Pst DC3000-inoculated Arabidopsis thaliana Col-0 plants at normal and elevated temperature

city: East Lansing

first: Sheng Yang

state: MI - Michigan

address: 612 Wilson Rd.

department: DOE Plant Research Lab

institute: Michigan State University

summary: We performed RNA sequencing of mock-inoculated and Pseudomonas syringae pv. tomato (Pst) DC3000-infected A. thaliana (Col-0 accession) plants at normal (23C) and elevated (30C) temperatures. 4-week-old Col-0 plants were pre-incubated at 23C and 30C for 48h and then leaves were syringe-infiltrated with either mock (MgCl2) or DC3000 bacterial inoculum. Plants were incubated at their respective temperatures (23C or 30C) for another 24h post-inoculation before tissue collection for RNA extraction. RNA samples for submitted for RNA sequencing and we found different clusters of DC3000-regulated genes that were downregulated, upregulated and unchanged at elevated temperature. Temperature-downregulated DC3000-induced genes were enriched for a whole suite of defense-related genes, including those essential for host salicylic acid (defense hormone) biosynthesis and accumulation.

overall_design: 4 treatments were used: (1) 23C mock; (2) 23C DC3000; (3) 30C mock; and (4) 30C DC3000. For each treatment, three individual plants (independent biological replicates) were sampled.


title: Transcriptome changes in human endothelial cells with constitutively active YAP, TAZ and TEAD mutants

summary: Transcriptome profiling of human umbilical vein endothelial cells (HUVECs) overexpressing constitutively nuclear YAP (YAP S127A), TAZ (TAZ S89A) or TEAD-binding deficient YAP (YAP S94A/S127A) or TAZ (TAZ S51A/S89A) to identify YAP and TAZ target genes.

overall_design: Analysis of HUVECs transduced with a lentivirus encoding for a nuclear YAP and TAZ mutant compared to HUVECs transduced with a control lentivirus (Ctrl). Expression analysis was performed 48h post doxycycline induction.


title: Deeper insight into Pancreatic Ductal Adenocarcinoma (PDAC) survival heterogeneity using integrative analyses of individual and global transcriptome based networks

city: liege

first: Kristel

last: Van Steen

state: BELGIUM

address: BAT B34, GIGA-R Medical Genomics-BIO3

institute: GIGA-R, Medical Genomics, University of Liege

summary:
Purpose: The goals of this study are to delineate genes when comparing long-term (LT) and short-term (ST) PDAC survivors, and to exploit the merits of extensive integrative individual- and group-based transcriptome profiling.
Method: Using a discovery cohort of 19 PDAC patients, we first performed differential gene expression (DGE) analysis comparing LT to ST PDAC groups. Second, we adopted unsupervised systems biology approaches to obtain meaningful gene modules showing associations to clinical features. Third, we created individual-level gene expression perturbation profiles and identified key regulators across the perturbed profiles of LT patients at the pathway and motif level. Furthermore, we applied two network context gene prioritization approaches for the depiction of PDAC specific regulatory genes. In particular, we used the random walk-based DADA method to develop PDAC disease modules considering the use of PDAC seed genes (via prior biological knowledge). As an alternative, we used NetICS to prioritize PDAC survival associated genes, by integrating information regarding group-based and individual-specific perturbed genes.
Result: DGE analysis resulted in differences in the expression of genes involved in immune responses, cell cycle and metabolic pathways. Validation of a selection of DGEs in the molecular lab suggested a role of REG4 and TSPAN8 in PDAC survival. Detailed inspection of individual-specific omics changes across LT survivors revealed biological signatures associated with focal adhesion and extracellular matrix (ECM) receptors, commonly perturbed in at least 2 out of 9 LT survivors, implying a potential role in molecular-level heterogeneity of LT PDAC survivors. Network centric approaches such as NetICS (integrating group-based and individual-specific perturbed genes) and DADA (degree-aware disease gene prioritizing), identified various known oncogenes such as CUL1, SCF62, EGF, FOSL1, MMP9, and TGFB1. In addition, we identified TAC1, KCNH7, IRS4, DKK4, further warranting detailed follow-up investigations.
Conclusion:Our proposed analytic workflow, combining clinical and omics data, and individual-level and group-level transcriptome profiling, highlighted transcriptome marks of PDAC long-term survival heterogeneity. The identified genes open up avenues towards better understanding the mechanisms underlying PDAC survival extension.

overall_design: Examination of 2 survival groups (short term and long term)  in PDAC using transcriptome profiling

first: Ingrid

last: Sturman

first: Claire

last: Josse

first: Archana

last: Bhardwaj


title: Expression data from Gata3+/- and Gata3-/- ESC-derived T-cell progenitors

status: Public on May 01 2022

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

state: Ontario

address: 2075 Bayview Avenue

country: Canada

institute: University of Toronto

summary: GATA3 plays a crucial role during early T-cell development and also dictates later T-cell differentiation outcomes. However, its role and collaboration with the Notch signaling pathway in the induction of T-lineage specification and commitment have not been fully elucidated. We show that GATA3 deficiency in hematopoietic progenitors results in an early block in T-cell development despite the presence of Notch signals, with a failure to up-regulate Bcl11b expression, leading to a diversion toward myeloid lineage fate.  GATA3 deficiency results in dysregulated Cdkn2b expression, leading to apoptosis of early T-lineage cells due to inhibition of CDK4/6 function. We also show that GATA-3 induces Bcl11b, and together with Bcl11b represses Cdkn2b expression. Our findings provide a signaling and transcriptional network by which the T-lineage program in response to Notch signals is realized.

overall_design: Gata3+/- and Gata3-/- ESCs were maintained in vitro in ES media. ESCs were cultured on OP9/OP9-DL1 cells for differentiation towards the hematopoietic and T-cell lineages. T-cell progenitors were FACS sorted, RNA isolated, and cDNA/cRNA generated for subsequent microarray gene expression analysis.

first: Patrycja

middle: K

last: Thompson

first: Edward

last: Chen

first: Renee

last: de Pooter

first: Catherine

last: Frelin

first: Walter

last: Vogel

first: Christina

last: Lee

first: Thomas

last: Venables

first: Divya

last: Shah

first: Norman

last: Iscove

first: Mark

last: Leid

first: Michele

last: Anderson

first: Juan

middle: C


title: Transcriptomic analyis of donor (B6:SJL.C20) and host follicular and marginal zone B cells after adoptive transfer of follicular B cells into into lymphopenic (Rag2-/-) or replete animals (C57BL6)

first: Brian

middle: Thomas

last: Gaudette

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

summary: The generation of marginal zone (MZ) B cells is a Notch2 dependent process. We observed that transdifferentiation of follicular (FO) B cells to an MZ-like phenotype is dependent on a lymphopenic environment.  We therefore adoptively transftered congenically marked SJL.C20 (CD45.1) mature naive FO B cells into either lymphopenic Rag2-/- or intact C57BL6 (CD45.2) recipient mice and recovered and double sorted intermediate phenotype (MZ-FO) donor B cells at day 4 post transfer from Rag2-/- recipients or both MZ and FO phenotype donor B cells at day 8 post transfer from both recipient groups and performed RNA sequencing.

overall_design: Samples are double sorted donor (B6:SJL.C20) and host follicular and marginal zone B cells after adoptive transfer into lymphopenic (Rag2-/-) or replete animals (C57BL6). cDNA was prepared from RNA with 3' polyA capture method.  Transcript abundance was measured by Kallisto psuedo-alignment and normalized (voom) and differential expression was assessed using limma.

