title: Elucidating the CodY regulon in Staphylococcus aureus USA300 lineage using ChIPexo

status: Public on Aug 29 2022

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

summary: CodY is a conserved broad acting transcriptional factor that regulates the expression of genes related to amino acid metabolism and virulence in Staphylococcus aureus. CodY target genes have been studied by using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). In this study we performed the first in vivo determination of CodY target genes using a novel CodY monoclonal antibody in established ChIP-exo protocols. Our results showed, 1) The same 165 CodY target genes in both strains; 2) That the differential binding intensity for the same target genes under the same conditions were due to sequence differences in the same CodY binding site in the two strains; 3) Based on transcriptomic data, a CodY regulon comprising 72 target genes that revealed that CodY is mainly involved in amino acid transport and metabolism, inorganic ion transport and metabolism, and cellular transcription and translation; and 4) CodY systematically regulated central metabolic flux to generate branched-chain amino acids (BCAAs) by mapping the CodY regulon onto a genome-scale metabolic model of S. aureus. Our study performed the first system-level analysis of CodY in two closely related dominant USA300 TCH1516 and LAC strains, thus expanding the size of the known CodY regulon, and giving new insights into the similarities and differences of CodY regulatory roles between closely related strains.

overall_design: Expression profiling data for wild type S. aureus JE2 and  its corresponding codY mutant strains were generated by RNA-seq, in duplicate

first: Bernhard

last: Palsson


title: Hypoxia-Induced Transcriptional Differences in African and Asian Versus European Diabetic Cybrids

status: Public on Aug 22 2022

city: Irvine

first: Maria

middle: Cristina

last: Kenney

state: CA

address: 843 Health Science Rd

department: Ophthalmology

country: USA

institute: University California Irvine

type: Expression profiling by high throughput sequencing

summary:
We then performed gene expression profiling analysis using data obtained from RNA-seq of 16 different cybrid lines at normoxia and hypoxia conditions.
The goal was to compare the impact of mitochondrial haplogroup (European vs Non-European) on gene expression in the above conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Andrew

middle: H

last: Dolinko

first: Marilyn

last: Chwa

first: Kevin

last: Schneider

first: Jie

last: Wu

first: Cristina

last: M Kenney


title: Chromatin Accessibility differentiates Invasive Lobular from Invasive Ductal Breast cancer and Dictates Response to Endocrine Treatment

status: Public on Aug 31 2022

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Unique microRNA expression profiles in plasmic exosomes from intrahepatic cholestasis of pregnancy

status: Public on Aug 09 2022

city: chengdu

first: wang

last: xiaodong

state: China

address: Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University.

country: China

summary: Intrahepatic cholestasis of pregnancy (ICP) is strongly associated withan increased risk of adverse perinatal outcomes. Total bile acid (TBA) levels in the late second or third trimester are a major factor in the diagnosis. Here, we sought to establish the miRNA expression profile of plasma exosomes of ICP and identify possible biomarkers for the diagnosis of ICP.

overall_design: This case-control study involved 14 ICP patients as the experimental group and 14 healthy pregnant women as the control group. Among them, three ICP patients and three controls were used for isolation plasmic exosome and preliminary miRNA array analysis. The Agilent miRNA array was utilized to dynamically monitor the miRNA expression inplasmic exosomes of includedpatients in the first trimester(T1), second trimester(T2), third trimester (T3),and delivery (T4).

first: Yao

last: Kong

first: Yongchi

last: Zhan

first: Daijuan

last: Chen

first: Xixi

last: Deng

first: Xinghui

last: Liu

first: Tingting

last: Xu

first: Xiaodong

last: Wang


title: Voluntary running exercise after focal cerebral ischemia modifies astrocytic population and features

status: Public on Aug 08 2022

city: Kusatsu

first: Natsumi

last: Yamaguchi

state: Shiga

address: 1-1-1 Noji-Higashi

country: Japan

institute: Ritsumeikan University

summary: Voluntary running exercise after focal cerebral ischemia promotes functional recovery and prevents the ischemia-induced dendritic spine loss in the peri-infarct motor cortex layer 5. Neuronal morphology is affected by the perineuronal environmental change. Glia exert crucial roles in the formation of perineuronal environment, and exercise-induced changes of glial phenotype are expected. Here, we demonstrated that voluntary running exercise increased the population of newborn astrocytes in the acute phase after cerebral ischemia at late phase. Transcriptome analysis detected 10 upregulated genes and 70 downregulated genes by exercise in the ipsilateral cortex astrocytes. Gene cluster downregulated by exercise were significantly associated with neuronal morphology. The expression of Lipocalin 2, a factor of decreasing dendritic spines, tended to be decreased in the postischemic astrocytes by exercise. Our results suggest that exercise modifies the phenotype of postischemic astrocytes, which relate to the exercise-induced amelioration of postischemic dendritic spine loss.

overall_design: To induce permanent focal cerebral ischemia, middle cerebral artery occlusion (MCAO) was performed for seven-weeks old male C.B-17/Icr-+/+Jcl mice. Mice were divided into MCAO + non-exercise group and MCAO + exercise group. MCAO + exercise group mice were exposed to running wheel after MCAO for voluntary exercise for 15 days. To detect the newborn cells after cerebral ischemia, 5-bromo-2’-deoxyuridine (BrdU) was administered to each group through intraperitoneal injection with a dose of 50 mg/kg/day at postoperative day (POD) 0 (immediately after MCAO), 1, 2 and 3. Transcriptome of postischemic astrocytes were compared between MCAO + non-exercise group and MCAO + exercise group at POD15 by sorting ACSA-2-positive astrocytes from the ipsilateral cortices.

first: Toshinori

last: Sawano

first: Jin

last: Nakatani

first: Akiko

last: Nakano-Doi

first: Takayuki

last: Nakagomi

first: Tomohiro

last: Matsuyama

first: Hidekazu

last: Tanaka


title: Topo1cc siganls are presented at the KCl induced acutely activated enhancers [CUT&RUN]

status: Public on Aug 04 2022

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

summary: Topo1cc siganls are serving as the marker for the KCl induced acutely enhancer activation in cortical neurons.

overall_design: CUT&RUN assays  were designed to investigate the Topo1cc signals at KCl induced neuronal active enhancers.


title: PRO-seq assay in human breast cancer MCF7 cells

summary: PRO-seq assay was performed to detect the function of Top1 in the activation of acutely activated phase-separated MegaTrans enhancers.

overall_design: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. For knock-down of Top1 genes, the siTop1_1  and siTop1_3  were employed.


title: Detection and localization of early- and late-stage cancers using tumor-educated platelet RNA

status: Public on Aug 05 2022

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

summary: We report RNA-sequencing data of 2351 blood platelet samples, including 1628 patients with stage I-IV cancer (of which 18 different tumor types), 390 asymptomatic controls and 333 symptomatic controls. This dataset highlights the ability of TEP RNA-based 'liquid biopsy' diagnostics for the detection and localization of early- and late-stage cancers.

overall_design: Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 or 4000 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the humane reference genome using STAR, and intron-spanning reads were summarized using HTseq.

middle: G

first: Sjors

last: In 't Veld

first: Thomas

last: Wurdinger


title: The Deciphering of Mouse Uterine Microenvironment during Early Pregnancy [scRNA-seq]

status: Public on Jul 30 2022

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: The mouse uterine microenvironment at pregnancy D7.5 was investigated by Visium spatial transcriptome. Ten distinct uterine microenvironments were identified with diverse biological functions, different endocrine regulations and intensive interactions. The single cell RNA-seq of D7.5 mouse uterus has been intergrated with the spatial visium results and predicted the presence of mutiple types of cells in each microenvironment.

overall_design: The mosue uterus were collected at D7.5, either sectioned for Visium spatial transcriptome, or isolated into single cell for scRNA-Seq.

first: Rong

last: Li

first: Tianyuan

first: Xin

first: Olivia

last: Emery

first: Myeongjin

last: Jin

first: San-Pin

last: Wu

first: Francesco

middle: J

last: DeMayo


title: The Deciphering of Mouse Uterine Microenvironment during Early Pregnancy


title: Ku70/HP1g are presented at the KCl induced acutely activated enhancers [ChIP-seq]

summary: Ku70/HP1g are serving as the marker for the KCl induced acutely enhancer activation in cortical neurons.

overall_design: All ChIP-Seq experiments were designed to investigate the Ku70/HP1g signals at KCl induced neuronal active enhancers.


title: Circular RNA hsa_circ_0064559 is identified to affect the progression of colorectal cancer

status: Public on Jul 29 2022

city: Jinan

first: Ya'nan

last: Zhen

state: Shandong

address: No.38 Wuyinshan Road

department: Department of Gastrointestinal Surgery

institute: The Third Affiliated Hospital of Shandong First Medical University

summary:
In the present study, six pairs of matched CRC and normal colorectal tissue samples were searched for genes that may influence proliferation.
Affymetrix Clariom D array research revealed 13 genes that may be engaged in the progression of CRC.

overall_design: We identified differentially expressed genes (DEGs) between colorectal tumor tissues and matched adjacent normal tissues, using Affymetrix Clariom D array

first: YA’NAN

last: ZHEN

first: GUODONG

last: SUN

first: CUNBAO

last: CHEN

first: JIANQI

last: LI

first: RUIXUE

last: XIAO

first: ZHONGFA

last: XU


title: MiRNA expression patterns in anaplastic thyroid cancer and papillary thyroid cancer cell lines

status: Public on Jul 22 2022

city: Baltimore

first: Bonita

last: Powell

address: 733 N Broadway, MRB 8 829

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Anaplastic thyroid carcinoma (ATC) is a rare but deadly thyroid cancer. In contrast, papillary thyroid carcinoma (PTC) is common and highly curable. Minimally invasive biomarkers are needed to distinguish ATC and PTC. Here, by small RNA-seq we show the differential expression levels of several miRNAs, which include miR-34a and miR-210 in ATC compared to PTC cell lines.

overall_design: Total RNA was extracted from SW1736, C643, TPC-1 and BCPAP cell lines then subject to small RNA sequencing to identify differentially expressed miRNAs between anaplastic thyroid cancer and papillary thyroid cancer cell lines.

first: Liliana

last: Florea

first: Kenneth

last: Witwer


title: Gene expression profile of hyaluronan-induced cell clusters in multiple myeloma

status: Public on Jul 31 2022

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

summary: We identified the changes in gene expression profile in hyaluronan-induced spheroids to elucidate the mechanisms of drug resistance of extramedullary disease in multiple myeloma.

