title: AHNAK, regulated by the OSM/OSMR signaling, enhances keratinocyte proliferation and differentiation in PLCA patients

city: Guangzhou

first: Huiting

last: Liu

state: Guangdong

address: Lujing road NO.2

institute: Dermatology Hospital, Southern Medical University

overall_design: Total RNA samples of AHNAK knockout HaCaT cells was examined by nextGen RNA sequencing

first: Wen

last: Zheng

first: Huan

last: Yang

first: Biying

last: Qiu

first: Yingying

last: Luo

first: Yadan

last: Zhong

first: Bin

first: Jun


title: Gene expression analysis of predestined heterogeneity in neutrophil progenitor clones (ER-HoxB8 conditionally immortalized)

status: Public on Sep 27 2022

city: Boston

first: Michael

middle: K.

last: Mansour

state: MA

address: 55 Fruit Street

country: USA

institute: Massachusetts General Hospital

type: Expression profiling by high throughput sequencing

summary: Transcriptional profiling of clonal neutrophil progenitor populations. Conditionally immortalized CD45.1 naive paired granulocyte-monocyte progenitors (GMPs) and their mature neutrophil counterpart were profiled in an in vitro cell system. Clones demonstrated an overall similar transcriptional profile within the GMP or neutrophil states, however, individual clones had several differentially expressed genes (DEGs) between each other at both the progenitor and mature cell stages.

overall_design: We utilized a technique of retroviral ER-Hoxb8 expression (Wang et al. Nature Methods 2006) to examine clonal granulocyte-monocyte progenitors (GMPs) and the corresponding mature neutrophil from a C57Bl/6-CD45.1-STEM mouse. The GMPs are will grow indefinitely in the presence of stem cell factor and beta-estradiol. Eight paired naïve granulocyte monocyte progenitors (GMPs) and neutrophil clones were processed for RNA-seq using the Qiagen RNeasy Plus Mini Kit (Qiagen) with DNaseI treatment.

first: Allison

middle: K

last: Scherer

first: Murat

last: Cetinbas

first: Ruslan

middle: I

last: Sadreyev


title: RNA-seq Analysis of Tgfbr2f/f and Tgfbr2HKO Mouse Liver Transcriptomes

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

country: China

institute: Changzheng hospital

summary:
Purpose: To identify the alterations of genes transcriptional profile of livers obtained from Tgfbr2f/f mice and Tgfbr2HKO mice treated with CCl4.
Methods: we generated hepatocyte-specific Tgfbr2 knockout (Tgfbr2HKO) mice by AAV8-TBG-Cre injection via the tail vein of Tgfbr2f/f. Tgfbr2f/f mice and Tgfbr2HKO were intraperitoneally injected with 0.25 ml/kg CCl4 (diluted 1:3 (v/v) in olive oil) twice a week for 4 weeks to induce liver fibrosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of 12-week old Tgfbr2f/f mice and Tgfbr2HKO mice treated with CCl4.

first: Shu-Qing

first: Xing

last: Deng


title: Mediator 1 Regulation of the BMP/TGF-b Signaling in Endothelium: Implications for Pulmonary Hypertension

city: La Jolla

first: John

last: Shyy

state: CA

address: 9500 Gilman Dr

institute: UC San Diego

summary: We investigate the MED1/KLF4 co-regulation of the BMP/TGF-beta axes in endothelium by studying the epigenetic regulation of BMP receptor type II (BMPR2), ETS-related gene (ERG), and TGF-beta receptor 2 (TGFBR2) and their involvement in the PH. High throughput screening involving data from RNA-seq, MED1 ChIP-seq, H3K27ac ChIP-seq, KLF4 ATAC-seq, and high-throughput chromosome conformation capture (HiC) together with in silico computations were used to explore the epigenetic and transcriptional regulation of BMPR2, ERG, and TGFBR2 by MED1 and KLF4. In vitro experiments with cultured pulmonary arterial endothelial cells (PAECs) and bulk assays were used to validate results from these in silico analyses. Lung tissue from patients with idiopathic pulmonary arterial hypertension (IPAH), animals with experimental PH, and mice with endothelial ablation of MED1 (EC-MED1-/-) were used to study the PH-protective effect of MED1. Levels of MED1 were decreased in lung tissue or PAECs from IPAH patients and rodent PH models. Mechanistically, MED1 acted synergistically with KLF4 to transactivate BMPR2, ERG, and TGFBR2 via chromatin remodeling and enhancer-promoter interactions. EC-MED1-/- mice showed PH susceptibility. In contrast, MED1 overexpression mitigated the PH phenotype in rodents. A homeostatic regulation of BMPR2, ERG, and TGFBR2 in ECs by MED1 synergistic with KLF4 is essential for the normal function of the pulmonary endothelium. Dysregulation of MED1 and the resulting impairment of the BMP/TGF- signaling is implicated in the disease progression of PAH in humans and PH in rodent models.

overall_design: PAECs were transfected with MED1 siRNA or control siRNA for 48 hr before RNA isolation followed by RNA-seq analysis.

first: Chen

last: Wang

first: Yuanming

last: Xing

first: Jiao

last: Zhang

first: Chih-Hung

last: Chou

middle: Y


title: Defining mongolia sheep organogenesis at single-cell resolution reveals a role for the Hippo pathway in regulation Hulunbuir short-tailed sheep

city: Inner Mongolia

first: Hong

last: Su

state: Inner Mongolia

address: No. 306, Zhaowuda Road, Saihan District, Hohhot, Inner Mongolia Autonomous Region

institute: Inner MongoliaAgricultural University

summary: Analyze the mechanism of short tail formation

overall_design: Hulunbeier sheep is the experimental group, Uzhumuqin sheep is the control group, each group (n=3), take 16-day embryos of each type of sheep, digest them into single cells with enzymes, and perform 10Xgenomic sequencing.

first: Guifang

last: Cao


title: RNA-seq of 3D-culture balding and non-balding dermal papilla cells

city: London

last: Philipott

address: 4 Newark St

department: Center for Molecular Medicine Cologne

country: United Kingdom

institute: Blizard Institute Barts and The London School of Medicine and Dentistry

summary: Androgenetic alopecia (AGA, male patterned baldness) is a prevalent hair loss condition in males that develops due to the influence of androgens and genetic predisposition. With the aim of elucidating genes involved in AGA pathogenesis, we cultured immortalised balding human dermal papilla cells (BAB) and immortalised non-balding human dermal papilla cells (BAN) in 3-dimensional culture format, and compared gene expression using RNA-seq between BAB and BAN cells.

overall_design: Examination of transcriptome difference between immortalised balding human dermal papilla cells (BAB) and immortalised non-balding human dermal papilla cells (BAN), technical triplicate.

first: M

last: Philpott

first: A

middle: M

last: Hillmer


title: MicroRNAs in the exosome-like nanoparticles from orange juice inhibit Citrus blue mold caused by Penicillium italicum [RNA-Seq]

status: Public on Sep 26 2022

first: chunxiao

last: yin

address: Xingke Road

department: Agriculture and Biotechnology Research Center

institute: South China Botanical Garden, Chinese Academy of Sciences

summary: Identification of miRNAs in citrus reticulata exosomes；Identification of potential target genes of exosomal miRNAs in penicillium italicum； Comparison of differentially expressed genes between citrus exosome-treatedpenicillium italicum and wild type

overall_design: Extraction of citrus exosomes and miRNA sequencing；mRNA sequencing and degradome sequencing of penicillium italicum spores incubated with exosomes

first: Liang

last: Gong

first: Chunxiao

last: Yin

first: Yuli

last: Lao

last: Zhu

first: Yueming

last: Jiang


title: Next generation sequencing for quantitative analysis of double-negative (DN) thymocyte transcriptomes from Toxf/f and Toxf/fPdcd1Cre mice.