first: Ivan

last: Maillard

first: David

last: Allman


title: Restoration of genome-wide 5-hydroxymethylation by azacitidine and ascorbate in TET2-deficient human pre-leukemic HSPCs

city: Stanford

first: Ravindra

last: Majeti

state: CA

address: 875 Blake Wilbur Dr Clinic F

institute: Stanford University

summary: The conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) is a key step in DNA demethylation that is mediated by ten-eleven-translocation (TET) enzymes, which require ascorbate/vitamin C. Here, we report the 5hmC landscape of normal hematopoiesis and identify cell type-specific 5hmC profiles associated with active transcription and chromatin accessibility of key hematopoietic regulators. We utilized CRISPR/Cas9 to model TET2 loss-of-function mutations in primary human HSPCs. Disrupted cells exhibited increased serial replating and competitive advantage, defective erythroid/megakaryocytic differentiation, and in vivo myeloid skewing coupled with reduction of 5hmC at erythroid regulators. Azacitidine and ascorbate restored 5hmC abundance and slowed/reverted the expansion of TET2-mutant clones in vivo. These results demonstrate the key role of 5hmC in normal hematopoiesis and TET2-mutant phenotypes, and raise the possibility of utilizing these agents to treat pre-leukemia/clonal hematopoiesis and prevent leukemogenesis.

overall_design: 5hmC pulldown sequencing profiles of healthy hematopoietic cell types and TET2-edited and AAVS1 control human HSPCs. RNA sequencing data of TET2-edited and AAVS1 control human HSPCs

first: Yusuke

last: Nakauchi

first: Armon

last: Azizi

first: Daniel

last: Thomas

first: M

last: Corces

first: Andreas

last: Reinisch

first: Rajiv

last: Sharma

last: Cruz Hernandez

last: Köhnke

first: Daiki

last: Karigane

first: Amy

last: Fan

last: Martinez-Krams

first: Melissa

last: Stafford

first: Satinder

last: Kaur

first: Ritika

last: Dutta

first: Paul

last: Phan

first: Asiri

last: Ediriwickrema

first: Erin

last: McCarthy

first: Yuhong

last: Ning

first: Tierney

last: Phillips

first: Christopher

last: Ellison

first: Gulfem

middle: D

last: Guler

first: Anna

last: Bergamaschi

first: Chin-Jen

last: Ku

first: Samuel

last: Levy


title: Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2

city: Melbourne

first: Kelly

last: Smith

state: Victoria

address: Grattan Street

department: Department of Anatomy & Physiology

country: Australia

institute: The University of Melbourne

summary: The endocardium plays important roles in the development and function of the vertebrate heart; however, few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here, we describe the Gt(SAGFF27C); Tg(4xUAS:egfp) line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan-endothelium confirms molecular distinction between these populations and time-course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity, we employed npas4l, etv2 and scl loss-of-function models. Endocardial expression is lost in npas4l mutants, significantly reduced in etv2 mutants and only modestly affected upon scl loss-of-function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression, whereas Bmp inhibition decreased expression. Finally, epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast, overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together, these results describe the differentiation of the endocardium, distinct from vasculature, and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation.

overall_design: Differential gene expression analysis of RNA-seq data from GFP positive endocardial (Gt(SAGFF27C); Tg(4xUAS:egfp)) and endothelial (Tg(fli1a:egfp)) cells at the 15 somite stage in zebrafish, three independent biological replicates were collected for each condition

last: Capon

first: Veronica

last: Uribe Sokolov

first: Nicole

last: Dominado

first: Ophelia

last: Ehrlich


title: Latent HIV infection disrupts cell-intrinsic innate immunity

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Bulk RNA Sequencing of Jurkat E6-1 & JLat9.2 CD4+ T cells Treated with 100IU/mL IFNb

overall_design: Jurkat E6-1 & JLat9.2 CD4+ T cells were treated with 100IU/mL IFNb and sampled at 4 hours, 8 hours, and 12 hours post-treatment. An untreated "Mock" group for both Jurkat E6-1 & JLat9.2 CD4+ T cells were sampled at 4 hours.

first: Rebecca

last: Olson

first: Leanne

middle: S

last: Whitmore

first: Daniel

last: Newhouse

first: Elise

last: Gale Jr


title: prrA mutant RNA-seq

city: Ramat-Gan

first: Ilana

last: Lebenthal-Loinger

address: Bar-Ilan University

department: The Mina & Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

summary: We performed transcriptomic analysis of prrA antitoxin mutant and WT strain of the clinical isolate 39016 of Pseudomonas aeruginosa. The purpose: understanding the gene expression pattern in the mutant with and without prophage induction- in compaarison to the WT strain with and without induction.

overall_design: The RNA samples were extracted in triplicates for WT and prrA mutant strains with and without the addition of 0.4mM Norfloxacin.

first: Ehud

last: Banin


title: Retinoic acid supplementation rescues the social deficits in Fmr1 knockout mice

status: Public on Apr 30 2022

city: shanghai

first: zhixiong

last: xia

address: yueyang road 320

institute: SIBCBs

summary: Autism spectrum disorder (ASD) is a hereditary intellectual disability. Fragile X syndrome (FXS) is the leading cause of ASD and mainly results from the abnormal CGG amplification (>200 repeats) of the fragile X mental retardation 1 (Fmr1) gene. All-trans retinoic acid (RA) is involved in synaptic plasticity, neuronal differentiation and brain maturation. RA-mediated synaptic strength regulation was abolished in FXS patient-derived induced pluripotent stem (iPS) cells. Previous work on the ASD model with excessive UBE3A expression, of which the ASD-like behaviors caused by repression in RA signaling were successfully ameliorated by oral supplementation of RA. In this study, we used male Fmr1 knock-out (KO) mice to explore the effect of RA exerting on the behaviors. Our results indicated that RA supplementation can alleviate the defects in social novelty. We performed RNA sequencing to find out the differentially expressed genes (DEGs) in the Fmr1 KO group, of which the expression levels were restored to the similar level as those in the wild-type (WT) group after RA supplementation, such as Per1, Per2 and Foxp2. Besides, several DEGs associated with neuronal functions were also identified, like Arc, Ccn2, Foxp2, Xdh, Lepr, Serpina3n andTnfsf10. our findings that RA supplementation improved social novelty behavior in Fmr1 KO mice provided a potential therapeutic intervention method for FXS, which may further be used in other disease models with defective RA signaling.

overall_design: mRNA sequencing data of prefrontal cortex tissue from six WTmale mice treated with Oil; six WTmale mice treated with RA; and six KO male mice treated with Oil;  six KO male mice treated with RA. Two mice of the same genotype and treatment were pooled together as one sample. A total of three samples from six male mice were used for high-throughput sequencing in each group, including WT+Oil; WT+RA;Fmr1 KO+Oil; Fmr1 KO+RA.