overall_design: We cultured human myeloma cell lines KMS12 and MM.1S with hyaluronan under shear stress to facilitate cell cluster formation and subjected them to gene expression profiling using an Agilent GeneChip Array with corresponding myeloma cells cultured without shear stress as controls.

first: Jiro

last: Kikuchi


title: Transcriptomic analysis of TCF-7 cKO CD4 T cells

city: Syracuse

first: Mobin

last: Karimi

state: NY

address: 766 Irving Ave Suite 2281

department: Microbiology/Immunology

institute: Suny Upstate Medical University

summary: The transcription factor T Cell Factor-1 encoded by (TCF-7) is critical for T cell development. However, the role of TCF-7 on peripheral CD4 T cells mediated allo-immunity was not known. In this report using a clinically relevant model we presented novel finding of how TCF-7 regulates CD4 T cells functions, including CD4 T cells activation, proliferation, differentiation and impacts effector and central memory formation. We uncovered how TCF-7 regulates chemokine receptor which are essential for CD4 T cells migration to the site of inflammation. Our data uncovered how TCF-7 plays critical role in CD4 T cells survival, apoptosis. Using in vivo allo-immunity models and in-vitro studies we demonstrated how TCF-7 plays central role in CD4 T cells mediated damaged to organs like liver, skin and small intestine.   We provided both molecular and biochemical and transcriptomic evidence how TCF-7 functionally regulates CD4 T cells mediated apoptosis and cell death, T cell mediated processes, pro-inflammatory and anti-inflammatory cytokines productions in both basal level and after allo-activation. These findings novel findings represent a stem forward to designing target specific approach for CD4 T cells mediated diseases while understand molecular mechanism the role of CD4 T cells in allo-immunity.

overall_design: We analyzed FACS purified CD8 T cells of 3 different  TCF-7 cKO and WT mouse labeled this group of samples as pre-transplanted samples. For post-transplanted samples 1 x10^6 CD3 T Cells from  TCF-7 cKO and WT mice were initially transplanted into lethally irradiated recipent Balb/c mouse and at day 7 post-transplant H2kb+ donor CD4 and CD8 T cells  FACS sorted  from the spleen of recipients into the Trizol.

first: Mahinbanu

last: Mammadli


title: Impact of pregnancy status on the transcriptome of peripheral white blood cells

status: Public on Aug 10 2022

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Pregnancy poses an immunological challenge because the fetus must be supported within the pregnant female during the entire gestational period. Indeed, the mechanisms behind the maternal immune respond to pregnancy are not fully understand yet. As such, the goal of this study was to compare the gene expression profiles of peripheral blood leukocytes between pregnant and non-pregnant dairy cows 21 after embryo transfer.

overall_design: Nulliparous Holstein heifers were subjected to embryo transfer using fresh IVF embryos. Pregnancy diagnosis was performed on day 21 after embryo transfer. A total of 10 heifers, 5 pregnant and 5 non-pregnant, were used in this study.

first: Jorge

last: de los Santos


title: The diapause-like colorectal cancer cells induced by SMC4 attenuation are characterized by low proliferation and chemotherapy insensitivity [CUT&TAG]

status: Public on Jul 17 2022

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

summary: CUT-Tag for histone H4K12la in  HCT116 cells and its shSMC4.

first: xuedan

last: sun

first: lifang

last: he

first: mian

last: wu

first: lianxin

last: liu


title: Single-cell RNA-seq of mouse thymus iNKT cells

city: Detroit

first: Indra

last: Adrianto

state: MI

address: 1 Ford Place

department: Public Health Sciences

institute: Henry Ford Health System

summary: Invariant natural killer T cells (iNKT) cells are innate-like T cells, selected from thymic cortex-resident CD4+CD8+ double positive (DP) thymocytes.  Despite major advances in the understanding of iNKT cells development, the heterogeneity of iNKT subsets and underlying molecular programs that guide iNKT cell-lineage remain unclear.

overall_design: We profiled the transcriptome patterns of individual mouse thymic iNKT cells across their developmental stages (stages 0 to 3) using a droplet-based single-cell RNA-sequencing (scRNA-seq) approach.

first: Jie

last: Wang

first: Xiaojun

last: Wu

first: Li

last: Zhou

first: Qing-Sheng

last: Mi


title: Cluster Analysis of Plasma Cytokines and Neutrophil Transcriptomic Profiling of Children with Asthma in the Pediatric Intensive Care Unit

status: Public on Jul 15 2022

city: Atlanta

first: Milad

last: Rad

state: GA

address: 266 Ferst Dr NW

department: School of Electrical and Computer Engineering

institute: Georgia Institute of Technology

summary:
We determined whether we could identify clusters of children with critical asthma by plasma cytokine concentration. Differences in gene expression between the two clusters were analyzed using a targeted Nanostring immunology array.
We performed a single-center, prospective, observational cohort study of 64 children ages 6 – 17 years admitted to a pediatric intensive care unit for an asthma attack between July 2019 to February 2021.

overall_design: Neutrophils were isolated from children and mRNA was analyzed using a targeted Nanostring immunology array. Network analysis of the differentially expressed transcripts for the clusters defined by plasma cytokine concentrations was performed.

first: Jocelyn

middle: R

last: Grunwell

first: Rishikasan

last: Kamaleswaran


title: Effect  of organic nitrogen on gene expression of clavulanic acid biosynthesis in Streptomyces clavuligerus F613-1

status: Public on Aug 25 2022

first: Guangxiang

last: Cao

address: 18877 jingshi Road

institute: Shandong Academy of Medical Sciences

summary:
To investigate the function of organic nitrogen on clavulanic acid biosynthesis in Streptomyces clavuligerus, we established  F613-1 strain cells cultured in MH fermentation medium and ML fermentation medium.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different medium at three time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for F613-1 strains cultured in MH fermentation medium and ML fermentation medium.

first: Jiafang

last: Fu


title: Chromatin Accessibility differentiates Invasive Lobular from Invasive Ductal Breast cancer and Dictates Response to Endocrine Treatment

first: Rinath

last: Jeselsohn

summary: Invasive lobular breast cancer (ILC) is the second most common histological sub-type of breast cancer. Although the majority of ILC are strongly hormone receptor positive and are of low-intermediate grade, they present a number of clinical challenges. These challenges include limitations in physical exam and breast imaging for early detection, decreased response to chemotherapy and prospective evidence for differences in the benefit from specific adjuvant endocrine treatment regimens when compared to invasive ductal cancer (IDC). In addition to loss of e-cadherin, ILCs possess genetic alterations that are suggestive of a unique estrogen receptor(ER) axis, including an increase in the frequency of FOXA1 mutations and decrease in GATA3 truncating mutations. We performed a randomized Phase II clinical trial, Palbociclib and Endocrine therapy for LObular breast cancer Preoperative Study (PELOP), in which patients were stratified by histological subtype and found that the magnitude of the difference between the benefit from letrozole compared tamoxifen is significantly higher in ILC versus IDC. To elucidate the mechanism underlying this divergent response we comprehensively studied the ER axis in experimental models of ILC and IDC and clinical samples and show that ILC harbors a unique ER transcriptional axis that stems from increased FOXA1 chromatin binding and an altered chromatin state. These findings provide insights to the unique pattern of response to endocrine treatment in ILC and mechanisms of resistance to endocrine treatment, and offer new treatment strategies to improve outcomes for patients with this breast cancer subtype."

overall_design: RNA-seq of ductal (MCF7 and T47D) and lobular (MDA134 and SUM44) in full medium, hormone deprivation (WM), WM plus estrogen or tamoxifen, in presence of CDH1 Knockout (KO) or overespression (OE), with shRNA for FOXA1, with siRNA control (CTR) or for CASZ1; in 2-3 replicates, using Illumina NextSeq 500.


title: Evolution of gene regulatory networks during human cardiogenesis

first: Christopher

last: Benner

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: The heart, a vital organ which is first to develop, has adapted its size, structure and function in order to accommodate the circulatory demands for a broad range of animals. Although heart development is controlled by a relatively conserved network of transcriptional/chromatin regulators, how the human heart has evolved species-specific features to maintain adequate cardiac output and function remains to be defined. Here, we show through comparative epigenomic analysis the identification of enhancers and promoters that have gained activity in humans during cardiogenesis. These cis-regulatory elements (CREs) are associated with genes involved in heart development and function, and may account for species-specific differences between human and mouse hearts. Supporting these findings, genetic variants that are associated with human cardiac phenotypic/disease traits, particularly those differing between human and mouse, are enriched in human-gained CREs. During early stages of human cardiogenesis, these CREs are also gained within genomic loci of transcriptional regulators, potentially expanding their role in human heart development. In particular, we discovered that gained enhancers in the locus of the early human developmental regulator ZIC3 are selectively accessible within a subpopulation of mesoderm cells which exhibits cardiogenic potential, thus possibly extending the function of ZIC3 beyond its conserved left-right asymmetry role. Genetic deletion of these enhancers identified a human gained enhancer that was required for not only ZIC3 and early cardiac gene expression at the mesoderm stage but also cardiomyocyte differentiation. Overall, our results illuminate how human gained CREs may contribute to human-specific cardiac attributes, and provide insight into how transcriptional regulators may gain developmental roles through the evolutionary acquisition of enhancers.

overall_design: Chromatin accessibility by ATAC-seq, histone mark mapping by ChIP-seq, expression profiling by RNA-seq

first: Eugin

last: Destici

first: Fugui

last: Zhu

first: Bing

last: Ren

first: Neil

middle: C

last: Chi


title: Vitreous of proliferative diabetic retinopathy patients

city: Zunyi

first: Lan

last: Zeng

state: Guizhou

address: No.98, Fenghuang Road

institute: The First People’s Hospital of Zunyi

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
We identified lncRNA expression profiles in vitreous samples between proliferative diabetic retinopathy (PDR) patients and idiopathic macular hole (IMH) patients, and between PDR patients who had received preoperative anti-vascular endothelial growth factor (anti-VEGF) therapy and PDR patients who had received surgery alone.
There had been the systemic expression differences in vitreous at the microarray level from PDR patients and IMH patients, and from PDR patients after anti-VEGF treatment and untreated PDR patients.

overall_design: This study was divided into 3 groups, which were group A consisting of IMH patients without diabetes, group B consisting of PDR patients pretreated with conbercept 3-7 days before surgery, and group C consisting of PDR patients who received surgery alone.