status: Public on Sep 28 2022

city: Nanjing

first: qifeng

last: he

state: JIANGSU

address: zhongshan Road

department: general surgery

institute: nanjing university

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the difference of NGS-derived transcriptome profiling between DN thymocytes from Toxf/f and Toxf/fPdcd1Cre mice.
Methods: mRNA profiles of DN thymocytes sorted by FACS from 3-4-week-old Toxf/f and Toxf/fPdcd1Cre mice were generated by deep sequencing, in triplicate, using Illumina Novaseq6000. The sequence reads that passed quality filters were analyzed at the transcript level with qRT–PCR using TaqMan and SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (Build Ensembl_release100) and identified 19,045 transcripts in the DN thymocytes of Toxf/f and Toxf/fPdcd1Cre mice with BWA workflow. RNA-seq data showed approximately 1.4% of the transcripts which were differentially expressed between the DN thymocytes from Toxf/f and Toxf/fPdcd1Cre mice, with the parameter of false discovery rate (FDR) < 0.05 and absolute fold change ≥ 2.
Conclusions: Our study exhibits the detailed analysis of DN thymocyte transcriptomes with biologic replicates, generated by RNA-seq technology. The optimized data analysis here provides a framework for comparative investigations of expression profiles. The RNA-seq data allow researchers to identify the transcripts affected by TOX and to better understand the role of TOX in the development of thymocytes.

overall_design: mRNA profiles of DN thymocytes from 3-4-week-old Toxf/f and Toxf/fPdcd1Cre mice

first: Qifeng

last: He

first: Yijun

last: Lu

first: Runqiu

first: Beicheng

last: Sun


title: Ten-day human unilateral lower limb suspension and active recovery in young healthy men

city: BALTIMORE

first: Luigi

last: Ferrucci

state: MD

address: 251 BAYVIEW BLVD.

department: Translational Gerontology Branch

institute: National Institute on Aging, National Institutes of Health

summary: Human skeletal muscle disuse-atrophy is one of the main problems associated with spaceflight, bed rest, lower limb unloading, or immobilization. This study investigates the effects of 10-day unilateral lower limb suspension (ULLS) followed by 21 days of active recovery (AR) in young healthy men.

overall_design: 9 subjects with 3 time points each (baseline, 10-day ULLS, 21-day AR), 2 subjects with 2 time points each (baseline, 10-day ULLS), sequenced with RNA-Seq. This submission consists of 31 paired-end RNA-Seq samples.

first: Julian

last: Candia


title: Molecular dynamics and experimental verification studies of the mechanism of dihydroartemisinin in the treatment of colorectal cancer

city: Chengdu

first: dunshui

last: liao

address: chengdu

institute: West China Hospital,sichuan University,Chengdu,China

summary: SW480 cells were used to study the mechanism of dihydroartemisinin in the treatment of colorectal cancer. The cells in the experimental group were treated with 20 μg/ml dihydroartemisinin, and the control group was treated with culture medium containing 0.1% DMSO. The experimental group and the control group were divided into 3 groups of samples to examine the RNA transcriptome.

overall_design: The SW480 cells were cultured until logarithmic growth phase. Then DHA was added to a final concentration of 20 μg/ml (treatment group) and 0.1% DMSO (solvent control group) , and 3 replicate wells were set up for each group. Cells were continued to be cultured for 4h and then the culture was terminated and the supernatant was discarded. Total RNA was extracted from fresh tissues using the TRIzol reagent (Invitrogen Beijing Office, Beijing, China) based on the manufacturer’s instructions. The extracted total RNA was verified by purity, concentration, and integrity; then, the library was prepared. After RNAseq and reads filtering, clean reads were mapped to the reference genome  and calculated the gene expression level for each sample. The differential expression genes (DEGs) between treatment groups and control groups were calculated using the DESeq2. All analyses were performed with the R 4.0.3 framework.

first: Qingjie

last: Xia

first: Dunshui

last: Liao

first: Zengliang

first: Qijie

last: Li

first: Xiao

last: Zhang

first: Jun-Feng


title: Effect of RRM2 knockdown on gene expression of NF1-associated MPNST cells

first: Zhichao

last: Wang

address: 639 Zhizaoju Road, Shanghai 200011, P.R. China

department: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

institute: Department of Plastic and Reconstructive Surgery

summary:
To investigate the role of RRM2 in the progression of NF1-associated MPNST, we established S462TY cell in which target gene has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of control and knockdown of target gene group

overall_design: Comparative gene expression profiling analysis of RNA-seq data for S462TY cells and its KD derivative (shRRM2).

first: Man-Hon

last: Chung

first: Rehanguli

last: Aimaier


title: MicroRNAs in the exosome-like nanoparticles from orange juice inhibit Citrus blue mold caused by Penicillium italicum [miRNA-Seq]

first: chunxiao

last: yin

type: Non-coding RNA profiling by high throughput sequencing

first: Liang

last: Gong

first: Chunxiao

last: Yin

first: Yuli

last: Lao

first: Hong

first: Yueming


title: MicroRNAs in the exosome-like nanoparticles from orange juice inhibit Citrus blue mold caused by Penicillium italicum [degradome]

last: Zhu

last: Jiang


title: HBP1 inhibits the development of type 2 diabetes mellitus through transcriptional activation of the IGFBP1 gene

city: beijing

first: ZHANG

last: Tongjia

address: xueyuan Road 38

institute: peking university

summary: Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that is highly prevalent worldwide and characterized by glucose and lipid metabolism disorders. However, the pathogenic mechanisms have not been fully established. Here, we found that HMG-box transcription factor 1 (HBP1) is involved in T2DM and that its deficiency in mice aggravates the features of diabetes. In addition, we undertook screening by RNA sequencing and found that HBP1 activates the transcription of the insulin-like growth factor binding protein 1 (IGFBP1) gene. Moreover, Insulin and palmitic acid reduced HBP1 protein expression and inhibited its binding to the IGFBP1 promoter. Furthermore, HBP1 reduced the serum free insulin-like growth factor 1 (IGF-1) concentration through IGFBP1 and inhibited the PI3K/AKT signaling pathway. This forms an insulin/HBP1/IGFBP1 negative feedback regulatory loop to dynamically regulate blood glucose and insulin concentrations. These findings have elucidated a mechanism whereby HBP1 and its negative feedback regulatory loop influence the development of T2DM, thereby providing a new theoretical basis and potential therapeutic target for T2DM.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse liver tissue and its KD derivatives (KO-HBP1).

first: Yuning

last: Cheng

first: Ruixiang

last: Yang

first: Yue

last: Zhou

first: Jiyin

first: Tongjia

first: Shujie

first: Hui

first: Wei

first: Xiaowei


title: Transcriptome sequencing analysis of lncRNA and mRNA expression profiles in bone nonunion

city: ChangSha

first: Tang

last: Liu

state: Hunan

address: No. 139 Renmin Middle Road

department: Department of Orthopedics

institute: The Second Xiangya Hospital

summary: Background: Bone nonunion is a serious complication of fracture. This study explored the differentially expressed lncRNAs (DELs) and mRNAs (DEGs) and identified potential lncRNA-mRNA interactions in bone nonunion.   Methods: We extracted total RNA from three bone nonunion and three bone union patient tissue samples. RNA sequencing was performed to detect DELs and DEGs between bone nonunion and union tissue samples. The lncRNAs and genes with absolute log2-fold change (log2FC) > 1 and adjusted p value < 0.05 were further chosen for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. lncRNA and targeted mRNA interaction networks were constructed.   Results: We observed 179 DELs and 415 DEGs between the bone nonunion and union tissue samples. GO analysis indicated that DELs and DEGs were mainly enriched in chondroitin sulfate proteoglycan biosynthetic process. DELs and DEGs were enriched in 'ECM-receptor interaction' and 'Staphylococcus aureus infection' KEGG pathways. Several potential lncRNA-mRNA interactions were also predicted.  Conclusions: This study identified bone nonunion-associated lncRNAs and mRNAs using deep sequencing that may be useful as potential biomarkers for bone nonunion.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for bone nonunion patients
**RAW DATA not provided due to patient privacy concerns**

first: Jian

first: Rongjun

last: Wan

first: Qunyan

last: Tian


title: MicroRNAs in the exosome-like nanoparticles from orange juice inhibit Citrus blue mold caused by Penicillium italicum

first: chunxiao

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Penicillium italicum
Citrus reticulata

platform_organism:
Penicillium italicum
Citrus reticulata

overall_design: Refer to individual Series


title: Drought induced transcriptomic changes in tobacco

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

institute: Nanjing Agricultural University

summary: The drought stress is one of key adverse environmental factors limiting plant growth and development, even threating global crop productivity in many arid and semi-arid regions. Drought stress usually causes huge economic losses for tobacco industries. Understanding how plants respond and adapt to the drought stress helps generate engineered plants with enhanced drought resistance. In this study, integrative analyses of multiple time point-related transcriptome and metabolome generated from K326 and its derived mutant 28 (M28) with contrasting drought tolerance. We found that dramatic changes of gene expression  profiles between M28 and K326 before and after drought treatment.