first: Liqin

last: Yang

first: Zhixiong

last: Xia

first: Jianhua

last: Feng

first: Menghuan

last: Zhang

first: Pu

last: Miao

first: Xiangyan

first: Zijian

last: Hao

first: Ronggui

last: Hu


title: Neonatal murine cardiomyocyte transcriptome

city: Darlinghurst

first: Amy

last: Nicks

state: NSW

address: 405 Liverpool Street

institute: Victor Chang Cardiac Research Institute

summary: Cardiomyocyte poly(A) RNA was sequenced from purified bulk cardiomyocytes collected from one male and female murine heart at postnatal day 2 (P2).  Neonatal cardiomyocytes were isolated and purified (96% cardiomyocytes at P2) by Langendorff retrograde perfusion and immunomagnetic cell separation, respectively. We found evidence of sexual dimorphism with 9 differentially expressed genes (FDR<0.05) encoded on XY chromosomes in this RNA-Seq dataset.

overall_design: Cardiomyocytes were collected from one male and female heart from 4 different litters (n=4 per biological sex) of an average C57BL6/J litter size of 6-8 mouse pups.

first: Paul

last: Young

first: David

last: Humphreys


title: BRAF-V600E utilizes post-transcriptional mechanisms to amplify LPS-induced TNF production in dendritic cells of Langerhans Cell Histiocytosis

first: Danielle

last: Minichino

address: 3400 civic center blv

department: Pediatric Rheumatology

institute: Children's Hospital of Philadelphia

summary: Langerhans Cell Histiocytosis (LCH) is an inflammatory disease characterized by abnormal dendritic cells (DCs) with hyperactive ERK signaling, called “LCH cells”.  Since DCs rely on ERK signaling to produce inflammatory signaling molecules in response to pathogenic cues, we hypothesized that hyperactive ERK will enhance DC inflammatory responses.  We utilized the BRAF-V600E fl/+: CD11c-Cre mouse model of LCH which hyperactivates MAPK/ERK signaling in DCs.  We cultured bone-marrow derived dendritic cells (BMDCs) from LCH and control mice (BRAF-V600E fl/+: Cre0) and stimulated them with LPS with or without a specific BRAF-V600E inhibitor.  Polysome Profiling revealed a large and irreversible increase in levels of polysome bound RNA in the LCH-BMDCs compared to WT.  We defined the LCH translatome by analyzing total and polysome-bound RNA from BMDCs using the Anota2seq program, which revealed a BRAF-V600E-mediated selective increase in LPS-induced inflammatory proteins.

overall_design: Paired total and polysome-bound RNA from LPS-stimulated BMDCs (WT vs LCH; n=3 biological repeats) was used to define the LCH translatome via Anota2seq.

first: Edward

last: Behrens

first: Kaosheng

last: Lv

first: Wei

last: Tong


title: OCA-T1 and OCA-T2 are coactivators of POU2F3 in the tuft cell lineage

city: Cold Spring Harbor

first: Xiaoli

middle: Sky

last: Wu

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: ChIP-Seq of C11orf53(OCA-T), COLCA2 and POU2F3(OCT11) in tuft cell lung cancer cell lines. Gene expression changes upon CRISPR knockout of different genes in tuft cell lung cancer cell lines and upon over-expression of C11orf53/POU2F3 alone or in combo in YT330 (a murine Notch high small cell lung cancer cell line)

overall_design: ChIP-Seq in NCIH211, NCIH526, CORL311, and NCIH1048 cell lines with endeneous and lentivirally over-expressed construct. Gene expressoin changes in above mentioned cells and YT330 with CRISPR knockout or lentivirally over-expression. Single cell RNA-seq of wild-type and knockout mice.

first: Jonathan

middle: B

last: Preall

first: Christopher

last: Vakoc


title: RNA sequencing facilitates quantitative analysis of 28ζ CAR, BBζ CAR and aTCR T cell transcriptomes

city: 上海市

first: yansha

last: sun

address: 斜土路2200弄25号上海市肿瘤研究所新大楼403

institute: Shanghai Jiaotong University

summary:
Purpose: Analyzing the cytokine transcription and associated signalings of human 28ζ CAR, BBζ CAR and aTCR T cells
Methods: Human 28ζ CAR, BBζ CAR and aTCR T cells were stimulated with antigen peptides for four hours
Results:  Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the human genome (build GRCh38).

overall_design: The mRNA profiles of human 28ζ CAR, BBζ CAR and aTCR T cells upon stimulation with antigen peptides for four hours. There are two sample replicates for the human 28ζ CAR, BBζ CAR and aTCR T cells.

first: Yansha

last: Sun

first: Yiwei

last: Dong


title: Human fetal lung tip progenitor cells

city: Cambridge

first: Dawei

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

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

overall_design: Refer to individual Series


title: E-Selectin/AAV2/2 Gene Therapy Alters Angiogenesis and Inflammatory Gene Profiles in Mouse Gangrene Model [Inflammation]

status: Public on Apr 29 2022

city: Miami

first: Zhao-Jun

last: Liu

state: FL

address: 1600 NW 10th Ave, RMSB 1010

department: Surgery

institute: University of Miami Miller School of Medicine

summary: For patients with chronic limb-threatening ischemia and limited revascularization options, alternate means for therapeutic angiogenesis and limb salvage are needed. E-selectin is a cell adhesion molecule that is critical for inflammation and neovascularization in areas of wound healing and ischemia. Here, we tested the efficacy of modifying ischemic limb tissue by intramuscular administration of E-selectin/AAV2/2 (adeno-associated virus serotype 2/2) to modulate angiogenic and inflammatory responses in a murine hindlimb gangrene model. Limb appearance, reperfusion, and functional recovery were assessed for 3 weeks after induction of ischemia. Mice receiving E-selectin/AAV2/2 gene therapy had reduced gangrene severity, increased limb and footpad perfusion, enhanced recruitment of endothelial progenitor cells, and improved performance on treadmill testing compared to control group. Histologically, E-selectin/AAV2/2 gene therapy was associated with increased vascularity and preserved myofiber integrity. E-selectin/AAV2/2 gene therapy also upregulated a panel of pro-angiogenic genes yet downregulated another group of genes associated with the inflammatory response. This novel gene therapy did not induce adverse effects on coagulability, or hematologic, hepatic, and renal function. Our findings highlight the potential of E-selectin/AAV2/2 gene therapy for improving limb perfusion and function in patients with chronic limb-threatening ischemia.

overall_design:
FVB mice were treated with intramuscular injection of 1x10^11 VG of E-selectin/AAV2/2 (treatment) or LacZ/AAV2/2 (control). Hindlimb ischemia was then induced by femoral artery ligation and intraperitoneal L-NAME (40 mg/kg). Ischemic adductor and gastrocnemius muscles were harvested 21 days after induction of ischemia. Ischemic muscle was homogenized and total RNA extracted for analysis of angiogenesis-related gene expression using Qiagen RT2 Profiler PCR Array (Inflammatory Cytokines and Receptors, PAMM-011Z).
RT-qPCR gene expression profiling. Equal amount of total RNA was pooled from 3 mice each for treatment and control groups prior to gene expression analysis. PCR array was performed twice and mean 2^-deltaCt calculated for fold-change in gene expression.

first: Antoine

last: Ribieras


title: RNA sequencing of the Murine Oviduct Infundibulum

city: Riverside

first: Ameae

last: Walker

address: 900 University Ave.

department: Biomedical Sciences

institute: University of California Riverside

summary: Changes in gene expression in the infundibulum after a prolonged prolactin treatment (3 μg/h/mouse, 7 days, subcutaneous Alzet osmotic minipump) showed prolactin down regulation of genes necessary for cilium development and function. Collectively, these results suggest that prolactin regulates cyclic changes in ciliated cell function in the infundibulum. They also suggest an additional mechanism whereby prolonged prolactin elevation would negatively impact fertility.