title: Reading the Covalent Topoisomerase1-DNA Intermediate: A Transcriptional Code Broadly Required for Signal-dependent Enhancer Activation [Human CUT&RUN]

first: Yuliang

last: Tan

summary: Acutely activated enhancers require the actions of Topo1cc, including those induced by 17β-oestradiol (E2), dihydrotestosterone (DHT) and tumor necrosis factor alpha (TNFa). Topo1cc at these acutely activated enhancers is “read” by Ku70, which in this context serves as a required transcriptional coactivator, based on nucleating a Ku70/heterochromatin protein1 gamma (HP1γ) complex to facilitate the recruitment of mediator subunit Med26 for eRNA transcription.

overall_design: CUT&RUN experiments were designed to disclose the presence of Topo1cc at acutely activated enhancers.


first: Shaina

last: Tran

address: 9500 Gilman Dr

summary: Here, we show through comparative epigenomic analysis the identification of enhancers and promoters that have gained activity in humans during cardiogenesis. These cis-regulatory elements (CREs) are associated with genes involved in heart development and function, and may account for species-specific differences between human and mouse hearts. Supporting these findings, genetic variants that are associated with human cardiac phenotypic/disease traits, particularly those differing between human and mouse, are enriched in human-gained CREs. During early stages of human cardiogenesis, these CREs are also gained within genomic loci of transcriptional regulators, potentially expanding their role in human heart development. In particular, we discovered that gained enhancers in the locus of the early human developmental regulator ZIC3 are selectively accessible within a subpopulation of mesoderm cells which exhibits cardiogenic potential, thus possibly extending the function of ZIC3 beyond its conserved left-right asymmetry role. Genetic deletion of these enhancers identified a human gained enhancer that was required for not only ZIC3 and early cardiac gene expression at the mesoderm stage but also cardiomyocyte differentiation. Overall, our results illuminate how human gained CREs may contribute to human-specific cardiac attributes, and provide insight into how transcriptional regulators may gain developmental roles through the evolutionary acquisition of enhancers.

overall_design: Mesoderm cells from three independent differentiations were dissociated with Accutase (STEMCELL) at 37ºC for 10 min and processed fresh for single cell combinatorial indexing (sci)ATAC-seq6,7. Dissociated cells were stained with DAPI (Thermo Fisher Scientific). 500,000 viable cells (DAPI negative) were sorted using a SH800 sorter (Sony) and processed for snATAC-seq


title: Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome

status: Public on Jul 14 2022

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

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

overall_design: Refer to individual Series


title: Ultra-deep 3D genome structure mapping with Region Capture Micro-C

status: Public on Jul 12 2022

first: Viraat

middle: Y

last: Goel

state: MA

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: In an effort to map the deeply map the structure of the genome at loci of interest, we applied Region Capture Micro-C and revealed focal patterns of contact between enhancers & promoters that we term microcompartments. We have mapped genomic structure at 0.4-1.9 Mb-sized regions at the Klf1, Ppm1g, Fbn2, Sox2, and Nanog loci across 4 conditions: wild-type and transcriptionally inhibited mouse Embryonic Stem Cells (mESCs), and cohesin-depletion & control treatments in a RAD21-AID genome-edited mESC line.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Micro-C with capture of five genomic regions in mouse embryonic stem cells, including triptolide treatment and depletion of cohesin subunit RAD21 using the AID system and IAA treatment.

first: Miles

middle: K

last: Huseyin

first: Anders

middle: S

last: Hansen


title: Novel circulating transcriptomic predictors of changes in maximal aerobic capacity in response to endurance training in healthy women

status: Public on Jun 22 2022

city: Fort Collins

first: Thomas

last: LaRocca

state: CO

address: 1582 Campus Delivery

institute: Colorado State University

summary: Maximal aerobic exercise capacity (V̇O2max) is one of the strongest predictors of morbidity and mortality. Aerobic exercise training can increase V̇O2max, but inter-individual variability is marked and unexplained physiologically. The mechanisms underlying this variability have major clinical implications for extending human healthspan. Here, we report the first comprehensive, RNA-seq study of circulating transcriptome signatures related to ΔV̇O2max. We used RNA-seq to characterize transcriptomic predictors of ΔV̇O2max in healthy women who completed a 16-week, randomized controlled trial comparing higher vs. lower aerobic exercise training volume and intensity (four training groups, fully crossed). We found striking baseline gene expression differences in subjects who responded to aerobic exercise training with robust (R) vs. little/no (NR) ΔV̇O2max.

overall_design: PolyA RNA-seq on PBMCs isolated from healthy adult women.


title: Muc1-C Induces Pbrm1-Mediated Chromatin Remodeling in Driving Chronic Inflammation and DNA Damage Resistance in Triple-Negative Breast Cancer

status: Public on Jun 21 2022

first: Nami

last: Yamashita

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: STAT1 and IRF1 are essential effectors of the type I and II interferon (IFN) pathways. Here, we report that the oncogenic MUC1-C protein is necessary for inducing chromatin accessibility and activation of the STAT1 and IRF1 genes in triple-negative breast cancer (TNBC) cells. Our results demonstrate that MUC1-C activates the PBRM1 subunit of the SWI/SNF PBAF chromatin remodeling complex and forms a nuclear complex with PBRM1. We show that MUC1-C associates with PBRM1 and STAT1 on the IRF1 gene at (i) a proximal enhancer-like signature (pELS), and (ii) distal enhancer-like signatures (dELSs). We also show MUC1-C and PBRM1 are necessary for opening chromatin at these signatures and for the induction of IRF1 expression. In extending these results, we found that MUC1-C binds directly to IRF1 and forms nuclear complexes with PBRM1 and IRF1, which are necessary for inducing chromatin accessibility at pELSs of the (i) STAT1 gene, (ii) type II IFN pathway IDO1 and WARS genes, and (iii) type I IFN pathway RIG-I, MDA5 and ISG15 genes. Consistent with involvement of chronic inflammation in promoting the cancer stem cell (CSC) state, we show that MUC1-C, PBRM1 and IRF1 are required for self-renewal of TNBC CSCs. Of translational relevance, we report that targeting MUC1-C, PBRM1 and IRF1 circumvents intrinsic DNA damage resistance of TNBC CSCs and that MUC1-C is necessary for acquired resistance to the PARP inhibitor olaparib. These findings demonstrate that MUC1-C activates PBRM1 and thereby chromatin remodeling of IFN pathway genes that promote chronic inflammation, the CSC state and DNA damage resistance.

overall_design: RNA-seq in breast cancer cell lines


title: ISL1 controls pancreatic alpha cell fate and regulates beta cell differentiation and maturation

status: Public on Jun 17 2022

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science


title: Effect of aging on mitochondrial gene expression using C57BL/6N liver mitochondria

city: Göttingen

first: Abhishek

last: Aich

state: Please Select…

address: Humboldtallee 23,

country: Germany

institute: Universitätsmedizin Göttingen

summary:
To investigate the effect of aging on mitochondrial gene expression we isolated liver mitochondria from 4 12-week and 4 65-week C57BL/6N  WT mice.
We then isolated RNA and prepared the barcoded library using PCR-cDNA Barcoding Kit SQK-PCB109 and ran it on MinIOn R9.4.1 Flow cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from 12-week and 65-week C57BL/6N liver mitochondria.

first: Witte

last: Steffen

first: Rehling

last: Peter

first: Aich

last: Abhishek


title: The diapause-like colorectal cancer cells induced by SMC4 attenuation are characterized by low proliferation and chemotherapy insensitivity [ATAC-seq]

first: sun

last: xuedan

summary: ATAC-seq for  HCT116 cells and its shSMC4.

first: xuedan

last: sun

first: lifang

last: he

first: mian

last: wu

first: lianxin

last: liu


title: The transcriptomic profile of rabiës virus (RABV) exposed human monocyte-derived macrophages.

status: Public on Jun 16 2022

city: Rotterdam

first: Carmen

last: Embregts

address: Wytemaweg 80

department: Department of Viroscience

institute: Erasmus Medical Center

summary: Macrophages are amongst the first immune cells that encounter rabies virus (RABV) at injured sites, but insights into if and how RABV affects macrophage activation are scarce. We undertook this study to characterize the transcriptional profile of human monocyte-derived macrophages that were exposed to RABV in vitro, to examine the antiviral response and potential RABV-induced immunosuppression mechanisms in these cells.

overall_design: RNA-seq was performed on RNA extracted from three individual blood donors. For each donor, M0 (non-polarized macrophages, control), M1, M2a, and M2c polarized macrophages, as well as RABV-exposed macrophages were sequenced.

middle: W

first: Annelieke

last: Wentzel

first: Alexander

middle: T

last: den Dekker

first: Wilfred

middle: F

last: van Ijcken

first: Ralph

last: Stadhouders

first: Corine

last: GeurtsvanKessel


title: Shared enhancer gene regulatory networks between wound and oncogenic programs

status: Public on Jun 15 2022

city: Leuven

first: Stein

last: Aerts

state: Flemish-Brabant

address: Herestraat 49

department: Department of Human Genetics / VIB Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven


title: Reprograming responsiveness of tolerogenic CD8+ T cells using a CXCR4 antagonist-armed oncolytic virus requires reversal of M2 macrophage polarization

status: Public on Jun 30 2022

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Overcoming barriers to the generation of antitumor immunity to self-and neo-antigens is a central concern of cancer immunotherapy. This study investigated the effect of interactions between ovarian cancer (OC) cells and the tumor microenvironment (TME) on the ability of oncolytic virotherapy to activate responsiveness of self antigen-specific and neoantigen-specific CD8+ T lymphocytes in tolerogenic and wild-type (WT) murine tumor models, respectively

overall_design:
The expansion of self antigen-specific CD8+ T cells using a CXCR4 antagonist-expressing oncolytic vaccinia virus (OV) was investigated using transplantable SV40 T antigen (TAg)-positive MOVCAR 5009 OC cells grown orthotopically in non-tumor prone syngeneic TgMISIIR-TAg-Low transgenic (Tag) mice expressing TAg as a self-antigen. MOVCAR 5009-challenged in WT mice served as a model for studying responses to a tumor-expressed neoantigen. Using immunostaining and single-cell RNA sequencing (scRNAseq) analyses, we compared phenotypic and transcriptomic changes in the TME during the induction of CD8+ T cells by OV in Tag mice to those in MOVCAR 5009-challenged WT mice.