overall_design: we conducted transcriptional  analyses using K326 and its derived mutant 28 (M28) with contrasting drought tolerance. Through integration of RNA-seq  and construction of gene regulatory networks, we revealed that some key genes directly or indirectly regulate  in drought responses.

first: Yangyang

last: Li


title: to be updated

city: Pittsburgh

first: David

last: Peters

state: PA

address: 204 Craft Avenue

institute: Magee-Womens Research Institute

type: Methylation profiling by high throughput sequencing

summary: to be updated

overall_design: We performed high-resolution genome-wide epigenomic analysis using solution-phase hybridization and next-generation sequencing of bisulfite-converted DNA from blood on patients with and without NEC.


title: Effect of tet-inducible expression of individual MAP3Ks (COT, MEKK1, MEKK2, MEKK3, ASK1, ASK3, ARAF, RAF1, BRAF, NIK, ZAK1, MLK3, MLK1) in MCF10A mammary epithelial cells.

city: Baltimore

first: Amy

middle: Fukumoto

last: Peterson

address: 735 N Wolfe St. PCTB 502

department: MBG

institute: Johns Hopkins University

summary:
To investigate the cooperative function ERK, JNK and p38 signaling in cell behavior decisions, we established MCF10A cell lines in which each target gene has been overexpressed by stable integration of a TRE3G (TET) inducible promoter driver the expression of each target gene.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 independent repliatse at 18 hours post induction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF10A cells and inducible overexpression of individual MAP3Ks.

first: Sergi

last: Regot


title: CONSTANS and jasmonate signaling coordinate floral senescence in Arabidopsis

city: Sevilla

first: Federico

last: Valverde

address: c/Americo Vespucio 49

country: Spain

institute: CSIC

summary: Photoperiodic floral initiation in the leaf is controlled by the hub gene CONSTANS (CO) while jasmonates (JAs) control flower senescence. Although both processes are chronologically ordered, no association between them has been described to date. We show that CO protein remains in Arabidopsis flowers after the floral induction, although displaying a different tissue and diurnal pattern than in leaves. We found that changes in CO expression alter flower senescence and abscission by interfering with the JA response, supported by petal specific analysis as well as CO overexpression in JA synthesis and signaling mutants. CO has a ZIM-like domain that mediates interaction with the JA response repressor JAZ3 (jasmonate ZIM-domain 3), inhibiting its repressor activity and activating downstream transcription factors involved in flower senescence. The complex CO-JAZ3 also interacts with the E3 ubiquitin ligase Coronatine Insensitive 1 (COI1) leading to its degradation in the presence of jasmonates. Therefore, the coordinated recruitment of photoperiodic and jasmonate signaling pathways would be an efficient way for plants to chronologically order the floral process and ensure the success of offspring production.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for seedlings and petals of Col-0 (WT), 35S:CO (CO overexpressor) vs co-10 (CO null mutant) Arabidopsis thaliana plants.

first: Gloria

last: Serrano-Bueno

first: Pedro

last: de los Reyes

first: Andrea

last: Chini

first: Gabriel

last: Ferreras-Garrucho

first: Víctor

last: Sánchez de Medina-Hernández

first: Marta

last: Boter

first: Roberto

last: Solano


title: Transcriptional evaluation of the ductus arteriosus at the single cell level uncovers a requirement for vimentin for complete closure

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Failure to close the ductus arteriosus immediately post-birth, patent ductus arteriosus (PDA), accounts for up to 10% of all congenital heart defects. Despite significant advances in PDA management options, including pharmacological treatment targeting the prostaglandin pathway, a proportion of patients fail to respond and must undergo surgical intervention. Thus, further refinement of the cellular and molecular mechanisms that govern vascular remodeling of this vessel is required. As anticipated, single-cell RNA sequencing on the ductus arteriosus in mouse embryos at E18.5, P0.5, and P5, revealed broad transcriptional alterations in the endothelial, smooth muscle, and fibroblast cell compartments. After close evaluation of the transcriptomic dataset, we predicted that vimentin might be required for complete closure of the vessel. Subsequent studies demonstrated that, in fact, mice with genetic deletion of vimentin fail to fully remodel the ductus arteriosus. Through single-cell RNA-sequencing and by tracking closure of the ductus arteriosus postnatally in mice, we uncovered the unexpected contribution of vimentin in driving complete closure of the ductus arteriosus potentially through regulation of the Notch signaling pathway.

overall_design: Single cell RNA sequencing on the aorta and ductus arteriosus in mouse embryos at E18.5, P0.5, and P5.

first: Jocelynda

last: Salvador

middle: E

last: Hernandez

first: M

middle: L

last: Iruela-Arispe


title: Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1925 Eastchester Road, Apt 20D, Apt 208

institute: Albert Einstein College of Medicine

summary:
To investigate epigenetic dynamics in a 3D liver spheroid model, liver spheroids were treated with sodium butyrate for 3 days and allowed to recover for 1 week.
We then performed gene expression profiling analysis using data obtained from RNA-seq of spheroids at 4 time points

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 liver spheroids

first: Stephanie

last: Stransky

first: Simone

last: Sidoli


city: kunming

first: Yi-Cheng

email: 290361200@qq.com, mayc@ynu.edu.cn

state: yunnan

address: NO.2 North Cuihu Road

institute: Yunnan University

summary: To identify the mechanism underlying AdipoR1-mediated beneficial effect of exercise, we used RNA-Seq analysis to study the transcriptomic profiles of mice after 4-month wheel running exercise. Differential expression analysis was performed by comparing exercised mice to control mice, and exercised mice subjected to AdipoR1 shRNA versus exercised mice.

overall_design: The transcriptional profiles of gastrocnemius muscle of exercised mice, control mice, and exercised mice subjected to AdipoR1 shRNA were generated by deep sequence, in quadruplicate, using Illumina Novaseq™.

first: Yuan-Li

last: Chen

first: Cheng-Gang

last: zou

first: Lan-Qing


title: Reduced mitochondrial transcription sensitizes acute myeloid leukemia cells to BCL-2 inhibition

city: Gothenburg

first: Cleas

middle: M.