overall_design: Animals were treated with recombinant murine PRL or saline as a control for 7 days. Infundibula were dissected and immediately snap frozen for RNA extraction. Both infundibular regions were pooled per mouse and two animals were pooled for each RNAseq sample (4 infundibula per sample, 5 samples per treatment). Whole transcriptome sequencing was performed using the Illumina NovaSeq 6000 system. Samples were enriched for mRNA (stranded) and sequenced by 100 base pair (bp) paired end (PE) reads (PE100, 80 million reads per sample). Reads were quality assessed using FastQC quality assessment software and trimmed using a quality threshold of 15 and Truseq adapter sequences (reads shorter than 20bp were discarded, Trimmomatic). Reads were aligned to the mouse mm10 reference genome with a splice aware short read aligner (Hisat2, Samtools). FeatureCounts was used to quantify raw counts and two group comparison, using DESeq2 to identify differentially expressed genes between control and PRL-treated animals.

first: Kelly

last: Radecki

first: Mary

last: Lorenson


title: Expression data from KDM4 inhibition

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

summary:
KDM4B shRNA knockdown in Rh30 cells or QC6352 treatment of Rh30 or Rh41 cells
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: KDM4B shRNA knockdown or siKDM4C in Rh30 cells for 72hours. 200nM QC6352 treatment of Rh30 or Rh41 cells for 48hours. Total RNA extracted for affymetrix analysis.

first: Jun

last: Yang

first: Ahmed

last: Abuzaid


title: Genome-wide maps of YAP, TAZ and TEAD1 binding sites in human endothelial cells

city: Almada

first: Ana

last: Grosso

address: Campus de Caparica

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

summary: ChIP-Seq profiling using human umbilical vein endothelial cells (HUVECs) to identify endogenous YAP, TAZ and TEAD1 DNA binding sites.

overall_design: HUVECs were cultured for 48 hours and analyzed by ChIP-seq with antibodies targeting YAP1, TAZ or TEAD1.

first: Yu

last: Ong

first: Jorge

last: Andrade

first: Michael

last: Potente


title: Evolution of transcription factor binding through sequence variations and turnover of binding sites

city: Rehovot

first: Gat

last: Krieger

address: Herzl St 234

institute: Weizmann Institute of Science

summary: Variations in noncoding regulatory sequences play a central role in evolution but interpreting such variations remains difficult even in the context of defined attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in cis-regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, which contains two related genomes within the same nucleus. TFs localize preferentially to sites containing their known binding motifs, but occupy only a small fraction of the potential motif-coding genomic sites. Differential binding of TFs to the two orthologues is well explained by sequence variations that alter the consensus core motif, while changes in chromatin accessibility were of little apparent effect. Motif variations that abolish binding when present in one allele show only moderately reduced binding when common to both alleles, suggesting evolutionary compensation. At the promoter level, we report cases of turnover, where binding in the two orthologues localized to different promoter regions, yet most interspecies differences resulted from higher number of binding sites in one of the alleles. Our results suggest that cis variations affecting TF binding occur primarily through the gain and loss of cis-regulatory motifs at accessible regions.

sample_organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

overall_design: Examiniation of DNA binding of 27 yeast transcription factors to a hybrid genome (S. cerevisiae x S. paradoxus), with at least two biological replicates per TF.

first: Offir

last: Lupo

first: Naama

last: Barkai


title: RNA-sequencing of PRMT1 proficient and deficient microglia

city: Montreal

first: Stephane

last: Richard

address: 3755 Côte Ste-Catherine Road

institute: McGill University

summary:
RNA_sequencing analysis defined a novel role for the PRMT1 in microglia during normal and 0.2% cuprizone diet 5weeks
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Microglia mRNA profiles of 4-6 weeks-old wild-type (PRMT1Ifl/fl) and microglia specific knockout (PRMT1fl/fl; cx3r1cre-ert2) mice during normal and 0.2% cuprizone diet 5 weeks

first: Jeesan

last: Lee


title: An induced pluripotent stem cell t(7;12)(q36;p13) acute myeloid leukemia model shows high expression of MNX1 and a block in differentiation of the erythroid and megakaryocytic lineages

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

summary: Acute myeloid leukemia (AML) results from aberrant hematopoietic processes and these changes are frequently initiated by chromosomal translocations. One particular subtype, AML with translocation t(7;12)(q36;p13), is found in children diagnosed before two years of age. The mechanisms for leukemogenesis induced by t(7;12) is not understood, in part because of the lack of efficient methods to reconstruct the leukemia-associated genetic aberration with correct genomic architecture and regulatory elements. We therefore created induced pluripotent stem cell (iPSC) lines that carry the translocation t(7;12) using CRISPR/Cas9. These t(7;12) iPSC showed propensity to differentiate into all three germ layers, confirming retained stem cell properties. The potential for differentiation into hematopoietic stem and progenitor cells (HSPC) was shown by expression of CD34, CD43 and CD45. Compared with the parental iPSC line, a significant decrease in cells expressing CD235a and CD41a was seen in the t(7;12) iPSC derived HSPC (iHSPC), suggesting a block in differentiation. Moreover, colony formation assay showed an accumulation of cells at the erythroid and myeloid progenitor stages. Gene expression analysis revealed significant down-regulation of genes associated with myeloid differentiation and megakaryocyte differentiation pathways. Compared with the parental iHSPC the t(7;12) iHSPC expressed high levels of MNX1, a characteristic strongly associated with pediatric AML with t(7;12). Thus, we have created an iPSC t(7;12) leukemia model that has strong similarities with the t(7;12) AML subtype and therefore constitutes a valuable tool for further studies of the mechanisms for leukemia development to find new treatment options.

overall_design: Gene expression profiling of iPSC differentated into hematopoietic stem and progenitor cells (HSPC) with or without the translocation t(7;12)

first: Tina

last: Nilsson


title: scRNAseq from WT and PRMT1-KO microglia

summary: scRNAseq of WT and PRMT1-KO microglia during CPZ diet 5 weeks

overall_design:
Microglia were isolated from PRMT1FL and PRMT1cx3cr1-cre mice using CD45+ and CD11b+ surface markers.

Grant number: FDN-154303
Grant title: Molecular and Genetic Analysis of Arginine Methylation and RNA binding proteins in Health and Disease
Funding source: Canadian Institute of Health Research


title: Multi-modal single-cell sequencing identifies cellular immunophenotypes associated with juvenile dermatomyositis disease activity

city: San Francisco

first: Jessica

last: Neely

state: California

address: 550 16th Street

department: Pediatrics

institute: UCSF

summary: Juvenile dermatomyositis (JDM) is a rare autoimmune condition with insufficient biomarkers and treatments, in part, due to incomplete knowledge of the cell types mediating disease. We investigated immunophenotypes and cell-specific genes associated with disease activity using multiplexed RNA and protein single-cell sequencing applied to PBMCs from 4 treatment-naïve JDM (TN-JDM) subjects at baseline, 2, 4, and 6 months and 4 subjects with inactive disease.