CMO assignments:
CMO301 WT_C
CMO302 WT_OV
CMO303 Tag_C
CMO304 Tag_OV

first: Anna

last: Mistarz

first: Sebastiano

last: Battaglia

first: Prashant

last: Singh

first: Danuta

last: Kozbor


title: Single cell RNA-seq by mostly-natural sequencing by synthesis

status: Public on May 31 2022

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

summary: Massively parallel single cell RNA-seq (scRNA-seq) for diverse applications, from cell atlases to functional screens, is increasingly limited by sequencing costs, and large-scale low-cost sequencing can open many additional applications, including patient diagnostics and drug screens. Here, we adapted and systematically benchmarked a newly developed, mostly-natural sequencing by synthesis method for scRNA-seq. We demonstrate successful application in four scRNA-seq case studies of different technical and biological types, including 5’ and 3’ scRNA-seq, human peripheral blood mononuclear cells from a single individual and in multiplex, as well as Perturb-Seq. Our data show comparable results to existing technology, including compatibility with state of the art scRNA-seq libraries independent of the sequencing technology used – thus providing an enhanced cost-effective path for large scale scRNA-seq.

overall_design: We generated and analysed single cell RNA-seq (10x Chromium) data for 4 samples. 1) PBMC sample with 3' technology, 2) PBMC sample (same as 1) with 5' single cell technology, 3) a mixture of PBMCs from 8 individuals with  5' technology, and 4) a mixture of 8 Perturb-seq samples (mixed using cell hashing) with 3' technology. For each we sequenced with both Illumina and Ultima sequencing.

first: Sean

last: Simmons

middle: Z

first: Gila

last: Lithwick-Yanai

first: Xian

last: Adiconis

first: Florian

last: Oberstrass

first: Nika

last: Iremadze

first: Kathryn

last: Geiger-Schuller

first: Pratiksha

middle: I

last: Thakore

first: Chris

last: Frangieh

first: Omer

last: Barad

first: Gilad

last: Almogy

first: Orit

last: Rozenblatt-Rosen

first: Aviv

last: Regev

first: Doron

last: Lipson


title: Next Generation Sequencing Facilitates Quantitative Analysis Transcriptomes of dHL-60 cells after capsaicin processed

city: Chengdu

first: Kexin

last: Chen

state: Sichuan

address: No.37 guoxue Lane, Wuhou District, Chengdu city

department: Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China

institute: West China hospital

summary: To uncoverthe capsaicin effects on the neutrophil activation, we performed transcriptomic of dHL-60 cells after capsaicin stimulation in degree of different time. this study revealed the functional changes of neutrophils in the presence of capsaicin. The transcriptomic data with different time stimulation gradients can contribute to the revealing of dynamic alternation in gene expression and annotate the time-dependent effect of the neutrophil respond to capsaicin.

overall_design: dHL-60 cells were processed by 400uM capsaicin for 8 hours, 16 hours, and 24 hours.

first: Yiding


title: miRNA expression in tracheal aspirates [sBPD, BPD-PH]

status: Public on Jun 01 2022

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

summary: Extreme preterm infants are a growing population in the neonatal intensive care unit.  Multiple factors play a role in preterm birth, resulting in complications including severe bronchopulmonary dysplasia (sBPD) without or with and pulmonary hypertension (BPD-PH).  The goal of this study was to identify biomarker signatures associated with sBPD and BPD-PH.  We analyzed profiles in tracheal aspirates (TAs) from 46 extremely preterm infants receiving invasive mechanical ventilation (25 sBPD, 21 BPD-PH) . We found specific miRNA signatures in TAs that may serve as biomarkers for the two disease phenotypes.

overall_design:
We extracted RNA  from 0.5 mL of tracheal aspirates from premature neonates with BPD and BPD-PH using the Plasma/Serum RNA Purification Kit (Norgen). The expression of 1,066 human miRNAs was quantified using the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z). Results (Ct values) were normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.
variables: sBPD, BPD-PH

first: Roopa

last: Siddaiah

first: Christiana

last: Oji-Mmuo


title: Gene expression analysis of granulosa cells from animals that are wildtype or knockout for total PGR, PGR-A or PGR-B (RNA-seq)

status: Public on May 18 2022

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

summary: Progesterone receptor (PGR) is essential for various functions in the female reproductive tract, especially ovulation in the ovary. PGR consists of two main isoforms, PGR-A and PGR-B, that possess different expression patterns and are responsible for various unique roles in different tissue contexts. While both are present in the reproductive tract, PGR-A is the only one known to be essential for ovulation while PGR-B plays a lesser role in the reproductive tract. However, the specific roles of PGR isoforms on gene expression in peri-ovulatory granulosa cells have not been previously investigated in detail. In this study, we identified the unique role of PGR-A and PGR-B in peri-ovulatory granulosa cells through RNA-seq of knockout mouse models for total PGR (PGR KO) or specific isoforms (PGR-A KO and PGR-B KO)

overall_design: RNA-seq was performed on 3 replicates of granulosa cells obtained from wildtype and knockout animals from the PGR KO, PGR-A KO and PGR-B KO strains for comparative analysis

middle: D

first: James

last: Breen

first: Rebecca

middle: L

last: Robker

first: Darryl

last: Russell


title: DNA Methylation Profiling Reveals Novel Pathway Implicated in Cardiovascular Diseases of Diabetes

status: Public on Jul 01 2022

city: Wuhan

first: Shengqing

last: Hu

state: China

address: NO.1277, jiefang road

institute: wuhan union hospital

summary: Epigenetics was reported to mediate the effects of environmental risk factors on disease pathogenesis. To unleash the role of DNA methylation modification in the pathological process of cardiovascular diseases in diabetes, we screened differentially methylated genes by methylated DNA immunoprecipitation chip (MeDIP-chip) among the enrolled participants.

overall_design: Comparison of DNA methylation in  normal control (NC group, n=3), diabetes without cardiovascular diseases (DM group, n=3), and diabetes with cardiovascular diseases (CVD group, n=3). DNA methylation data were obtained using  NimbleGen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Microarray.

first: Yunfei

last: Liao

first: Lulu

first: Tianshu

last: Zeng

first: Wenyi

last: Wang

first: Yan

last: Yan

first: Kangli

last: Qiu

first: Yajuan

last: Xie


title: Dynamic differentiation of F4/80+ tumor-associated macrophage and its role in tumor vascularization in a syngeneic mouse model of colorectal liver metastasis

status: Public on Jun 18 2022

city: ShenZhen

first: Huan

last: Ren

address: 1088 Xueyuan Avenue

institute: Southern university of science and technology

summary:
Tumor-associated macrophages (TAMs) are highly heterogeneous, derived from myeloid monocyte/macrophages or tissue-resident macrophages, and play vital role in tumor progression. Here we adopted a C57BL/6 mouse model imitating the late-stage colorectal liver metastasis (CRLM) by Mc38 colorectal cancer cell injection via the portal vein. We defined the critical period at 7 to 9 days post injection (dpi) for tumor neovascularization on serial sections of CRLM biopsies. The tumor neovascularization was initiated from one of the liver blood vessels via vessel cooption and extended by vascular mimicry and growth of CD34+cells. In samples with increasing sized liver metastases of CRLM, infiltrated Ly6C+ CD11b+ F4/80 monocytes steadily gained the expression of F4/80, a Kupffer cell marker, and then transformed into Ly6C CD11bint F4/80+ cells, which, the same phenotype was also adapted by Ly6C CD11b F4/80+ Kupffer cells. F4/80+ TAMs showed proximity to neovascularization and tumor vessels. Depletion of macrophages or disturbance on macrophage polarization during the crucial period of neovascularization impeded tumor growth and vascularization and resulted in greatly reduced F4/80+ TAMs, yet increased CD11b+ cells due to inhibition of TAM differentiation. In summary, we showed dynamic F4/80+ TAM differentiation within the tumor microenvironment and strengthened its role as perivascular TAMs in CRLM.
A set of aliquot samples (about 0.25 cm3) from for flow cytometry preparations (the above method and Fig. 4A) were used for bulk RNA-Sequencing, among these samples, Ht1 and Ht3 were identical samples;  F4/80+cells and CD11b+ cells were selected from medium-sized CRLM (Mt2) with microbeads and MS column;A total of 20 samples were sent for analysis. These collected tissues were flash-frozen in liquid nitrogen, stored at - 80°C and shipped on dry ice to the sequencing provider (Novogene, www.novogene.com), who then extracted RNA from these samples and confirmed that all sample RNA were in good quality and adequate concentrations. The resulted RNA-Sequencing data were verified as the clean reads > 95%, Q30 > 90%, and error rate < 0.05%; Square of Pearson Correlation Coefficient (R2) between the biological replicates was > 0.89; R2 of the identical samples (Ht-1 and Ht-3) was > 0.98.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver biopsy samples with/out varied metastases in syngeneic mouse model of colorectal liver metastasis.

first: Ting

last: Qiao

first: Xiaoli

last: Yang

first: Yudan

last: Gao

first: Xiao


title: GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation (HEP)

status: Public on May 04 2022

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary:
Background: Hepatocytes comprise a major cell type of the human liver and function for metabolism, detoxification, and production of secreted proteins. During the hepatocyte differentiation process, whereas the gene regulation and master transcription factors have been extensively investigated, little is known about the epigenome regulation, particularly DNA methylation dynamics, and their responsible upstream factors.
Results: Examining changes in transcriptome and methylome during in vitro hepatocyte differentiation, we identified putative DNA methylation-regulating transcription factors, which are likely involved in DNA demethylation and hypo-methylation maintenance in a differentiation stage-specific manner.

overall_design: Examination of methylome in hematopietic  differentiation in vitro

first: Erina

last: Furuhata

first: Shiori

last: Maeda

first: Mami

last: Kishima

first: Yurina

last: Miyajima

first: Yuki

last: Tanaka

first: Joanne

last: Lim

first: Hajime

last: Nishimura

first: Yuri

last: Nakanishi

first: Aiko

last: Shojima

first: Harukazu


title: Evidence for toxic CAG trinucleotide repeats contributing to Huntington’s disease though RNA interference

status: Public on Apr 27 2022

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: Mutant huntingtin CAG trinucleotide repeat mimetic hairpins are loaded into the RISC and kill cells through RNAi

overall_design: NB7 cells were transfected with different HP mimicking two different mHTT variants or CAG control siRNAs. Subsequently, Ago protein associated short RNAs were pulled down using a GW182 peptide and subjected to smRNA Seq

first: Andrea

last: Murmann

middle: E

first: Elizabeth

last: Bartom


title: GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation (DE CAGE)

overall_design: Examination of transcriptome in definitive endoderm differentiation in vitro by CAGE


title: GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation


title: GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation (ChIPmentation)

overall_design: Examination of GATA6 binding in definitive endoderm differentiation in vitro by ChIPmentation


title: GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation (DE ATAC-Seq)

overall_design: Examination of chromatin accessibility in definitive endoderm differentiation in vitro by OmniATAC-seq


title: ISL1 controls pancreatic alpha cell fate and regulates beta cell differentiation and maturation [RNA-seq]

first: Šárka

last: Benešová

summary: Glucose homeostasis is dependent on functional pancreatic α and ß cells. Mechanisms underlying generation and maturation of these endocrine cells remain unclear. Here, we unravel the molecular mode of action of ISL1 in controlling α cell fate and endocrine differentiation in the pancreas. By combining transgenic mouse models, transcriptomic and epigenomic profiling, we uncover that elimination of Isl1 results in a diabetic phenotype with a complete loss of α cells, disrupted pancreatic islet architecture, downregulation of maturation markers of ß cells, and an enrichment in an intermediate endocrine progenitor transcriptomic profile. Mechanistically, apart from the altered transcriptome of pancreatic endocrine cells, Isl1 elimination results in altered silencing H3K27me3 histone modifications in the promoter regions of the essential genes for endocrine cell differentiation. Our results thus show that ISL1 transcriptionally and epigenetically controls α cell fate competence, and ß cell maturation, suggesting that ISL1 is a critical component for generating functional α and ß cells.