last: Gustafsson

address: Medicinaregatan 9A

department: medical biochemistry and cell biology

country: Sweden

institute: university of Gothenburg

summary: Leukemia cells resistant to standard treatment are sensitive to a recently developed inhibitor of mitochondrial gene expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human AML cells isolated from bone marrow of the mice treated with single and combination compounds

first: Laleh

middle: S

last: Arabanian

first: Jenni

last: Adamsson

first: Anke

last: Unger

first: Raffaella

last: Di Lucrezia

first: Tim

last: Bergbrede

first: Peter

last: Nussbaumer

first: Bert

last: Klebl

first: Lars

last: Palmqvis

first: Claes


title: PIF4/HEMERA-mediated daytime thermosensory growth requires the Mediator subunit MED14

city: University

first: Yongjian

last: Qiu

state: MS

address: 30 University Ave

department: Biology

institute: University of Mississippi

summary: Warm ambient temperatures do not trigger stress responses in plants but stimulate the growth of specific organs. The basic helix-loop-helix transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) plays a central role in regulating thermomorphogenetic hypocotyl elongation in various plant species, including the model dicotyledonous plant Arabidopsis thaliana. Although it is well known that PIF4 promotes plant thermosensory growth by activating key genes involved in the biosynthesis and signaling of the phytohormone auxin, the detailed molecular mechanism of such transcriptional activation is still not clear. Our previous studies demonstrated that HEMERA (HMR), a transcription co-activator of PIF4, promotes the thermo-induced expression of PIF4 target genes through the nine-amino-acid transactivation domain (9aaTAD) in its carboxy-terminus. In this report, we investigate the role of the Mediator complex in the PIF4/HMR-mediated thermoresponsive gene expression. Through the characterization of various mutants of the Mediator complex, a tail subunit named MED14 is identified as an essential factor for thermomorphogenetic hypocotyl growth. MED14 is required for the thermal induction of key PIF4 target genes but has a marginal effect on the levels of PIF4 and HMR. Further transcriptomic analyses confirm that the expression of numerous PIF4/HMR-dependent, auxin-related genes requires MED14 at a warm temperature. Moreover, PIF4 and HMR physically interact with MED14 and both are indispensable for the association of MED14 with the promoters of these thermoresponsive genes. Together, these results unveil an important thermomorphogenetic mechanism, in which PIF4 and its coactivator HMR recruit the Mediator complex to activate auxin-related growth-promoting genes when plants sense moderate increases in ambient temperature.

overall_design: RNA-seq analysis was performed on Col-0 (WT), pif4-2, hmr-22, and med14 seedlings that were grown at 20°C or 27°C under continuous red light for 96 hours. RNA was extracted from four biological replicates, resulting in a total of 32 samples.

first: Abhishesh

last: Bajracharya

first: Jing

last: Xi

first: Ameeta

last: Agarwal

first: Scott

middle: R

last: Baerson


title: Single-Cell Transcriptomic Atlas of Human Hepatic ILCs Reveals the Enrichment of ILC2 in Liver Cancer

city: Hefei

first: Cheng

last: Sun

state: Anhui

address: 17, Lujiang Road

department: the First Affiliated Hospital of USTC

institute: University of Science and Technology of China

summary: Here, we show the scRNA-seq-based analysis of 9 ILC samples sorted by flow cytometry, from blood, healthy livers, hepatocellular carcinoma (HCC) tumors, and HCC tumor-adjacent liver tissues. Unbiased transcriptional clustering revealed seven distinct ILC subpopulations in healthy liver and six in liver cancer, among which there were two tissue-resident NK cell subpopulations (CXCR6+CD16+ and CXCR6+CD16-) in healthy liver but only one tissue-resident NK cell subpopulation (CXCR6+CD16-) in tumor tissues. Notably, ILC2s were significantly accumulated in the HCC tissues, and bulk RNA sequencing of SLAMF1+ ILC2s and SLAMF1- ILC2s identified their function.

overall_design: scRNA-seq-based analysis of 9 ILC samples sorted by flow cytometry, 1 from blood, 3 from healthy livers, 4 from hepatocellular carcinoma (HCC) tumors, and 1 from HCC tumor-adjacent liver tissues. Bulk RNA sequencing samples including 2 from SLAMF1+ ILC2s and 2 from SLAMF1- ILC2s in HCC tumor sorted by flow cytometry.

first: Huan

last: Liu

first: Rongrong

last: Qin

first: Qiang

last: Huang

first: Rui


title: RNAseq of livers from WT mice or livers with Rbfox2 knockout fed CD with 30% (w/v) Fructose in the drinking water

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: Rbfox2 is required for maintaining hepatic metabolic homeostasis. Here we carry out RNAseq to of WT and aged matched litter mate Rbfox2 knockout mice under CD or HFD in order to determine changes in alternative splicing and mRNA expression caused by knockout of this splicing factor in the context of metabolic health and disease.

first: Santiago

last: Vernia

first: Yi-Fang

last: Wang

first: Helen

middle: A

last: Paterson


title: eiCLIP analysis of RBFOX2 in primary mouse hepatocytes

summary: Rbfox2 is required for maintaining hepatic cholesterol levels under high fructose.  Here we carry out an enhanced iCLIP (eiCLIP) protocol in order to determine the targets of Rbfox2 in primary mouse hepatocytes.

overall_design: Primary hepatocytes from control diet mice were harvested and plated, cells were left overnight and then UV irradiated at 150mJ/cm2 before carrying out the eiCLIP protocol

first: Nejc

last: Haberman


title: RNAseq of liver of CD and HFD fed mice in fed or fasted conditions

summary: The liver is key for maintaining metabolic homeostasis between feeding and fasting in healthy conditions. However, this is dysregulated during high fat diet feeding. What are the transcriptomic changes required for rapid adaptation of the liver to respond to feeding and fasting and how is this altered in the development of metabolic disease?

overall_design: RNAseq of liver tissue from control diet and high fat diet (60% cal. from fat) mice harvested under fed (ad libitum) or fasted (16h) status


title: CD4 T cell stimulation with or without chronic lymphocytic leukemia (CLL) cells present

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

summary: In this experiment we in vitro activated T cells from CLL patients either in the presence or absence of their autologous CLL cells. After 48 hours of antiCD3/antiCD28 stimulation, the CD4 cells were FACS sorted from two condition and RNA sequencing was performed on these cells.

overall_design: Comparison of condition with and condition without CLL cells in culture

first: F


title: Transcriptomic and epigenetic analysis of iPSC-endothelial cells treated with statin

city: Palo Alto

first: Yu

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: In the present study we created and analyzed endothelial cells  from two separate iPSC clones from the PBMCs of three different normal individuals using footprint-free Sendai virus, under highly coontroled differentiation and treatment

overall_design: Endothelial differentiation of iPSCs grown in EGM2 media, using RPMI-B27 medium with 6uM CHIR induction for 2 days (d0-d2) and 2 uM CHIR treatment for two days (d3-d5). iPSC differentiated endothelial cells (ECs) were treated with simvastatin (1uM ) for 72 hrs. For diabetic modeling, iPSC-ECs were treated with 25mM glucose and 20 nM insulin and for 1 week.

first: Chun


title: A single-cell transcriptomic inventory of murine smooth muscle cells [colon]

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

institute: Karolinska Institutet

summary: Smooth muscle cells (SMC) execute important physiological functions in numerous vital organ systems, including the vascular, gastrointestinal, respiratory and urogenital tracts. SMC differ morphologically and functionally at different anatomical locations, but the molecular underpinnings of these differences remain poorly understood. Here, using deep single-cell RNA sequencing combined with in situ gene and protein expression analysis in four organs - heart, aorta, lung and colon - we reveal the molecular basis for high-level differences between vascular, visceral and airway SMC, and more subtle differences between SMC in elastic versus muscular arteries as well as zonation of elastic artery SMC along the direction of blood flow. Arterial SMC exhibit extensive organotypic heterogeneity, whereas venous SMC conversely display high similarity across organs. We further identify a unique SMC phenotype of terminal pulmonary arterioles. This study provides the first comparative SMC cross-organ resource, offering new insight into SMC subtypes and their specific functions.