overall_design:
This study includes single-cell RNA and ADT (protein) measurements of PBMCs from 4 treatment-naïve JDM (TN-JDM) subjects at baseline, 2, 4, and 6 months and 4 subjects with inactive disease.  Samples were multiplexed across four 10X reactions.  Provided in GEO are the filtered RNA and ADT matrices we used for clustering and differential gene expression analysis.  We have also included a metadata file with cell annotations and file with UMAP coordinates to re-create our cell clusters.
>>> Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns. <<<


title: E-Selectin/AAV2/2 Gene Therapy Alters Angiogenesis and Inflammatory Gene Profiles in Mouse Gangrene Model [Angiogenesis]

first: Zhao-Jun

last: Liu

overall_design:
FVB mice were treated with intramuscular injection of 1x10^11 VG of E-selectin/AAV2/2 (treatment) or LacZ/AAV2/2 (control). Hindlimb ischemia was then induced by femoral artery ligation and intraperitoneal L-NAME (40 mg/kg). Ischemic adductor and gastrocnemius muscles were harvested 21 days after induction of ischemia. Ischemic muscle was homogenized and total RNA extracted for analysis of angiogenesis-related gene expression using Qiagen RT2 Profiler PCR Array (Angiogenesis, PAMM-024Z).
RT-qPCR gene expression profiling. Equal amount of total RNA was pooled from 3 mice each for treatment and control groups prior to gene expression analysis. PCR array was performed twice and mean 2^-deltaCt calculated for fold-change in gene expression.

first: Antoine

last: Ribieras


title: Single Cell Analysis of Wild Type and HHEX-/- Embryonic Stem Cell Derived Pancreatic Progentiors.

city: New York

first: Dapeng

state: NY

address: 1275 YORK AVE

institute: Memorial Sloan Kettering Cancer Center

summary: scRNA-seq reveals cellular complexity and differentiation trajectory of pancreatic-differentiated WT and HHEX KO cells.

overall_design: Transcriptional profiling of WT and HHEX-/- hESC-derived cells (in two experiments) at different stages of pancreatic differentiation (DE, GT, PP1, and PP2).

first: Huangfu

last: Danwei

first: Leslie

last: Christina

first: Tayyebi

last: Zakieh

first: Yang

last: Dapeng


title: Genes that escape X chromosome inactivation modulate sex differences in valve myofibroblasts

city: Boulder

first: Kristi

last: Anseth

state: CO- COLORADO

address: 3415 Colorado Ave, 596 UCB

institute: University of Colorado - Boulder

summary: Aortic valve stenosis (AVS) is a sexually dimorphic disease, with women often presenting with sustained fibrosis and men with more extensive calcification.  However, the intracellular molecular mechanisms that drive these clinically important sex differences remain under explored. Hydrogel scaffolds were designed to recapitulate key aspects of the valve tissue microenvironment and serve as a platform for culture of sex-specific valvular interstitial cells (VICs; precursors to pro-fibrotic myofibroblasts). The hydrogel culture system was used to interrogate intracellular pathways involved in sex-dependent VIC-to-myofibroblast activation and deactivation. RNA-seq was used to define pathways likely to be involved in driving sex-dependent activation. Interventions using small molecule inhibitors were performed to provide mechanistic insight into sex-specific cellular responses to microenvironmental cues, including matrix stiffness and exogenously delivered biochemical factors. In both healthy porcine and human aortic valves, female leaflets had higher baseline activation of the myofibroblast marker, α-smooth muscle actin (α-SMA), compared to male leaflets. When isolated and cultured, female VICs had higher levels of basal α-SMA stress fibers that further increased in response to the hydrogel matrix stiffness, both of which were higher than male VICs. A transcriptomic analysis of male and female porcine VICs revealed Rho-associated protein kinase (RhoA/ROCK) signaling as a potential driver of this sex-dependent myofibroblast activation. Further, we found that genes that escape X-chromosome inactivation, such as BMX and STS (encoding for Bmx non-receptor tyrosine kinase and steroid sulfatase, respectively) partially regulate the elevated female myofibroblast activation via RhoA/ROCK signaling. This finding was confirmed by treating male and female VICs with endothelin-1 and plasminogen activator inhibitor-1, factors that are secreted by endothelial cells and known to drive myofibroblast activation via RhoA/ROCK signaling. Together, in vivo and in vitro results confirm sex-dependencies in myofibroblast activation pathways, and transcriptome analyses and small molecule interventions implicate genes that escape X-chromosome inactivation in regulating sex differences in AVS progression. Our results underscore the importance of considering sex as a biological variable to understand the molecular mechanisms of AVS and help guide sex-based precision therapies.

overall_design: Male and female porcine VICs were isolated, seeded on PEG-norbornene hydrogels (elastic modulus ~5.8 kPa) or tissue culture plastic, and cultured in Media 199 (Life Technologies) supplemented with 1% fetal bovine serum, 50 U/mL penicillin, 50 μg/mL streptomycin, and 1 μg/mL amphotericin B for 48 hours. 4 male and 4 female biological replicates are provided, resulting in 16 total samples. VICs cultured on hydrogels were considered to be quiescent fibroblasts, and VICs cultured on tissue culture plastic were considered to be myofibroblasts.

first: Brian

last: Aguado


title: KDM5A inhibits anti-tumor immune response through downregulation of antigen presentation pathway in ovarian cancer

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

institute: The Wistar Institute


title: Transcription Factor Binding Analysis of Wild Type and HHEX-/- ES-derived Pancreatic Progentiors

last: Yang

summary: The pancreas and liver arise from a common pool of progenitors in the foregut endoderm; however, the underlying molecular mechanisms driving this lineage diversification are not fully understood. We combined human pluripotent stem cell guided differentiation and sequential CRISPR-Cas9 loss-of-function screening to uncover regulators of  pancreatic specification. Here we report the discovery of a cell-intrinsic requirement for HHEX, a transcription factor (TF) associated with diabetes susceptibility. HHEX promotes pancreatic differentiation through cooperation with pancreatic TFs as well as common TFs like FOXA2 that are shared by both pancreas and liver differentiation programs. Furthermore, HHEX restricts differentiation plasticity, and deletion of HHEX shifts FOXA2 interaction towards cooperation with HNF4A, driving liver differentiation. Therefore, HHEX safeguards pancreatic differentiation by promoting lineage specification while simultaneously restricting cell fate plasticity, demonstrating how organ domain demarcation requires fine tuning of TF cooperation.

overall_design: Examination of duplicates per genotypes for each differentiation stage

first: Cho

last: Hyunwoo


title: Chromatin Landscape Analysis of Wild Type and HHEX-/- ES-derived Pancreatic Progentiors


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and RNF138-/- mice colorectal transcriptomes in DSS, AOM/DSS and organoids samples

city: Beijing

first: Rong

last: Huang

address: 5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis NGS-derived transcriptome profiling (RNA-seq) in DSS induced chronic inflammation, AOM/DSS induced colitis-associated colorectal tumorigenesis and organoids isolation from colitis-associated colorectal tumorigenesis
Methods: DSS, AOM/DSS and organoids mRNA profiles of  wild-type (WT) and RING Finger 3 (RNF138−/−) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads were trimmed for low-quality sequence, then mapped to mm10 whole genome using STAR v2.6.1d
Results: Using an optimized data analysis workflow, the padj <0.05 and fold change >2 were refered as differential expression. There are 987, 2649 and 2373 differential genes were found in  RNF138-/- compared with  Wild Type in DSS, AOM/DSS and organoids, respectively
Conclusions: Our study revealed NFκB pathway is the main activation pathway regulated by RNF138 loss

overall_design: DSS induced chronic inflammation, AOM/DSS induced colitis-associated colorectal tumorigenesis and organoids isolation from colitis-associated colorectal tumorigenesis (DSS, AOM/DSS and organoids samples ) mRNA profiles of  wild type (WT) and RNF138-/- mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500, The transcriptome analysis revealed NFκB pathway is the main activation pathway regulated by RNF138 loss


title: Sequential CRISPR screening uncovers an intrinsic requirement for HHEX in safeguarding human pancreatic differentiation


title: Stem cell-derived trophoblast organoids model human placental development and susceptibility to emerging pathogens