overall_design: Together 22 samples of 100 FACS-sorted  tdTomato+ endocrine cells were analyzed. 11 samples of P9 (biological replicates of 5 control and 6 mutant samples) and 11 samples of  E14.5 (biological replicates of 6 control and 5 mutant samples) were analyzed separately.

first: Romana

last: Bohuslavova

first: Valeria

last: Fabriciova

first: Jessica

last: Malfatti

first: Ondrej

last: Smolik

first: Lukas

last: Valihrach

first: Sarka

last: Benesova

first: Daniel

last: Zucha

first: Zuzana

last: Berkova

first: Frantisek

last: Saudek

first: Sylvia

last: Evans

first: Gabriela

last: Pavlinkova


title: ISL1 controls pancreatic alpha cell fate and regulates beta cell differentiation and maturation [CUT&Tag]

overall_design: 10 biological samples pooled from two to three pancreata (biological replicates of 4 control and 6 mutant samples) were analyzed at age P9/10. Approximately 14700 cells/sample  FACS-sorted  tdTomato+ endocrine cells were used for CUT&Tag sequencing. At age E14.5 were analyzed 12 samples (biological replicates of 6 control and 6 mutant samples). Each sample was pooled together from five to nine pancreata ( ~ 4700 cells/sample) and used for used for CUT&Tag sequencing. Two CUT&Tag validated primary antibodies anti-H3K4me3 and anti-H3K27me3 were used. All samples were analyzed separately. Each   developmental stage was enriched of one more sample were IgG antibodies were used for CUT&Tag on input cells mixed from control and mutant.


title: Shared enhancer gene regulatory networks between wound and oncogenic programs [scRNA]

first: Stein

last: Aerts

summary: Wound response programs are often activated during neoplastic growth in tumors. In both systems, cells respond to acute stress and balance the activation of multiple programs including apoptosis, proliferation, and cell migration. Central to this response are the JNK/MAPK and JAK/STAT signaling pathways. Yet, to what extent these signaling cascades interact at the cis-regulatory level, and how they orchestrate different phenotypic responses is still unclear. Here, we aim to characterize the cellular states that emerge and cooperate in the wound response, using the Drosophila melanogaster wing disc as a model system. We used single-cell multi-omics profiling to derive enhancer Gene Regulatory Networks (eGRNs) from chromatin accessibility, transcription factor binding motif and gene expression signals. We identify the eGRNs being activated following a transient wound induction, and compare them with the scRNA profiles obtained from a persistent induction of the rasv12 scrib-/- oncogenic driver. We detect a small cell population in the wound that activates a senescence program that is shared with cancer cells. This population is characterized by the C/EBP-like transcription factors Irbp18, Xrp1, slow-border and vrille. Our single-cell multiome and eGRNs resource offers a new perspective on gene regulation in the normal and wounded wing disc.

overall_design: Wild-type wing imaginal discs and eye-antennal discs with induced Ras/Scrib tumors were dissected and analysed using 10x scRNA experiments

first: Swann

last: Floc'hlay

first: Anne-Kathrin

last: Classen


title: Shared enhancer gene regulatory networks between wound and oncogenic programs [Multiome]

overall_design: Wing imaginal discs in wild-type condition or following a 40h-induction of the TNF ligand eiger (egr) in the pouch  were dissected and analysed using 10x multiome scATAC + scRNA experiments


title: A neural crest-specific overexpression mice model reveals the transcriptional regulatory effects of Dlx2 during maxillary process development

status: Public on Apr 14 2022

city: Shanghai

first: Jian

last: Sun

address: Quxi Road No.500

institute: Shanghai Ninth People's Hospital

summary: Craniofacial morphogenesis is an intricate process that requires precise regulation of cell proliferation, migration, and differentiation. Perturbations of this process cause a series of craniofacial deformities. Dlx2 is a critical transcription factor that regulates the development of the first branchial arch. However, the transcriptional regulatory functions of Dlx2 during craniofacial development have been poorly understood due to the lack of animal models in that the levels of Dlx2 can be precisely modulated. In this study, we constructed a Rosa26 site-directed Dlx2 gene knock-in mouse model Rosa26CAG-LSL-Dlx2-3xFlag for conditionally overexpressing Dlx2. By breeding with Wnt1cre mice, we obtained Wnt1cre; Rosa26Dlx2/- mice in which Dlx2 is overexpressed in neural crest lineage at about three times the endogenous level. The Wnt1cre; Rosa26Dlx2/-  mice exhibited consistent phenotypes that include cleft palate across generations and individual animals. Using this model, we demonstrated that Dlx2 caused cleft palate by affecting maxillary growth in the early-stage development of maxillary prominences. By performing bulk RNA-seq, we demonstrated that the overexpression of Dlx2 induced significant changes of many genes related to critical developmental pathways. In summary, our novel mouse model provides a reliable and consistent system for investigating the functions of Dlx2 during development and for dissecting the gene regulatory networks underlying craniofacial development.

overall_design: Bulk RNA sequencing of E12.5 WT and Wnt1cre; Rosa26Dlx2/-  mouse embryonic maxillary prominence tissue. Three biological replicates per group

first: Xudong

last: Wang

first: Qian

last: Bian

first: Nayoung

last: Ha

first: Zhixu

last: Liu


title: A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [scRNA-seq]

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

institute: VIB/KU Leuven

summary: Cancer cells outgrowing in distant organs of metastasis rewire their metabolism to fuel on the available nutrients. While this is often considered an adaptive pressure limiting metastasis formation, some nutrients available at the metastatic site naturally or through changes in organ physiology may inherently promote metastatic growth. We find that the lung, a frequent site of metastasis, is a lipid-rich environment. Moreover, we observe that pathological conditions such as pre-metastatic niche formation and obesity further increase the availability of the fatty acid palmitate in the lung. We find that targeting palmitate processing inhibits spheroid growth in vitro and metastasis formation in lean and obese mice. Mechanistically, we discover that breast cancer cells use palmitate to synthesize acetyl-CoA in a carnitine palmitoyltransferase 1a (CPT1a)-dependent manner. Lysine acetyltransferase 2a (KAT2a), whose expression is promoted by palmitate availability, relies on the available acetyl-CoA to acetylate the NF-B subunit p65. This favors nuclear location of p65 and activates a pro-metastatic transcriptional program. Accordingly, deletion of KAT2a phenocopies CPT1a silencing in vitro as well as in vivo and patients with breast cancer show co-expression of both proteins in metastases across palmitate-rich metastatic sites. In conclusion, we find that palmitate-rich environments foster metastasis growth by increasing p65 acetylation resulting in elevated NF-B signaling.

overall_design: scRNA from lungs of BALB/c mice injected with control media or tumor conditioned media for 3 weeks

first: Ginevra

last: Doglioni

first: Patricia

last: Altea-Manzano

first: Sofie

last: Demeyer

first: Sarah

middle: M

last: Fendt


title: Concentrations of progesterone prior to luteolysis modulates the uterine luminal transcriptome in the subsequent cycle in cattle

status: Public on Apr 13 2022

city: Madison

first: Francisco

last: Peñagaricano

address: 1675 Observatory Drive

institute: University of Wisconsin-Madison

summary: Sex-steroids concentrations throughout the estrous cycle modulate endometrial function and fertility in cattle. The objective of this study was to compare the post-estrus endometrial transcriptome of cows that were exposed to contrasting pre-estrus concentrations of progesterone before they displayed estrus and ovulated spontaneously. We hypothesized that greater pre-estrus concentration of progesterone alters post-estrus endometrial function even after the display of estrus and spontaneous ovulation.

overall_design: Bos indicus-influenced cross-bred beef cows exposed to either high (H) or low (L) pre-estrus concentrations of progesterone. On day -9, the cows assigned to the high progesterone treatment received a new CIDR and 2 mL GnRH i.m. while the cows assigned to low progesterone treatment received a CIDR used twice previously, 5 mL PGF2α i.m. and 2 mL GnRH i.m. Ovarian ultrasonography and blood collections were performed on d -9, d -2, d -0.5, d 0 (observed estrus), d 4, d 7, and d 14 for measurement of ovarian structures, progesterone, and estradiol. Luminal epithelial cells were collected using a cytology brush on d 4, d 7, and d 14 for RNA-sequencing analysis.

first: Mario

last: Binelli


title: A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation

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

overall_design: Refer to individual Series


title: Analysis of Amniotic Fluid-derived lncRNAs and mRNAs in Fetuses with ventricular septal defect

status: Public on May 27 2022

city: Fuzhou

first: Huaming

state: Fujian

address: No. 1 Xuefu North Road

institute: Fujian Medical University

summary: Ventricular septal defect (VSD) is one of the most prevalent birth defects. The pathogenesis of VSD remains unknown.  to analyze the expression of AF-derived lncRNAs and their roles in VSD development, Arraystar Human LncRNA Microarray V5.0 is employed for the global profiling of human lncRNAs and protein-coding transcripts.