overall_design: single-cell transcriptomes were generated of individual cells captured from adult male mice (8-21 weeks of age) by single-cell RNA-sequencing

first: Giuseppe

last: Mocci

first: Riikka

last: Pietilä

first: Jianping

first: Liqun

last: He

first: Guillem

last: Genové

first: Stefanos

last: Leptidis

first: Sonja

last: Gustafsson

first: Byambajav

last: Buyandelger

first: Elisabeth

last: Raschperger

first: Emil

last: Hansson

first: Johan

last: Björkegren

first: Michael

last: Vanlandewijck

first: Urban

last: Lendahl

first: Christer

last: Betsholtz


title: A single-cell transcriptomic inventory of murine smooth muscle cells [heart]

overall_design: single-cell transcriptomes were generated of individual cells captured from adult male mice (8-30 weeks of age) by single-cell RNA-sequencing

last: Liu


title: RNAseq of livers from WT mice or livers with Rbfox2 knockout fed CD

city: London

first: LMS

last: Bioinformatics Core

summary: Rbfox2 is required for maintaining hepatic metabolic homeostasis, here we carry out RNAseq to of WT and aged matched littermate Rbfox2 knockout mice under high fructose in order to determine changes in alternative splicing and mRNA expression caused by knockout of this splicing factor in this metabolic environment.

overall_design: RNAseq of liver tissue from control diet and high fat diet (60% cal. from fat) mice harvested under fasted (16h) status

first: Santiago

last: Vernia

first: Yi-Fang

last: Wang

first: Helen

last: Paterson


title: A single-cell transcriptomic inventory of murine smooth muscle cells [lung]

first: Lars

last: Muhl

first: Giuseppe

last: Mocci

first: Riikka

last: Pietilä


title: Characterization of the role of RBFOX2 in the liver

summary:
Here we investigate the role of the splicing factor RBFOX2 in the liver. Our work describes a new regulatory mechanism where RBFOX2 controls cholesterol level, by coordinating the inclusion/exclusion of alternatively spliced exons in the liver.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Integrative proteomics of primary hepatocytes during dedifferentiation

city: Hang Zhou

first: jiang

last: zhengyi

state: State...

address: Qingchun  79 Road

institute: Zhejiang University

summary: To understand the relationship between protein expression and mRNA translation during primary hepatocytes dedifferentiation, we have employed transcriptome microarrayas a discovery platform. Rat primary hepatocytes were isolated by the method of two-step enzymes perfusion and then cultured on mono-layer in vitro. Samples at 0h( just after perfusion, before planking) , 6h, 12h ,24h and 48h were collected.  Integrative analysis of transcriptome and whole cell proteomics (WCP) leaded us to realize the poor correlation of them. This discovery made us realize that targeting mRNA was far from enough in illustrating this process. It would provide new insights from the aspects of post-translational modifications(PTMs).Post-translational modifications play important role in numorous biological and pathological process, but a few reports are related to primary hepatocytes dedifferentiation process, and there is still no integrative proteomics analysis in this field yet. In this study, we perform ubiquitinome phosphorylated proteome, whole cell proteome and transcriptome simultaneously during the five different time points of dedifferentiation in vitro quantified over 6000 modified sites mapping to over 2000 proteins. And comprehensive analysis of these datasets provides novel insight in this field.

overall_design: Dedifferentiation induced gene expression in primary rat hepatocytes was measured at 0, 6, 12, 24 and 48 hours after cultured in vitro monolayer. Three independent experiments were performed at each time point using different biological replicates.

first: Zhengyi

last: Jiang


title: A single-cell transcriptomic inventory of murine smooth muscle cells [aorta]

first: Jianping

first: Liqun

last: He

first: Guillem

last: Genové

first: Stefanos

last: Leptidis

first: Sonja

last: Gustafsson

last: Buyandelger


title: mRNA expression analysis of several cell subset from peripheral blood of SLE patient and Healthy Control

city: Kyoto

first: Kenji

last: Okuma

state: Kyoto

address: 53, Shogoin Kawara-cho, Sakyo-ku, Medical Innovation Center

country: Japan

institute: Astellas Pharma Inc.

summary: Isolated T, B, monocyte, mDC, pDC, naiveB, memoryB and PBMC at spontaneous state from peripheral blood

overall_design: SLE, HC

first: Takuma

last: Oku

first: Yoshitaka

last: Hirayama

first: Koji

last: Kitagori

first: Hajime

last: Yoshifuji


title: Transcriptome of skin biopsies from Hidradenitis Suppurativa (HS) patients with anti-TNFalpha therapy.

status: Public on Sep 25 2022

city: Dublin

first: Walter

last: Kolch

address: School of Medicine, University College Dublin, Belfield, Dublin 4.

country: Ireland

institute: Systems Biology Ireland

summary: Hidradenitis suppurativa (HS) is a chronic inflammatory skin disorder with significant morbidity. The pathogenesis remains incompletely understood although immune dysregulation plays an important role. It is challenging to treat and approximately 50% of patients respond clinically to adalimumab, the only licensed treatment.

overall_design: We completed bulk RNA-sequencing on lesional and non-lesional skin samples of patients before and after 12-weeks treatment with adalimumab.

first: Róisín

last: Hambly

first: Solene

last: Gatault

first: Luis

middle: F

last: Iglesias-Martinez

first: Brian

last: Kirby


title: Variation in histone configurations correlates with gene expression across nine inbred strains of mice [ChIP-seq]

city: Bar Harbor

first: Petko

last: Petkov

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: It is well established that epigenetic features, such as  histone modifications and DNA methylation, are associated with gene expression across cell types. However, it is not well  known how variation in genotype affects epigenetic state,  or to what extent such variation contributes to variation in gene expression across genetically distinct individuals. Here we investigated the relationship between heritable epigenetic variation and gene expression in hepatocytes across nine inbred mouse strains. Eight of the inbred strains  were founders of the diversity outbred (DO) mice, and the ninth  was DBA/2J, which, along with C57BL/6J, is one of the founders  of the BxD recombinant inbred panel of mice. We surveyed four  histone modifications, H3K4me1, H3K4me3, H3K27me3 and H3K27ac,  as well as DNA methylation. We used ChromHMM to identify  14 chromatin states representing distinct combinations  of the four measured histone modifications. We found that variation  in chromatin state mirrored genetic variation across the inbred  strains. Furthermore, epigenetic variation was correlated with gene  expression across strains. The correspondence between epigenetic  state and gene expression was replicated in an independent population  of DO mice in which we imputed local epigenetic state. In contrast,  we found that DNA methylation did not vary across inbred strains and  was not correlated with variation in expression in DO mice. This  work suggests that chromatin state is highly influenced by local  genotype and may be a primary mode through which expression  quantitative trait loci (eQTLs) are mediated. We further  demonstrate that strain variation in chromatin state, paired  with gene expression is useful for annotation of functional  regions of the mouse genome. Finally, we provide a data  resource that documents variation in chromatin state across  genetically distinct individuals.

overall_design: We surveyed four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K4me3) in hepatocytes nine inbred mouse strains. We also surveyed patterns of DNA methylation and bulk gene expression in the same mice to relate genetic variation to variation in epigenetic modifications and gene expression.

first: Gregory

middle: W

last: Carter

first: Anna

last: Tyler

first: Catrina

last: Spruce

first: Romy

last: Kursawe

first: Annat

last: Haber

first: Robyn

last: Ball

first: Wendy

last: Pitman

first: Alexander

middle: D

last: Fine

first: Narayanan

last: Raghupathy

first: Michael

last: Walker

first: Vivek

last: Philip

first: J

last: Mahoney

first: Gary

last: Churchill

first: Jennifer

middle: J

last: Trowbridge

last: Stitzel

first: Kenneth

last: Paigen

first: Christopher

last: Baker


title: Variation in histone configurations correlates with gene expression across nine inbred strains of mice [RRBS]

first: Petko

last: Petkov

last: Carter


title: Variation in histone configurations correlates with gene expression across nine inbred strains of mice [RNA-seq]

first: Gregory

last: Tyler

last: Spruce


title: Effect of depletion of KLB or various combinations of FGFR1, FGFR3, and FGFR4 on gene expression in HuH-7 and JHH-7 cells

city: Beijing

first: yue

last: cui

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences，Beijing

summary: To investigate the impact of FGFR redundancy in regulating gene expression, we established HuH-7 and JHH-7 cell lines in which each target gene has been knocked out by CRISPR.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HuH-7 and JHH-7 cells and its KO derivatives (sgKLB, sgFGFR4, sgFGFR3/4 and sgFGFR1/3/4).