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Trophoblast organoids derived from placental villi provide a 3D model system of human placental development, but access to first-trimester tissues is limited. Here we report that trophoblast stem cells isolated from naïve human pluripotent stem cells (hPSCs) can efficiently self-organize into 3D stem cell-derived trophoblast organoids (SC-TOs) with a villous architecture similar to primary trophoblast organoids. Single cell transcriptome analysis reveals the presence of distinct cytotrophoblast and syncytiotrophoblast clusters and a small cluster of extravillous trophoblasts, which closely correspond to trophoblast identities in the post-implantation embryo. These organoid cultures display clonal X chromosome inactivation patterns previously described in the human placenta. We further demonstrate that SC-TOs exhibit selective vulnerability to emerging pathogens (SARS-CoV-2 and Zika virus), which correlates with expression levels of their respective entry factors. The generation of trophoblast organoids from naïve hPSCs provides an accessible 3D model system of the developing placenta and its susceptibility to emerging pathogens.

overall_design: Single cell RNA sequencing of trophoblast organoids derived from primary and naïve hTSCs.

first: Thorold

last: Theunissen

first: Rowan

last: Karvas


title: RNA-Seq analysis of strawberry fruit receptacles treated with Azacytidine vs control tissues treated with water

city: Cordoba

first: Antonio

middle: Rodriguez

last: Franco

state: CORDOBA

address: Rabanales. Ed Severo Ochoa

department: Bioquímica y Biología Molecular

country: Spain

institute: Universidad de Córdoba

summary:
We injected 0.1mM of the hypomethylating agent 5-azacytidine to halves of green, unripen strawberry receptacles. The other halves were injected with water and used as control.
Control tissues ripened normally whereas the 5-azacytidine treated tissues remained green and unripen
Both tissues were separated with a scalpel, and frozen at -80ºC until use

overall_design: RNA-Seq diffenential expression analysis with both type of tissues

first: Juan

last: Blanco


title: Transcription Landscape Analysis of Wild Type and HHEX-/- ES-derived Pancreatic Progentiors

summary: The pancreas and liver arise from a common pool of progenitors in the foregut endoderm; however, the underlying molecular mechanisms driving this lineage diversification are not fully understood. We combined human pluripotent stem cell guided differentiation and sequential CRISPR-Cas9 loss-of-function screening to uncover regulators of pancreatic specification. Here we report the discovery an unexpected, cell-intrinsic requirement for HHEX, a transcription factor (TF) associated with diabetes susceptibility. HHEX promotes pancreatic differentiation through cooperation with pancreatic TFs as well as common TFs like FOXA2 that are shared by both pancreas and liver differentiation programs. Furthermore, HHEX restricts differentiation plasticity, and deletion of HHEX causes a shift of FOXA2 interaction towards cooperation with HNF4A to drive liver differentiation. Our findings demonstrate a critical role for the fine tuning of TF cooperation in organ domain demarcation, as exemplified by how HHEX safeguards pancreatic differentiation by simultaneously promoting lineage specification and restricting cell fate plasticity.

overall_design: RNA-seq at various stages of ES-derived pancreatic progenitor differentiation in the context of WT and HHEX KO

first: Danwei

last: Huangfu

first: Richard

middle: P

last: Koche


title: Viral Mimicry by Endogenous Y-RNAs Contributes to Antiviral Immunity [HIV]

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Pattern recognition receptors (PRRs) protect against host invasion by detecting specific molecular patterns found in pathogens and initiating an immune response. While microbial-derived PRR ligands have been extensively characterized, the contribution and relevance of endogenous ligands to PRR activation during viral infection remain overlooked. In this work, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors upon infection by a positive-sense RNA virus, a negative-sense RNA virus or a retrovirus. We found that several endogenous RNAs transcribed by RNA polymerase 3 (Pol3), and in particular the Y-RNA family of small non-coding repeats, bind and activate RIG-I. We show that this recognition is dependent on Y-RNA mimicking viral secondary structure and its 5’-triphosphate extremity. Further, we found that HIV-1 infection triggers a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, leading to an increase of Y-RNA 5’-triphosphorylation that enables their immunogenicity. Importantly, we show that altering DUSP11 expression is sufficient to induce a type-I interferon and T cell activation transcriptional program associated with HIV-1 infection. Overall, our work uncovers the critical contribution of endogenous RNAs ligands to antiviral immunity and demonstrates the role of this pathway in HIV-1

sample_organism:
Homo sapiens
Human immunodeficiency virus 1

overall_design: For each experimental condition three biological replicates were performed each time. No data were excluded from analysis

first: Nicolas

last: VABRET

first: Valérie

last: NAJBURG

first: Alexander

last: SOLOVYOV

first: Petr

last: ŠULC

first: Sreekumar

last: BALAN

first: Guillaume

last: BEAUCLAIR

first: Maxime

last: CHAZAL

first: Hugo

last: VARET

last: LEGENDRE

first: Odile

last: SISMEIRO

first: Raul

last: DAVID

first: Christopher

last: McCLAIN

first: Ramya

last: GOPAL

first: Lise

last: CHAUVEAU

first: Olivier

last: SCHWARTZ

first: Nolwenn

last: JOUVENET

first: Martin

last: MARKOWITZ

first: Frédéric

last: TANGY

first: Nina

last: BHARDWAJ

first: Benjamin

last: GREENBAUM

first: Anastasia

middle: V

last: KOMAROVA


title: Viral Mimicry by Endogenous Y-RNAs Contributes to Antiviral Immunity [MV]

first: Rachel

last: Legendre

summary: Pattern recognition receptors (PRRs) protect against host invasion by detecting specific molecular patterns found in pathogens and initiating an immune response. While microbial-derived PRR ligands have been extensively characterized, the contribution and relevance of endogenous ligands to PRR activation during viral infection remain overlooked. In this work, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors upon infection by a positive-sense RNA virus, a negative-sense RNA virus or a retrovirus. We found that several endogenous RNAs transcribed by RNA polymerase 3 (Pol3), and in particular the Y-RNA family of small non-coding repeats, bind and activate RIG-I. We show that this recognition is dependent on Y-RNA mimicking viral secondary structure and its 5’-triphosphate extremity. Further, we found that HIV-1 infection triggers a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, leading to an increase of Y-RNA 5’-triphosphorylation that enables their immunogenicity. Importantly, we show that altering DUSP11 expression is sufficient to induce a type-I interferon and T cell activation transcriptional program associated with HIV-1 infection. Overall, our work uncovers the critical contribution of endogenous RNAs ligands to antiviral immunity and demonstrates the role of this pathway in HIV-1 infection.