overall_design: Arraystar Human LncRNA Microarray V5.0 was used to screen differentially expressed lncRNAs (DE-lncRNAs) and mRNAs (DE-mRNAs) in AF between the VSD group and the control group

first: H

first: G

last: Lyu


title: p53 wild-type colorectal cancer cells that express a fetal gene signature are associated with metastasis and poor prognosis

status: Public on Apr 08 2022

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

summary: Current therapy against colorectal cancer (CRC) is based on DNA-damaging agents that remain ineffective in a proportion of patients. Whether and how non-curative DNA damage-based treatment affects tumor cell behavior and patient outcome is primarily unstudied. Using CRC patient-derived organoids (PDO)s, we show that sublethal doses of chemotherapy (CT) does not select previously resistant tumor populations but induces a quiescent state specifically to TP53 wildtype (WT) cancer cells, which is linked to the acquisition of a YAP1-dependent fetal phenotype. Cells displaying this phenotype exhibit high tumor-initiating and metastatic activity. Nuclear YAP1 and fetal traits are present in a proportion of tumors at diagnosis and predict poor prognosis in patients carrying TP53 WT CRC tumors. We provide data indicating the higher efficacy of CT together with YAP1 inhibitors for eradication of therapy resistant TP53 WT cancer cells. Together these results identify fetal conversion as a useful biomarker for patient prognosis and therapy prescription.

overall_design: 14 samples analyzed

first: Laura

last: Solé

first: Teresa

last: Lobo-Jarne


overall_design: 2 samples analyzed, plus an input


title: A Chilling-induced Photosynthesis-Related Genes Inhibition as Integrated by TOP6 Complex via Fulfilling Two Distinct Regulatory Functions in Rice Mesophyll Cells

status: Public on May 05 2022

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

summary:
We conducted a global genomic analysis on the top6a3 mutant leaves by using an Illumina-type RNA sequencing
We firstly conducted a global transcription analysis in rice leaves after the γ-irradiation treatment.

overall_design: the leaves of WT (DJ) plants either untreated (control) or γ-irradiated with 40 Gy were harvested for the total RNA preparation on 6 h post IR.

first: Zhan

last: Xu

first: Zhang

last: Jianxiang


title: Transcriptome of tomato leaf tissue grown under OSC filters

status: Public on Apr 21 2022

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

summary: To characterize plant growth in net zero energy greenhouse models covered with semi-transparent organic solar cells (OSCs), RNA was extracted from tomato leaf tissue. Six experimental treatments were created with three OSC filters: FTAZ:IT-M, PTB7-Th:IEICO-4F, FTAZ:PCBM. Boxes with either a clear glass cover or a spectrally-neutral cover were used as the high light (HC) control and the comparative light intensity (PC) control, respectively. These treatments were divided into 2 experiments. 4 treatments (3 OSC boxes and control) had a consistent light intensity and were called the PPFD Controlled (PC) experiment. The other 4 treatments were the Height Controlled (HC) experiment and had more variation in light intensity between treatments due to a consistent distance from the growth chamber light source (height). Plants in the FP_PC treatment flowered one day later than the PC control. FI_PC flowered one day earlier. Gene expression in samples from the FP_PC treatment had a distinct pattern related to flowering initiation.

overall_design: Leaf tissue was sampled from 4 individual plants grown under one of eight light spectra and intensity conditions. Samples were collected under growth conditions.

first: Melodi

last: Charles

first: Brianne

last: Edwards

first: John

last: Calero


title: The change of transcriptomics profiles in osteoclast precurosors after addition of prostate cancer-derived extracellular vesicles

status: Public on Apr 04 2022

city: Tokyo

first: Fumihiko

last: Urabe

institute: The Jikei University School of Medicine

summary: Gene expression analysisi by next generation sequencer revealed osteoclast diferentiation after the addition of PC3M-derived extracellular vesicles (EVs) with or without RANKL. Finally, we found that PC3M-derived EVs promote osteoclast differentiation in the presence of RNAKL.

overall_design: To examine the effect of PC3M derived extracellular vesicles on osteoclast differentiation, we performed RNA seq. After an initial attachment period for 12 hours, the RAW264.7 were cultured in the presence or absence of recombinant mouse RANKL (GST-RANKL, Oriental Yeast Co., Tokyo, Japan) at a concentration of 10 ng/mL alone or in combination with PC3M derived EVs (30µg/mL)  for 48h or 72h. Total 16 samples were examined: only addition of PBS (48h and 72h), PC3M derived EV (48h and 72h), only RANKL (48h and 72h), and RANKL with PC3M derived EV (48h and 72h).

first: Yamamoto

last: Yusuke

first: Takahiro

last: Ochiya


title: Generation of resolving neutrophils with 4-PBA or genetic deletion of TRAM

status: Public on Apr 20 2022

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

summary: We have generated resolving neutrophils with anti-inflammatory potency, through applying the pharmacological agent 4-PBA or genetically depleting TRAM molecule.  WT murine neutrophils treated with PBS or 4-PBA for overnight were harvested for  scRNAseq analysis to examine the generated resolving neutrophil phenotype.  In addtion, we have cultured WT and TRAM KO neutrophils and compared the resolving phenotype via scRNAseq analysis.

overall_design: WT murine neutrophils were treated with either PBS or 4-PBA for 24hrs.

first: RuiCi

last: Lin

first: Ziyue

last: Yi


title: Gene expression profile of brains from Angptl2+/+ or Angptl2-/- mice

status: Public on Mar 28 2022

city: shanghai

first: wenqian

last: yang

address: 280 South Chongqing Road

institute: Shanghai Jiaotong University School of Medicine

summary: To identify the intracellular targets of  ANGPTL2/MAG mediate signals that enhance oligodendrocyte differentiatiaon, brains from Angptl2+/+ or Angptl2-/- mice borned at Day 15 were obtained, followed by the extraction of total RNA and subjected to the RNA-sequencing.

overall_design: Brains from Angptl2+/+ or Angptl2-/- mice borned at Day 15 were obtained to measure gene expression

first: J

last: Zheng

first: Y

last: Zhang

first: L

last: Chen


title: The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract

status: Public on Mar 31 2022

city: new haven

first: Yuping

last: Zhou

state: CT

address: 310 cedar street

department: OB/GYN

institute: Yale

type: Methylation profiling by genome tiling array

type: Methylation profiling by high throughput sequencing


title: Gene profile of human CD14+ monocytes and monocyte-derived macrophages

status: Public on Mar 24 2022

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

institute: Hospital General Universitario Gregorio Marañón

summary: Comparison of the transcriptome of CD14+ human monocytes and CD14+ human monocyte-derived macrophages generated in the presence of M-CSF (M-MØ) or GM-CSF (GM-MØ).

overall_design: mRNA profiles of human CD14+ monocytes isolated by immunomagnetic procedures from peripheral blood, and of monocyte-derived macrophages generated by culturing monocytes for 7 days in the presence of M-CSF (10 ng/ml) to generate M-MØ, or in the presence of GM-CSF (1000 U/ml) to generate GM-MØ.

first: Ittai

middle: B

last: Muller

first: Gerrit

last: Jansen

middle: P

last: Kröger


title: GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation (DE)

last: Suzuki

overall_design: Examination of methylome in definitive endoderm differentiation in vitro

first: Erina

last: Furuhata

first: Shiori

last: Maeda

first: Mami

last: Kishima

first: Yurina

last: Miyajima

first: Yuki

last: Tanaka

first: Joanne

last: Lim

first: Hajime

last: Nishimura

first: Yuri

last: Nakanishi

first: Aiko

last: Shojima

first: Harukazu


title: Single cell transcriptomics of lung retinoid-containing cells

status: Public on Mar 15 2022

city: New York

first: William

last: Blaner

state: NY

address: 630 West 168th Street

institute: Columbia University

summary: We undertook single cell RNA sequencing (scRNA-seq) and bioinformatic analyses to identify roles for different alveolar cell populations in retinoid metabolism and storage.

overall_design: Transcriptome analysis of lung retinoid-containing cells

first: Igor

middle: O

last: Shmarakov

first: María

last: Marhaenda-Muňoz


title: GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation (HEP CAGE)

first: Takahiro

summary:
Background: Hepatocytes comprise a major cell type of the human liver and function for metabolism, detoxification, and production of secreted proteins. During the hepatocyte differentiation process, whereas the gene regulation and master transcription factors have been extensively investigated, little is known about the epigenome regulation, particularly DNA methylation dynamics, and their responsible upstream factors.
Results: Examining changes in transcriptome and methylome during in vitro hepatocyte differentiation, we identified putative DNA methylation-regulating transcription factors, which are likely involved in DNA demethylation and hypo-methylation maintenance in a differentiation stage-specific manner.

overall_design: Examination of transcriptome in hematopietic differentiation in vitro by CAGE


title: The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract [methylation]

first: Yuping

last: Zhou

summary: We identify an unexpected functional role for E3 in fetal reproductive system and brain. We further identify a novel mechanism of estrogen action, through recruitment of epigenetic modifiers to estrogen receptors and their target genes, which doesn’t correlated with the traditional view of estrogen potency.”

overall_design: We administered E3 to pregnant mice, exposing the fetus to E3 and identified an unexpected functional role for E3 and a novel mechanism of estrogen action.

first: Hugh

last: Taylor


title: Group B Streptococcus (GBS) infection during pregnancy

status: Public on Feb 18 2022

first: Itai

last: Yanai

address: 435 East. 30th St.

institute: NYU Langone Health

summary: GBS infection in the placenta modules host innate inflammatory response

overall_design: Pregnant mice were infected with GBS and placentas were collected at time points post infection for analysis. Results were validated in human placental macrophages

first: Felicia

last: Kuperwaser

first: Gal

last: Avital

first: Michelle

last: Vaz

first: Kristen

last: Noble

first: Allison

last: Dammann

first: Tara

last: Randis

first: David

last: Aronoff

first: Adam

last: Ratner


title: Global changes in granulosa cell chromatin accessibility in response to the LH surge and to PGR (ATAC-seq)

status: Public on Feb 15 2022

city: Adelaide

first: Thao

last: Dinh

address: North Terrace

institute: University of Adelaide

summary: During ovulation, the LH surge leads to the activation of various signalling cascades in granulosa cells, resulting in a critical shift in chromatin landscape and correspondingly the ovarian gene expression profile. Such large-scale genomic reprogramming involves a specific suite of ovulatory transcription factors. An essential factor for ovulation is the progesterone receptor (PGR). One of the ways through which PGR can mediate transcription regulation is through interaction with histone and chromatin remodellers to facilitate chromatin reprogramming and thereby enabling transcription. However, it is unknown whether this mechanism is employed by PGR in granulosa cells. This study aims to characterise global changes in the chromatin landscape that are induced by the LH surge and to determine the role of PGR in facilitating chromatin accessibility in granulosa cells during ovulation.

overall_design: ATAC-seq was performed on granulosa cells from wildtype mice pre- and post-hCG stimulation, or from PGR wildtype and knockout mice post-hCG stimulation. 2 biological replicates were done for each condition, 2-3 mice pooled per replicate.