first: Yue

last: Cui

first: Zhanchao

last: Tao

first: Ting

last: Han


title: RNA-seq for NB4 cell line in either the absence or presence of LDB1

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for NB4 cell line in either the absence or presence of LDB1

overall_design: 2 NB4 samples with no treatment and 2 NB4 samples with LDB1 knockdown

first: Pan

last: Jian

first: Lu

last: Lihui


title: IRF8 regulates intrinsic ferroptosis through repressing p53 expression to maintain tumor cell sensitivity to cytotoxic T lymphocytes

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: Ferroptosis has emerged as a cytotoxic T lymphocyte (CTL)-induced tumor cell death pathway. The regulation of tumor cell sensitivity to ferroptosis is still incompletely understood. We report here that the interferon regulatory factor 8 (IRF8) functions as a regulator of tumor cell intrinsic ferroptosis. Genome-wide gene expression profiling identified ferroptosis pathway as an IRF8-regulated pathway in tumor cells. IRF8.KO tumor cells acquire resistance to intrinsic ferroptosis induction and IRF8-deficient tumor cells exhibit decreased ferroptosis in response to tumor-specific CTLs. Irf8 deletion increases p53 expression in tumor cells and knocking out p53 in IRF8.KO tumor cells restored tumor cell sensitivity to intrinsic ferroptosis induction. Furthermore, IRF8.KO tumor cells grew significantly faster than WT tumor cells in immune competent mice. To restore IRF8 expression in tumor cells, we designed and synthesized codon usage-optimized IRF8-encoding DNA to generate IRF8-encoding plasmid NTC9385R-mIRF8. Restoring IRF8 expression via a lipid nanoparticle-encapsulated NTC9385R-mIRF8 plasmid therapy suppressed established tumor growth in vivo. In human cancer patients, nivolumab responders have a significant higher IRF8 expression level in their tumor cells as compared to the non-responders. Our data determine that IRF8 represses p53 expression to maintain tumor cell sensitivity to intrinsic ferroptosis

overall_design: Examination of ferroptosis in 4 different fibrosarcoma cell lines, 2 IRF8KO and 2 wild type

first: Dakota

last: Poschel

first: Kebin

last: Liu


title: Transcriptome and QTL mapping analyses identifying major QTL genes controlling glucosinolates contents between vegetable-type and oilseed-type Brassica rapa plants

city: Anseong-si, Gyeonggi-do

first: Heewon

last: Moon

address: 4726,Seodong-daero, Daedeok-myeon

country: South Korea

institute: Chung-ang university

summary: We report here NGS RNA-seqencing datasets for two different light condition of two different Brassica rapa cultivars, vegetable-type "Chiifu" and oilseed-type "LP08" plants

overall_design: Two different light treatment (Light,Dark) to B. rapa whole plants: Light; 1week old (16hours light, 8hours dark); Dark; 1week old (24hours dark)

first: Dong

middle: H

last: Kim


title: Salmonella subverts autophagy balancing bacterial fate and cellular inflammation

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

summary: Salmonella Typhimurium (S. Typhimurium) is an enteric bacterium capable of invading a wide range of host cell types and adopting different intracellular lifestyles for survival. Host endocytic trafficking and autophagy have been implied to regulate the S. Typhimurium subcellular localization and survival. To reveal alternative host regulators on S. Typhimurium lifestyle, we combined a novel fluorescent reporter, Salmonella Intracellular Analyzer (SINA) with haploid forward genetic screening. This identified transcription factor c-MYC as a negative regulator of S. Typhimurium cytosolic lifestyle via stabilizing the Salmonella-containing vacuole (SCV). We further confirmed that c-MYC downstream regulated LC3 acts to maintain SCV stability and limits S. Typhimurium cytosolic lifestyle. We demonstrated that LC3 is recruited to the SCV prior to the endomembrane damage marker Galectin 3, and it regulates SCV stability independent of the autophagosome adaptor NDP52. The LC3 processing enzymes ATG3 and ATG4 reciprocally act on SCV stability, where the loss of LC3-PE conjugation in the absence of ATG3 limits SCV damages. We further identified the dosage-dependent function of the S. Typhimurium effector SopF in mediating SCV stability by actively avoiding LC3 recruitment to the proximity of the SCV to reduce its catastrophic rupture and host cell death. Altogether, we offer insights on the significance of cellular transcription profile in the determination of S. Typhimurium pathophysiology as well as the underlying host-evasion strategy of S. Typhimurium.

overall_design: Identification of alternative host regulators on S. Typhimurium lifestyle by haploid forward genetic screening

first: Chak

last: Luk

first: Wei

last: Yu

first: Jost

last: Enninga


title: The impact of the carbon-regulation protein SbtB on CO2-dependent gene expression in Synechocystis sp. PCC 6803 [cyal]

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

summary: Gene expression changes were followed in cultures of the cyanobacterium Synechocystis sp. PCC 6803 three and 24 hours after shift from high carbon (HC) to low carbon (LC) concentrations. The acclimation to fluctuating inorganic carbon (Ci) concentrations is crucial for photoautotrophic organisms living in aquatic environments such as cyanobacteria. The PII-like regulator protein SbtB binds the second messengers cAMP or c-diAMP and is involved in the acclimation to LC. Here, we investigated the impact of SbtB and of second messengers on gene expression changes during this acclimation response. We analyzed cultures of the wild type (WT), the ΔsbtB mutant lacking the PII-like regulator protein SbtB, the ΔcyaI mutant, lacking the main soluble adenylate cyclase for cAMP production and ΔdacA, lacking the diadenylate cyclase for c-diAMP production. The majority of LC-induced genes behaved in these mutants like in wild type. However, a defined subset of LC-regulated genes in WT was found to be changed in mutant ΔsbtB already under high CO2. Collectively, the results indicate that SbtB regulates a particular subset of genes during the LC acclimation response.

overall_design: Total RNA was prepared from cells of Synechocystis sp. PCC 6803 wild type and the ΔcyaI mutant, lacking the main soluble adenylate cyclase for cAMP production. Samples were taken in biological replicates. For data analysis, the same raw data from wild type were taken as in the experiment with the ΔsbtB mutant but normalized here together with the data obtained for the ΔcyaI mutant.

first: Oliver

last: Mantovani

first: Viktoria

last: Reimann

first: Felix

middle: P

last: Herrmann

first: Khaled

last: Selim

first: Karl

last: Forchhammer

first: Martin

last: Hagemann


title: Development of gene expression signatures for lnc-URIDS knock down rat dermal fibroblast

status: Public on Sep 24 2022

city: guangzhou

first: Meng

last: Ren

address: 107 Yanjiang West Road

department: endocrinology department

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: In previous study we found that Lnc-URIDS increased in diabetic dermal fibroblast and delayed wound healing.To further verify the roles of lnc-URIDS in fibroblast during wound heaing, A lnc-URIDS shRNA lentivirus and a control lentivirus were transfected into rat dermal fibroblast respectively (three independent replicates for each group) for 48h. Then, differential expressed genes between Control fibroblast and Lnc-URIDS knockdown fibroblast were detected by using microarray expression profiling though Agilent rat 4 x 44K gene expression microarrays (Agilent Technologies, Santa Clara, CA) .

overall_design: Three replicate samples in control group and KD group.