sample_organism:
Homo sapiens
Measles virus strain Schwarz

overall_design:
for each experimental condition three biological replicates were performed each time. No data were excluded from analysis
HEK293 cells described in DOI: 10.7554/eLife.11275;

first: Nicolas

last: VABRET

first: Valérie

last: NAJBURG

first: Alexander

last: SOLOVYOV

first: Petr

last: ŠULC

last: BALAN


title: Viral Mimicry by Endogenous Y-RNAs Contributes to Antiviral Immunity [mock]

first: Sreekumar

first: Guillaume

last: BEAUCLAIR

first: Maxime

last: CHAZAL

first: Hugo

last: VARET

last: LEGENDRE

first: Odile

last: SISMEIRO

last: DAVID


title: Viral Mimicry by Endogenous Y-RNAs Contributes to Antiviral Immunity [DV-4]

sample_organism:
Homo sapiens
dengue virus type 4

platform_organism:
Homo sapiens
dengue virus type 4

overall_design:
for each experimental condition three biological replicates were performed each time. No data were excluded from analysis
HEK293 cells described in DOI: 10.7554/eLife.11275; Dengue virus 4 in doi: 10.1016/j.celrep.2018.06.047

first: Raul

first: Christopher

last: McCLAIN

first: Ramya

last: GOPAL

first: Lise

last: CHAUVEAU

first: Olivier

last: SCHWARTZ

last: JOUVENET

last: MARKOWITZ


title: Viral Mimicry by Endogenous Y-RNAs Contributes to Antiviral Immunity

last: Legendre

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

sample_organism:
Homo sapiens
dengue virus type 4
Measles morbillivirus
Human immunodeficiency virus 1
Measles virus strain Schwarz

overall_design: Refer to individual Series


title: Brain motor and fear circuits differentially regulate leukocyte distribution and function during acute stress [single-cell RNA-seq]

status: Public on Apr 28 2022

first: Wolfram

middle: Christian

last: Poller

address: One Gustave L. Levy Place

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

summary: The nervous and immune systems are intricately linked. Although psychological stress is known to affect immune function, direct mechanistic pathways linking stress networks in the brain to peripheral leukocytes remain poorly understood. Here, we show that distinct brain regions shape leukocyte distribution throughout the body during acute stress in mice. Using optogenetics and chemogenetics, we demonstrate that the motor cortex induces rapid neutrophil mobilization to peripheral tissues via skeletal muscle-derived neutrophil-attracting chemokines. Conversely, the paraventricular hypothalamus controls monocyte and lymphocyte egress from secondary lymphoid organs and blood to the bone marrow via direct and cell-intrinsic glucocorticoid signaling. These stress-induced counter-directional and population-wide leukocyte shifts are associated with altered disease susceptibility. On the one hand, acute stress changes innate immunity by reprogramming neutrophils and precipitating their recruitment to atherosclerotic plaques. On the other hand, stress-induced leukocyte shifts impair adaptive immunity, increasing susceptibility to SARS-Cov-2 and influenza infection but protecting against autoimmunity in a model of multiple sclerosis. Collectively, these data show that distinct brain regions differentially and rapidly tailor the leukocyte landscape during psychological stress, thus calibrating the immune system’s capacity to respond to physical threats.

overall_design: We FACS sorted blood neutrophils (CD45+;LIN-;CD11b+;Ly-6G+) from wild type mice under three different conditions: 1. relaxed; 2. 1h restraint stressed; 3. 1h restraint stressed followed by 3 hours of recovery

first: Filip

last: Swirski


title: Brain motor and fear circuits differentially regulate leukocyte distribution and function during acute stress


title: Brain motor and fear circuits differentially regulate leukocyte distribution and function during acute stress [bulk RNA-seq]


title: Centromere interactions promote the maintenance of the multipartite genome in Agrobacterium tumefaciens

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

institute: Indiana University at Bloomington

summary: Many pathogens and symbionts contain multipartite genomes, but how they are stably maintained is poorly understood. The plant pathogen, Agrobacterium tumefaciens, contains four replicons. Recent work indicates that their replication origins cluster at cell poles in a manner that depends on their ParB-family centromeric proteins. Here, we provide evidence that centromeric clustering is mediated by interactions between these centromeric proteins. We further show that the disruption of centromere clustering results in the loss of replicons. Our data establish the role of centromeric clustering in multipartite genome maintenance.

sample_organism:
Agrobacterium tumefaciens
Bacillus subtilis PY79

overall_design: Hi-C and ChIP-seq experiments were performed on wild type and mutant cells of Agrobacterium tumefaciens C58 or 15955 growing in LB, ATGN and mutant cells of Bacillus subtilis PY79 growing in rich media.

first: X


title: Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer [scRNA-seq]

city: Stanford

first: Winston

last: Becker

address: 1291 Welch Road, B259 Beckman Center

department: Genetics

institute: Stanford University

summary: To chart cell composition and cell state changes that occur during the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated single-cell chromatin accessibility profiles and single-cell transcriptomes from polyps, normal tissues, and CRCs collected from patients with or without germline APC mutations. We find that a large fraction of polyp and CRC cells exhibit a stem-like phenotype, and we define a continuum of epigenetic and transcriptional changes occurring in these stem-like cells as they progress from homeostasis to CRC.

overall_design: Nuclei from unaffected colon, polyps, and CRC samples were isolated with douncing. Following nuclei isolation, 10x scRNAseq and scATAC-seq assays were performed.

first: Stephanie

middle: A

last: Nevins

first: Derek

last: Chen

first: Roxanne

last: Chiu

first: Aaron

last: Horning

first: Tuhin

last: Guha

first: Rozelle

last: Laquindanum

first: Meredith

last: Mills

first: Hassan

last: Chaib

first: Uri

last: Ladabaum

first: Teri

last: Longacre

first: Jeanne

last: Shen

first: Edward

last: Esplin

first: Anshul

last: Kundaje

first: James

last: Ford

first: Christina

last: Curtis

first: Michael

last: Snyder

first: William

middle: J

last: Greenleaf


title: Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer [ATAC-seq]

first: Winston

last: Becker

first: Stephanie

last: Nevins


title: Quantitative single-cell transcriptome-based ranking of engineered AAVs in human retinal explants

city: Pittsburgh

first: Leah

last: Byrne

state: PA

address: 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

summary: Gene therapy is a rapidly developing field, and adeno-associated virus (AAV) is a leading viral vector candidate for therapeutic gene delivery. Newly engineered AAVs with improved abilities are now entering the clinic. It has proven challenging, however, to predict the translational potential of gene therapies developed in animal models, due to cross-species differences. Human retinal explants are the only available model of fully developed human retinal tissue, and are thus important for the validation of candidate AAV vectors. In this study, we evaluated 18 wildtype and engineered AAV capsids in human retinal explants using a recently developed single-cell RNA-Seq AAV engineering pipeline (scAAVengr). Human retinal explants retain the same major cell types as fresh retina, with similar expression of cell-specific markers, except for a photoreceptor population with altered expression of photoreceptor-specific genes. The efficiency and tropism of AAVs in human explants was quantified, with single cell resolution. The top performing serotypes, K91, K912, and 7m8, were further validated in non-human primate and human retinal explants. Together, this study provides detailed information about the transcriptome profiles of retinal explants, and quantifies the infectivity of leading AAV serotypes in human retina, accelerating the translation of retinal gene therapies to the clinic.

overall_design: Single cell RNA analysis of human explant retina

first: Zhouhuan

last: Xi

first: Bilge

middle: E

last: Öztürk

first: Molly

last: Johnson

first: Serhan

last: Turunç

last: Stauffer


title: Pseudomonas putida KT2440 transcriptomes for the putidaPRECISE321 study

city: San Diego

first: Bernhard

middle: O.

last: Palsson

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

summary: Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1,993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

overall_design: Ribosomal RNA removed RNA prepared from cell cultures of Pseudomonas putida KT2440 at the exponential phase.

first: Hyun

middle: G

last: Lim

first: Joshua

last: Mueller

first: Wei

last: Niu

middle: O


title: Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution.