first: James

last: Breen

first: Rebecca

last: Robker

first: Darryl

last: Russell


title: ENHANCED INTERFERON-SENSING BY AGGRESSIVE  CHRONIC LYMPHOCYTIC LEUKEMIA CELLS

city: Toronto

first: YU XUAN

last: LUO

state: ON

address: 2075 Bayview Avenue

department: Biological sciences

country: Canada

institute: Sunnybrook research institute

summary:
Purpose: to determine the CLL-B cells' interferome
Methods: CLL cells from 3 of the patients previously classified as responders were purified and treated with anifrolumab in vitro and RNA was analyzed by RNAseq.

overall_design: Gene expression in purified CLL cells before and 24h after treatment with anifrolumab at 9.25ug/ml in vitro were compared by RNAseq.

last: Spaner

first: YuXuan

last: Luo


title: Identification of Key LncRNAs and Pathways in Prediabetes and Type 2 Diabetes Mellitus for Hypertriglyceridemia Patients Based on Weighted Gene Co-Expression Network Analysis

city: Changchun

first: Weiwei

last: Cui

state: Jilin

address: Xinmin

institute: Jilin University

summary: We used WGCNA to construct a co‐expression network and obtain modules related to blood glucose, thus detecting key lncRNAs, and providing a reference for searching potential biomarkers of prediabetes and T2DM in hypertriglyceridemia patients.

overall_design: Examination of lncRNAs in blood sample of hypertriglyceridemia patients with different blood glucose.

first: Shoumeng

last: Yan

first: Mengzi

last: Sun

first: Lichao

last: Gao

last: Yao

first: Tianyu

last: Feng

first: Yixue

last: Yang

first: Xiaotong

last: Li

first: Wenyu

last: Hu

first: Bo


title: Mechanotherapy promotes extracellular matrix remodeling in aged rat muscle recovering from disuse by reprogramming intercellular communication

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

summary: A mechanistic understanding of the age-related impairment to skeletal muscle regrowth following disuse atrophy as well as therapies to augment recovery in the aged are currently lacking. Mechanotherapy in the form of cyclic compressive loading has been shown to benefit skeletal muscle under a variety of paradigms, but not during the recovery from disuse in aged muscle. To determine whether mechanotherapy promotes extracellular matrix (ECM) remodeling, a critical aspect of muscle recovery after atrophy, we performed single cell RNA sequencing (scRNA-seq) of gastrocnemius muscle cell populations, stable isotope tracing of intramuscular collagen, and histology of the ECM in adult and aged rats recovering from disuse, with and without mechanotherapy. ECM remodeling-related gene expression in fibro-adipose progenitor cells (FAPs) was absent in aged compared to adult muscle following 7 days of recovery, and instead were enriched in chemoattractant genes. There was a significantly lower expression of genes related to phagocytic activity in aged macrophages during recovery, despite enriched chemokine gene expression of numerous stromal cell populations, including FAPs and endothelial cells. Mechanotherapy reprogrammed the transcriptomes of both FAPs and macrophages in aged muscle recovering from disuse to restore ECM-and phagocytosis-related gene expression, respectively. Stable isotope labeling of intramuscular collagen and histological evaluation confirmed mechanotherapy-mediated remodeling of the ECM in aged muscle recovering from disuse. In summary, our results highlight mechanisms underlying age-related impairments during the recovery from disuse atrophy and promote mechanotherapy as an intervention that reprograms the muscle transcriptional environment more similar to that of adult skeletal muscle.

overall_design: Examination of how extracellular matrix related gene expression in skeletal muscle mononuclear cells changes with age during the recovery from disuse atrophy, and in response to a mechanotherapy

first: Zachary

middle: R

last: Hettnger

first: Esther

last: Dupont-Versteegden


title: Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase

status: Public on Feb 10 2022

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE

summary: Here, we described comparative transcriptomic analysis of B. subtilis strain stably expressing rho with the wild type and rho-deficient strains. We show that maintaining a stable Rho level caused global changes of B. subtilis transcriptome including both strong down-regulation of the antisense transcription and considerable modifications of the sense transcription. The observed changes were more noticeable upon entering the stationary phase and comprised majority of genes controlled by global transcription regulators AbrB and CodY, competence transcription factor ComK, and stringent response. Constitutively expressed rho reprograms stationary phase-specific cellular physiology, affects adaptation of cells to nutrient limitations by attenuating the stringent response and alters cell-fate decision-making to such an extent that it blocks competence development and sporulation.

overall_design: Impact of a stable Rho level on Bacillus subtilis global gene expression and physiology during exponential growth and upon entering the stationary phase.

first: Elena

last: Bidnenko

first: Vladimir

first: Pierre

last: Nicolas


title: Well-TEMP-seq characterizes the temporal dynamics of single-cell gene expression

status: Public on Feb 01 2022

city: Xiamen

first: Chaoyong

address: 422 Siming Road

institute: Xiamen University

summary: Single-cell RNA sequencing reveals the transcriptional heterogeneity of single cells, but offers static snapshots of gene expression and fails to reveal the temporal dynamics of transcription. Herein, we develop Well-TEMP-seq, a high-throughput, cost-effective, accurate, and efficient method for massively parallel profiling the time-resolved dynamics of single-cell gene expression. Well-TEMP-seq combines metabolic RNA labeling with our recently developed microwell-based single-cell RNA sequencing method (Well-Paired-seq) to distinguish newly transcribed RNAs marked by T-to-C substitutions from pre-existing RNAs in each of thousands of single cells. We further apply Well-TEMP-seq to profiling the dynamics of gene expression of colorectal cancer cells exposed to low-dose of 5-AZA-CdR, a clinically used DNA-demethylating anti-tumor drug. Well-TEMP-seq also for the first time reveals the activation of interferon responsive genes by 5-AZA-CdR induced viral mimicry in the first three days after treatment. Well-TEMP-seq will be broadly applicable to unveil the dynamics of single-cell gene expression in diverse biological processes.

overall_design: mRNA profiles of  K562 and HCT116

first: Fanghe

last: Lin

first: Jia

last: Song

first: Kun

last: Yin

first: Shichao

first: Yingkun

last: Zhang


title: RNA localization across the apicobasal axis of human epithelial cells

status: Public on Apr 05 2022

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: To assay the relative localization of RNA molecules in the apical and basal compartments of human intestinal epithelial cells, we performed Halo-seq using apically and basally localized HaloTag bait proteins.

overall_design:
We then used RNAseq to profile the RNA contents of these two compartments.
Comparative gene expression profiling of RNA in the apical and basal compartments of human epithelial cells.


title: Multilayer-omics Reveal Sex- and Depot-Dependent Adipose Progenitor Cell Heterogeneity

status: Public on Jan 26 2022

city: Durham

first: Rana

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

summary: White adipose tissue (WAT) harbors functionally diverse subpopulations of adipose progenitor cells that differentially impact tissue plasticity in a sex- and depot-dependent manner. To date, the molecular basis of this cellular heterogeneity has not been fully defined. Here, we describe a multilayered omics approach to dissect adipose progenitor cell heterogeneity in three dimensions: progenitor subpopulation, sex, and anatomical localization. We applied state-of-the-art mass spectrometry methods to quantify 4870 proteins in eight different stromal cell populations from perigonadal and inguinal WAT of male and female mice and acquired transcript expression levels of 15477 genes using RNA-seq. Notably, our data highlight the molecular signatures defining sex differences in PDGFRb+ preadipocyte differentiation and identify regulatory pathways that functionally distinguish adipose tissue PDGFRb+ subpopulations. Together, the multilayered omics analysis provides unprecedented insights into adipose stromal cell heterogeneity.

overall_design: Bulk RNA-seq experiment to analyze gene expression profile in gonadal white adipose tissue FIPs and APCs, and inguinal white adipose tissue DPP4_neg APCs and DPP4_pos APCs from male and female mice.

last: Shan


title: Organic vegetable juice supplement modulates microbial community in continuous colon simulation system

status: Public on Dec 31 2021

city: Gyeonggi-do

first: Jisoo

last: Kim

address: 22, Giheungdanji-ro 24beon-gil, Giheung-gu, Yongin-si

department: New growth team

country: South Korea

institute: hy R&BD center

summary: In this study, we investigated the effects of organic vegetable juice supplementation on modulating the microbial community, and how its consumption ameliorates blood lipid profiles in diet-induced obese mice. Here, we analyzed the effect of organic vegetable juice on the microbial community and fatty acid synthesis via animal experiments using diet-induced obese mice and continuous colon simulation system. Organic vegetable juice supplement influenced intestinal bacterial composition from phylum to genus level, including decreased Proteobacteria in the ascending colon in the phylum. At the family level, Akkermansia which are associated with obesity, were significantly augmented in the transverse colon and descending colon compared to the control juice group. In addition, treatment with organic vegetable juice affected predicted lipid metabolism function genes related to lipid synthesis. Organic vegetable juice consumption did not have a significant effect on weight loss but helped reduce epididymis fat tissue and adipocytes. Additionally, blood lipid profiles, such as triglyceride, high-density lipoprotein, and glucose, were improved in the organic vegetable juice-fed group. Expression levels of genes related to lipid synthesis, including SREBP-1, PPARγ, C/EBPα, and Fas, were significantly decreased. Analysis of antioxidant markers, including 8-OHdG and MDA, in the vegetable juice group, indicated that blood lipid profiles were improved by the antioxidant effect. These results suggest that organic vegetable juice supplementation may modulate gut microbial community  and reduce the potential role of hyperlipidemia in diet-obese mice.

overall_design: Stool samples were collected from three healthy adults who had not taken antibiotics for 3 months. Fecal samples were diluted with phosphate-buffered saline (PBS) at a 1:10 ratio in an anaerobic chamber. The stool slurry sample was inoculated into each vessel of continous colon simulation system at a final concentration of 2%.

first: Hyeonji


title: Loci-specific differences in blood DNA methylation in HBV-negative populations at risk for hepatocellular carcinoma development - pre-diagnostic HCC blood samples

status: Public on Jan 31 2022

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

institute: The University of British Columbia

summary: Genome wide DNA methylation profiling of blood samples collected from patients prior to diagnosis with hepatocellular carcinoma (HCC) vs. blood samples collected from healthy individuals without family history of cancer. The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human samples corresponding to cases (pre-diagnostic HCC) and controls. Samples included 21 cases and 21 controls. Cases were matched with controls on gender, age, ethnicity, hepatitis C infection, and diabetes. The presence or absence of HCC in our study was determined based on the AASLD criteria.