first: Mengdie

last: Hu

first: Li

last: Yan


title: Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease relevant pathologies

city: Toronto

first: Karun

last: Singh

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Krembil Research Institute

summary: There are hundreds of risk genes for autism spectrum disorder (ASD), but signaling networks at the protein level remain unexplored. We used neuron-specific proximity-labeling proteomics (BioID) to identify protein-protein interaction (PPI) networks for 41 ASD-risk genes. Neuron-specific PPI networks included synaptic transmission proteins, which are disrupted by de novo missense variants. The PPI network map revealed convergent pathways including mitochondrial/metabolic processes, Wnt signaling, ion channel activity and MAPK signaling. CRISPR knockout validations revealed an association between mitochondrial activity and ASD-risk genes. The PPI network showed an enrichment of 112 additional ASD-risk genes and differentially expressed genes from post-mortem ASD patients. Clustering of risk genes based on PPI networks identified gene groups corresponding to clinical behavior score severity. Our data reveal that cell type-specific PPI networks can identify previously unknown individual and convergent ASD signaling networks, provide a method to assess patient variants, and reveal biological insight into disease mechanisms and sub-cohorts of ASD.

overall_design: Cortices from Day 21-23 Taok2 WT and KO mice were used for RNA sequencing analysis, with 3 male mice per condition.

first: Nadeem

last: Murtaza

first: Annie

last: Cheng

first: Chad

middle: O

last: Brown

first: Durga

last: Meka

first: Shuai

last: Hong

first: Jarryll

last: Uy

first: Joelle

last: El-Hajjar

first: Neta

last: Pipko

first: Brianna

middle: K

last: Unda

first: Birgit

last: Schwanke

first: Sansi

last: Xing

first: Bhooma

last: Thiruvhindrapuram

first: Worrawat

last: Engchuan

first: Brett

last: Trost

first: Eric

last: Deneault

first: Froylan

last: Calderon de Anda

first: Bradley

last: Doble

first: James

last: Ellis

first: Evdokia

last: Anagnostou

first: Gary

last: Bader

first: Stephen

last: Scherer

first: Yu

last: Lu


title: Photoactivatable senolysis with single-cell resolution reverses aging

city: Haikou

first: Wenwen

last: Liu

address: 58 People's Avenue

department: College of Pharmacy

institute: Hainan University

summary: Emerging evidence supports the use of pharmaceutical interventions to target senescent cells (SnCs) and induce their death (senolysis) to extend a healthy lifespan. The challenge then becomes how to achieve precise, broad-spectrum and tractable senolysis. To this end, we have designed a novel senotherapeutic agent with an unprecedented integrated strategy

overall_design: Examination of Young control, Aged control and KSL0608-Se + irradiation groups in livers of mice by RNA-seq, five replicates

first: Donglei

last: Shi

first: Ying

last: Gao

first: Yuan

last: Guo

first: Jian

last: Li


title: Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive neoplasms in children and young adults II

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: We molecularly characterized a class of histologically aggressive childhood liver cancers and showed that these tumors are clinically aggressive and that their observed histological features are associated with underlying recurrent molecular features. We proposed a diagnostic algorithm to identify these cancers using a combination of histological and molecular features, and our analysis suggested that these cancers may benefit from specialized treatment strategies that may differ from treatment guidelines for hepatoblastomas and hepatocellular carcinomas.

overall_design: Genome-wide copy numbers were estimated using DNA isolated from fresh frozen and formalin-fixed paraffin-embedded (FFPE) tumor tissue (38 cases) using the Affymetrix OncoScan FFPE Assay Kit and OncoScan Console 1.3, and data were analyzed by Affymetrix CHAS 3.1 and OncoScan Nexus Copy Number 7.5 after BWA alignment to GRCh37/hg19.

first: Dolores

last: Lopez-Terrada


title: Long Noncoding RNA TINCR-mediated Regulation of Acetyl-CoA Metabolism Promotes Nasopharyngeal Carcinoma Progression and Chemoresistance

city: Guangzhou

first: Zi-Qi

last: Zheng

address: Dong Feng East Road No.651

institute: Sun Yat-sen University Cancer Center

summary: Our present study showed that lncRNA TINCR have impact on the ubiquitination-mediated degradation level of ACLY protein in nasopharyngeal carcinoma. Silencing of TINCR lead to downregulation of ACLY protein level. ACLY is a cytosolic homotetrameric enzyme catalyzing the ATP-dependent conversion of citrate and coenzyme A (CoA) to oxaloacetate and acetyl-CoA, a precursor for lipid biosynthesis, including cholesterol, free fatty acid and phospholipid. Meanwhile, the cellular acetyl-CoA pool is also required for acetylation reactions that modify proteins such as histone acetylation, including Histone H3 acetylation K27 (H3K27ac). To select the shared genes that were regulated by TINCR and were in response to acetyl-CoA alteration, we conducted RNA-seq in HONE-1 cells with or without TINCR or ACLY silencing, as well as H3K27ac Chromatin Immunoprecipitation sequencing (ChIP-seq) in HONE-1 cells with or without ACLY silencing. We also performed CLIP-seq in HONE-1 and SUNE-1 cells to validate the TINCR-ACLY interaction and identify the binding sites of TINCR with ACLY.

overall_design: We conducted RNA-seq in HONE-1 with or with out TINCR or ACLY silencing, H3K27ac Chromatin Immunoprecipitation sequencing (ChIP-seq) in HONE-1 cells with or without ACLY silencing, and ACLY crosslinking-immunprecipitation sequencing (CLIP-seq) in SUNE-1 and HONE-1 cells.

first: Zhi-Xuan

last: Sun


title: Ox40-Cre-mediated deletion of BRD4 reveals an unexpected phenotype of hair follicle stem cells in alopecia

status: Public on Sep 23 2022

first: Mou

last: Wen

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

summary: To identify the mechanisms of impaired hair regeneration in Brd4-deleted follicle stem cells, we FACS sorted HFSCs from Rag1-/-Ox40-Cre and Rag1-/-Brd4f/fOx40-Cre mice and performed RNA-seq analysis comparing the differences in their transcriptional profiles.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HFSCs from Rag1-/-Brd4f/fOx40-Cre mice and conrol Rag1-/-Ox40-Cre mice on postnatal day 20, 26, and 70.

first: Xiang

last: Xiao

first: Yuanlin

last: Ying

first: Xian


title: RNAseq of two mouse lung cancer cell lines in a DSTYK-altered context

city: Pamplona

first: Luis

last: Montuenga

state: Navarra

address: Avda. Pío XII, 55

institute: CIMA

summary:
We report RNAseq data from two independent mouse syngeneic lung cancer cell lines LLC and UN-SCC679 in an altered DSTYK context
Lung cancer remains the leading cause of cancer-related death worldwide. We identify DSTYK, a dual serine/threonine and tyrosine non-receptor protein kinase, as a novel actionable target altered in non-small cell lung cancer (NSCLC). We also show DSTYK´s association with a lower overall survival (OS) and poorer progression-free survival (PFS) in multiple patient cohorts. To ascertain the potential molecular carcinogenesis processes in which DSTYK was involved, we performed an RNAseq analysis of two different lung cancer cell lines with either overexpressed or inhibited DSTYK. Inhibition was achieved through shRNA technology. These cell lines were cultured in RPMI 1640 supplemented with 10% Fetalclone (Thermo Fisher Scientific) and 100 U/mL penicillin-100 µg/mL streptomycin (Thermo Fisher Scientific). All cells were grown in a humidified incubator containing 5% CO2 at 37°C. Cell lines were routinely tested for mycoplasma.

overall_design: Characterization of mouse syngeneic lung cancer cell lines (LLC and UN-SCC679) transcriptome in a DSTYK-altered context

first: Karmele

last: Valencia

middle: M


title: Loss of LOXL2 promotes uterine hypertrophy and tumor progression

city: Wenzhou

first: Xufeng

state: Zhejiang

address: Caolong Road

institute: Wenzhou Medical University

summary: Gene expression microarray was used to evaluate altered genes related to LOXL2 expression level in order to identify potential molecular mechanism in uterus.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Frozen tissues of 6 uterine endometrial carcinoma patients and 6 mice uterus were subjected to cDNA microarray analysis.