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

summary: Our findings reveal a high degree of both genomic and transcriptomic heterogeneity in established and globally utilized PDAC cell lines, custodial variation induced by growing apparently identical PDAC cell lines in different laboratories, and profound transcriptomic shifts in transitioning from 2D to 3D spheroid growth models. Our findings also call into question the validity of widely available immortalized, non-transformed pancreatic lines as contemporaneous “control” lines in experiments. Further, while patient-derived organoids (PDOs) are known to reflect the cognate in vivo biology of the parental tumor, we identify transcriptomic shifts during ex vivo passage that might hamper their predictive abilities over time. The impact of these findings on rigor and reproducibility of experimental data generated using established preclinical PDAC models between and across laboratories is uncertain, but a matter of concern.

overall_design: Single cell RNA (11 samples), single nuclei ATAC (2 samples), and single cell copy number variation (9 samples)sequencing analysis of pancreatic cancer cell lines and 2 passages of a patient-derived organoid.

first: Maria

last: Monberg

first: Heather

last: Geiger

first: Roshan

last: Sharma

first: Jaewon

last: Lee

first: Alexander

last: Semaan

first: Bret

middle: M

last: Stephens

first: Vincent

last: Bernard

first: Daniel

last: Swartzlander

first: Ken

last: Chen

first: Matthew

middle: H

last: Katz

first: Nicolas

last: Robine

first: Paola

last: Guerrero

first: Fang

last: Wang

first: Shaoheng

last: Liang

first: Justin

last: Wong


title: Transcriptome analysis of the wildtype and engineered Pseudomonas putida strains grown on different carbon sources (a part of putidaPRECISE321)

first: Bernhard

last: Palsson

summary: This dataset is a part of putidaPRECISE321, which was utilized to unveil the trnascriptional regulatory network of Pseudomonas putida KT244. Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1,993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

first: Hyungyu

last: Lim

first: Gayle

last: Bentley

first: Christopher

middle: W

last: Johnson

first: Gregg

middle: T

last: Beckham


title: MiR-181b targets semaphorin 3a to mediate TGF-β-induced endothelial-to-mesenchymal transition related to atrial fibrillation

status: Public on Apr 27 2022

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background:This study investigated if and how atrial endothelial cells may transform to mesenchymal cells and contribute to atrial fibrosis via endothelial-to-mesenchymal transition (EndMT).
Results:We show a novel mechanistic link between TGF-β1/SMAD signaling and decreased Sema3a expression through the induction of miR-181b; this pathway plays an important role in EndMT associated with the pathogenesis of AF. Both miR-181b and Sema3a are potential therapeutic targets in AF.

overall_design: A total of 8 mice were divided into two groups for study: wild-type mice(N=4) and TGFbeta transgene mice(N=4). Specimens of atrium from the mice were used for NGS study.

first: Ying-Ju

last: Lai

first: Feng-Chun

last: Tsai

first: Gwo-Jyh

last: Chang

first: Shang-Hung

first: Chung-Chi

last: Huang

first: Wei-Jan

first: Yung-Hsin

last: Yeh


title: Longitudinal and transversal comparison of iPSC-derived ALS_C9orf72 and healthy motor neurons at DIV21 and DIV42

city: ULM

first: Alberto

last: Catanese

address: Albert-Einstein-Allee 11

institute: Ulm University

summary: We performed total RNA sequencing in order to gain insights into the transcriptional differences between iPSC-derived ALS-diseased (2 patient cell lines, each harboring a C9orf72-mutation) and healthy (2 control cell lines) motor neurons at two different time points. Furthermore, we compared the transcriptomes of each genotype between the two time points to uncover alterations in neuronal maturation in ALS_C9orf72 motor neurons.

overall_design: Whole transcriptome analysis of control and ALS_C9orf72 motor neurons at DIV21 and DIV42

first: Daniel

last: Sommer

first: Tobias

last: Böckers


title: MAVS mediates a protective immune response in the brain to Rift Valley fever virus

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: Rift Valley fever virus causes severe disease in humans and livestock and in some cases can be fatal. There is concern about the use of Rift Valley fever virus as a bioweapon since it can be transmitted through the air, and there are no vaccines or antiviral treatments. Airborne transmission of the virus causes severe inflammation of the brain, yet little is known about the immune response against the virus in this organ. Here, we investigated the immune response in the brain to Rift Valley fever virus following intranasal infection. We determined that microglia, the resident immune cells of the brain, initiate a robust response to Rift Valley fever virus infection and identified a key immune pathway that is critical for the ability of microglia to respond to infection. When this immune pathway is rendered non-functional, mice have a dysregulated response to infection in the brain.

overall_design: C57BL/6J or Mavs-/- male and female mice (12 weeks old) were inoculated intranasally with 5x10^5 PFU RVFV MP-12. Brains were isolated from infected and uninfected control animals on day 7 post-infection. A single cell suspension was generated from whole brain and cells were sequenced to obtain single-cell level gene expression profiles.

first: Dina

last: Weilhammer

first: Nicholas

last: Hum


title: AOM/DSS tumors 5FU+Irinotecan treatment

city: Nashville

first: Ken

last: Lau

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary:
The tumor microenvironment plays a key role in the pathogenesis of colorectal tumors and contains various cell types including epithelial, immune, and mesenchymal cells. Characterization of the interactions between these cell types is necessary for revealing the complex nature of tumors. In this study, we used single-cell RNA-seq (scRNA-seq) to compare the tumor microenvironments between a mouse model of sporadic colorectal adenoma (Lrig1CreERT2/+;Apc2lox14/+) and a mouse model of inflammation-driven colorectal cancer induced by azoxymethane and dextran sodium sulfate (AOM/DSS). While both models develop tumors in the distal colon, we found that the two tumor types have distinct microenvironments. AOM/DSS tumors have an increased abundance of two populations of cancer-associated fibroblasts (CAFs) compared with APC tumors, and we revealed their divergent spatial association with tumor cells using multiplex immunofluorescence (MxIF) imaging. We also identified a unique squamous cell population in AOM/DSS tumors, whose origins were distinct from anal squamous epithelial cells. These cells were in higher proportions upon administration of a chemotherapy regimen of 5-Fluorouracil/Irinotecan. We used computational inference algorithms to predict cell-cell communication mediated by ligand-receptor interactions and downstream pathway activation, and identified potential mechanistic connections between CAFs and tumor cells, as well as CAFs and squamous epithelial cells. This study provides important preclinical insight into the microenvironment of two distinct models of colorectal tumors and reveals unique roles for CAFs and squamous epithelial cells in the AOM/DSS model of inflammation-driven cancer.
This series comprises the drug treatment set as well as the fibroblast enrichment set.

overall_design: post-treatment day 1 , 3 , 6. Untreated

first: Paige

last: Vega

first: Alan

last: Simmons

first: Hiroaki

last: Niitsu


title: E-Selectin/AAV2/2 Gene Therapy Alters Angiogenesis and Inflammatory Gene Profiles in Mouse Gangrene Model

city: Miami

first: Zhao-Jun

last: Liu

address: 1600 NW 10th Ave, RMSB 1010

institute: University of Miami Miller School of Medicine