overall_design: Bisulphite converted DNA from the 42 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Katarzyna

last: Lubecka

first: Kirsty

last: Flower

first: Megan

last: Beetch

first: Jay

last: Qiu

first: Lucinda

last: Kurzava

first: Hannah

last: Buvala

first: Adam

last: Ruhayel

first: Samer

last: Gawrieh

first: Suthat

last: Liangpunsakul

first: Tracy

last: Gonzalez

first: George

last: McCabe

first: Naga

last: Chalasani

first: James

last: Flanagan


title: Changes in nascent transcripts upon glucocorticoid stimulation in macrophages

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

summary: Glucocorticoids are widely prescribed anti-inflammatory drugs with tissue-specific effects. Beneficial anti-inflammatory effects are caused in cells of the immune system whereas metabolic adverse effects of glucocorticoid therapy are seen in metabolic tissues such as liver. The glucocorticoid receptor (GR), a nuclear receptor targeted by glucocorticoids, bind its DNA response elements upon ligand exposure in a tissue-specific manner. Tissue-specific GR binding patterns depend on the access of its binding sites, which determines the tissue-specific glucocorticoid response. Here, we investigated this response by nascent RNAseq in murine bone marrow-derived macrophages (BMDMs) after stimulation with lipopolysaccharide (LPS) and dexamethasone (Dex). After labelling newly synthesized transcripts with 4-thiouracile (4sU), we identified macrophage-specific non-coding transcripts expressed at intergenic GR binding sites. Those transcripts are regulated by the GR and correlate with its anti-inflammatory function in macrophages. Those findings add another layer to the mechanisms underpinning GR's tissue-specific gene regulation and represent potential drug targets in anti-inflammatory therapy and/or management of adverse effects in glucocorticoid therapy.

overall_design: We performed 4sU-seq in murine bone marrow-derived macrophages upon LPS (2h 100 ng/ml) and LPS plus Dex (2.5 h 1 mM Dex, 2h 100ng/ml LPS) stimulation. One hour before cell lysis nascent transcripts were labelled with 200 mM 4-thiouridine (4sU, Carbosynth, Cat.No: 13957-31-8). Three biological replicates were analyzed per treatment condition. For each sample, we performed total (Illumina Stranded Total RNA Library Prep Kit) and PolyA-specific (Illumina TrueSeq Stranded mRNA Library Prep Kit) RNAseq library preparation.

first: Kirsten

last: Bielefeld

first: Nina

middle: H

last: Uhlenhaut


title: Genomic and transcriptomic analysis of medulloblastoma

city: Cincinnati

first: Zaili

last: Luo

state: OH

address: 3333 Burnet Ave.

institute: CCHMC

type: Genome variation profiling by high throughput sequencing

summary: Identification of transcriptomic and genomic changes by RNA-seq, ATAC-seq and low coverage WGS in mouse and human tumor cells

overall_design: High throughput RNA-seq, ATAC-seq and low coverage WGS in mouse and human tumor cells

first: Q

last: Lu

first: Yunfei

last: Liao

first: Dazhuan

last: Xin

first: Sean

last: Ogurek


title: Screening of virus infection in suspected malaria patients in the city of Manaus in the Amazon region of Brazil

status: Public on Mar 01 2022

city: Ribeirao Preto

first: Victor

middle: Hugo

last: Aquino

state: Sao Paulo

address: Avenida do Cafe, s/n

department: Fculty of Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

summary: Arthropod-borne viruses (arboviruses) represent a threat to global public health, especially in the tropical and subtropical regions of the world. More than 150 arboviruses can infect humans; they cause mainly febrile illness, although hemorrhagic complications and diseases affecting the central nervous system (SNC) can also be observed. Arboviruses represent a threat to Brazil and, therefore, a permanent surveillance of these viruses is required to timely reduce the risk of epidemic outbreaks. The Brazilian Amazon region is where the highest number of arboviruses has been detected in the world. Besides, malaria is also endemic in the Amazon region, with a significant predominance of Plasmodium vivax. It is often difficult to differentiate between malaria and arboviral diseases, as they share similar clinical features and laboratory findings, mainly undifferentiated fever. This study aimed to estimate possible viral etiology in patients with febrile syndrome negative for Plasmodium infection, in the Brazilian Amazon. We initially analyzed serum samples of 124 participants with a DNA microarray platform designed for the detection of arboviruses and viruses transmitted by small mammals, but no virus was detected. Then, the serum samples of 76 participants were analyzed with a deep New Generation Sequencing, which showed evidence of the presence of only one arbovirus, the Zika virus in only one pool of 9 serum samples. This result is in contrast with our hypothesis, showing that arboviruses are not frequent in suspected malaria cases in Manaus, Brazil. Other viruses instead of arboviruses were found in this study. Primate erythrovirus 1 was the virus most frequently found virus in the suspected malaria patients, followed by Enterobacteria phage lambda. Besides, we detected, in a lower frequency, the Pegivirus C. In addition to the exogenous viruses, we also detected human endogenous retrovirus in all pools. Due to the high number of viruses that are important in the differential diagnosis of malaria, cost-effective and simple high throughput methods are required, helping molecular surveillance of misdiagnosed viral infections. Further studies with more robust sample sizes in other areas in the Amazon are needed.


title: Next-generation sequencing reveals the regulatory mechanism of transcription factor Foxk1 in the liver

city: Charlottesville

first: Shun

last: Fujinuma

state: Virginia

address: Jordan Hall, RM 4061B, 1340 Jefferson Park Ave

institute: University of Virginia

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

overall_design: Refer to individual Series


title: Hypercapnia impairs fibroblast cell activity and promotes cellular differentiation

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary:
Hypercapnia has deleterious effects on cell function, including inhibition of alveolar epithelial cells (AEC) and fibroblast proliferation without causing cell death.
Classical studies and lineage-trace models demonstrated that fibroblast cells can affect the structurally and functionally distinct alveolar type 1 cells (AT1) and alveolar type 2 cells.
This fibroblast cells reprogramming depends on certain signaling pathways that plays critical roles in tissue development and homeostasis throughout the organism lifespan.

overall_design: Transcriptomic profiles of flow sorted PDGFR alpha+ fibroblast cells from C57Bl/6 mice exposed to 10%  CO2 undernormoxic conditions for 0, and 10  days were generated by standard illumina RNA-Seq protocols.

first: Laura

middle: A

last: Dada

first: Jacob

last: Sznajder


title: Hypercapnia impairs AT2 cell progenitor activity and promotes differentiation to AT1 cells

summary:
Hypercapnia has deleterious effects on cell function, including inhibition of alveolar epithelial cells (AEC) and fibroblast proliferation without causing cell death.
Classical studies and lineage-trace models demonstrated that surfactant-producing AT2 cells can serve as stem cells for the structurally and functionally distinct alveolar type 1 cells (AT1)
This AT2 reprogramming depends on Wnt/βcat signaling, a pathway that plays critical roles in tissue development and homeostasis throughout the organism lifespan.
We found that high CO2 inhibits AT2 cell proliferation and self renewal, and promote their differentiation to ATEC and AT1 cells

overall_design: Transcriptomic profiles of flow sorted alveolar type 2 cells from C57Bl/6 mice exposed to 10%  CO2 undernormoxic conditions for 0, 7 and 21 days were generated by standard illumina RNA-Seq protocols.

first: Lynn

middle: C

last: Welch

first: Natalia

last: Magnani

first: Alexander

middle: V

last: Misharin


title: Short Stature, GH stimulation testing and RNASeq

status: Public on Dec 15 2021

city: Manchester

first: Philip

last: Murray

address: Oxford Road

institute: University of Manchester

summary: Case series of children and adolescents undergoing growth hormone stimulation testing for investigation of short stature. The aim of this study was to identify whether a machine learning approach utilising gene expression data could predict which short children would test positive for GHD and which would not.

overall_design: RNASeq of peripheral blood mononuclear cells  taken from patients at time of GH stimulation test

middle: G

first: Adam

last: Stevens

first: Terence

last: Garner

first: Ivan

last: Wangsaputra


title: RNA-seq of mouse liver samples from Alginate oligosaccharides and/or busulfan treatment groups

status: Public on Dec 01 2021

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: The goat of this project is to exploreAlginate oligosaccharides (AOS) effect on the recovery of liver function. RNA-seq of liver samples from different groups: Con, busulfan(B), AOS, B+AOS.

overall_design:
RNA-seq of liver samples from different groups: Con, busulfan(B), AOS, B+AOS. .
A0 means the treatment group is control (without any treatment). A10 means the animals were treated with Alginate oligosaccharides 10mg/kg for 5 weeks. B0 means the animal treated with busulfan at 40mg/kg once. BA10 means the animals were treated with busulfan once then dosed with Alginate oligosaccharides 10mg/kg for 5 weeks.

first: Xiangping

last: Ma


title: MNase-seq of Drosophila S2 cells

status: Public on Feb 12 2022

city: Srinagar

first: Ajazul

last: Wani

address: Hazratbal

country: India

institute: University of Kashmir

summary: We report the MNase-diestion coupled to Next Generation Sequencing of Wild type Drosophila S2 cells or S2 cells over-expressing polycomb protein PH

overall_design: Cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature, tumbling end over end. Crosslinking was quenched by 1M glycine (from 2.5M pH 7.9 stock) and cells were tumbled for 10min at RT. Cells were resuspended in cold PBS (+PI), pelleted through a sucrose cushion (20% sucrose in PBS), resuspended in PBS, and flash frozen in liquid nitrogen at 107 cells per tube and stored at -80oC. For MNase digestion, the cell pellet was resuspended in PBS with 0.1% Triton-X 100 (PBS-TX). Digestion of 10^6 cells per titration point took place in a volume of 400uL PBS-TX supplemented with 1mM CaCl2. Either 1.5 U, 6.25 U, 25 U, 100 U or 400 U of MNase (Worthington Biochemical) were added to pre-warmed cells and incubated at 37 oC for 3 minutes. Digestion was stopped by moving samples to ice and adding of 10 uL of 250 mM EDTA, 250 mM EGTA, and 10 uL of 20% SDS. For DNA cleanup, the digestion products were incubated with RNase (Roche) for 30 minutes at 37 oC, with proteinase K (2.5 ul of 20 mg/ml) (Roche) for 60 minutes at 55 oC, and incubated at 65 oC for overnight to reverse crosslinks. Following phenol-chloroform extraction and ethanol precipitation, the purified DNA was used input into the library preparation

first: Ajaz

first: Adfar

last: Amin