Please note that the raw data files for human samples include the incorrect Agilent design ID (Agilent-026655, instead of Agilent-014850), while generated using Agilent-014850 design.

first: Dazhuan

last: Xin

first: Y

last: chinn


title: Teratoma development in adult mice from extending pluripotency

city: Tianjin

first: chen

last: jiyu

address: Nankai university

institute: Nankai university

summary: Embryonic stem cells (ESCs) have practically unlimited proliferation capacity and unrivalled differentiation potential, thus providing an attractive source of cells for regenerative medicine. Numerous ESC culture systems have been established to achieve extended pluripotency. However, long-term safety evaluation on these extended pluripotent state cells (EPS) were largely overlooked. Here, we generate full ESC-mice through tetraploid embryo complementation assay from the prevailing extended pluripotent stem cells. Two years of safety evaluation show that all the EPS mice developed late onset retroperitoneal teratomas whereas no abnormality was observed in the conventional ESC mice. Whole exome sequencing and chromatin accessibility analysis on the EPS and the corresponding tumor tissues identify the global chromatin reconfiguration but only minor genetic variation in EPS. Correspondingly, the teratomas could be attributed to a proportion of undifferentiated cells from extended pluripotency. Our study uncovers the prevailing late onset tumorigenesis in EPS-mouse, highlighting the impact of early epigenetic variations on tumorigenicity in the adult.

overall_design: bisulfite sequencing of teratomas obtained after tetraploid embryo injection of ESCs cultured in different culture conditions

first: Chenglei

last: Tian

first: Jie

first: Jiyu

last: Chen

first: Xiaoying

last: Ye


title: Potentiation of Adipogenesis by Reactive Oxygen Species is a Unifying Mechanism in the Pro-adipogenic Properties of Bisphenol A and its New Structural Analogues

city: Calgary

first: Jennifer

last: Thompson

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

institute: University of Calgary

summary: Aims Structural analogues of bisphenol A (BPA), including BPS and BPF, are emerging environmental toxicants as their presence in the environment is rising since new regulatory restrictions were placed on BPA-containing infant products. The adipogenesis-enhancing effect of bisphenols may explain the link between human exposure and metabolic disease; Methods Adipose-derived progenitors were isolated from mice and exposed to various concentrations of BPS, BPA or BPF before induction of adipogenesis. RNAseq in BPS-exposed progenitors revealed modulation in redox pathways. The role of reactive oxygen species (ROS) was assessed by measuring the degree of adipogenesis in the presence or absence of antioxidants. ROS production and mitochondria function were determined by fluorescent assays. Fat mass was measured by TD-NMR in adult mice exposed to BPS during in utero establishment of the adipocyte progenitor pool, and in adult mice exposed to BPS after weaning. however, underlying molecular pathways remain unresolved. Results Exposure of progenitors to BPS, BPF, BPA or ROS generators enhanced lipid droplet formation and expression of adipogenic markers after induction of differentiation. ROS was higher in bisphenol-exposed cells, while co-treatment with antioxidants attenuated adipogenesis and abolished the effect of BPS. There was a loss of mitochondria membrane potential in BPS-exposed cells and mitochondria-derived ROS contributed to potentiation of adipogenesis by BPS and its analogues. Male mice exposed to BPS during gestation had higher adiposity, while postnatal exposure had no impact on adiposity in either sex. ROS act as signaling molecules in the regulation of adipocyte differentiation and mediate bisphenol-induced potentiation of adipogenesis.

overall_design: Comparative gene expression profiling analysis of RNA seq data for preadipocyte cells derived from wild-type murine inguinal subcutaneous adipose tissue, which were then exposed to vehicle or 2.5uM BPS.

first: Radha

last: Singh

first: Jessica

last: Wager

first: Taylor

middle: B

last: Scheidl

first: Liam

middle: T

last: Connors

first: Sarah

last: Easson

first: Mikyla

last: Callghan

first: Samuel

last: Alatorre-Hinojosa

first: Lucy

last: Swift

first: Pina

last: Colarusso

first: Anshul

last: Jadli

first: Timothy

last: Shutt

first: Vaibhav

last: Patel


title: Unified rhombic lip origins of Group 3 and Group 4 medulloblastoma [OTX2_KO]

city: Memphis

first: Kyle

last: Smith

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

summary: RNA-seq profiling of medulloblastoma OTX-knockout.

overall_design: Total RNAsequencing from medulloblastoma samples

first: Kye

first: Paul

last: Northcott


title: Muscle-specific cellular and molecular adaptations to late-life voluntary concurrent exercise in mice

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

summary: Aged mice (22-24 mo) underwent PoWeR for 8 weeks. RRBS on myonuclei from soleus muscles (n=3 sedentary and n=3 trained) were subjected to low-input RRBS.

overall_design: Human skeletal actin promoter reverse tetracycline transactivator tetracycline response element driven histone 2B green fluorescent protein mice (termed HSA-GFP) were generated to label resident myonuclei at the onset of experimentation. Myonuclera were isolated via fluorescent activated myonuclear sorting, then DNA was isolated from purified myonuclear using the Qiagen DNA Micro Kit using carrier RNA. Low-input reduced representation bisulfite sequencing was carried out by Zymo Research.

first: Kevin

last: Murach

first: Chris

last: Fry

first: Cory

last: Dungan


title: Inhibitor of prolyl-tRNA synthetase (PRS)  to reduce tubulointerstitial nephritis

city: Seoul

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

institute: Seoul National University Hospital

summary: Glutamyl-prolyl-transfer RNA synthetase (EPRS) is a class of enzymes that catalyze the attachment of 2 amino acids (i.e., glutamic acid and proline) to cognate transfer RNA for subsequent protein synthesis. Herein, we evaluated the effect of EPRS on the progression of tubulointerstitial nephritis using the mouse model with adenine-mixed diet. One single-cell RNA transcriptomic dataset was originated from wild-type mice, and other one was from heterozygous knockout mice, all of these were harvested at 2 weeks after adenine-mixed diet.

overall_design: Whole kidneys of C57BL/6 male (Eprs+/- and Eprs+/+) mice were prepared for scRNA. For a toxin-induced TIN model, mice were treated with AD and harvested at the indicated time points after reperfusion. To block the EPRS function, EPRS-targeting small molecule inhibitor was administered via peritoneal injection once daily.

first: Chaelin

last: Kang

last: Yun

first: Seung

last: Han


title: Single-cell transcriptome analysis of the in-vivo response to viral infection in the cave nectar bat Eonycteris spelaea

city: Singapore

first: Wharton

middle: O Y

last: Chan

state: Singapore

address: 8 College Road

department: Emerging Infectious Disease

country: Singapore

institute: Duke-NUS Medical School

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

overall_design: Refer to individual Series


title: RNA-seq analysis in uveal melanoma cells 92.1 and OMM1

city: Ghent

first: Shanna

last: Dewaele

address: Corneel Heymanslaan

country: Belgium

institute: Ghent University

summary: The goals of this study are to compare gene expression profiles between uveal melanoma cells treated with either a scrambled antisense oligonucleotide (NTC) or a SAMMSON inhibiting ASO wether or not in combination with mTOR inhibitor GDC-0349. GDC-0349 synergizes with SAMMSON ASO to further reduce cell viability. Based on the RNA seq data, we observed only a limited number of DEGs in the GDC-0349 treated cells, while the number of DEGs in the combination significantly increased compared to SAMMSON ASO alone with many overlapping genes showing a more pronounced log2foldchange.

overall_design: RNA-seq data of uveal melanoma cells 92.1 and OMM1 treated with NTC or SAMMSON inhibiting ASO in combination with 0.006% DMSO or mTOR inhibitor GDC-0349 with 4 replicates per condition

first: Pieter

last: Mestdagh


title: Unified rhombic lip origins of Group 3 and Group 4 medulloblastoma [scRNA-seq]

summary: Medulloblastoma, a malignant childhood cerebellar tumor, molecularly segregates into biologically distinct subgroups warranting personalized therapy. Murine modeling and cross-species genomics have provided mounting evidence of discrete, subgroup-specific developmental origins.

overall_design: Developing murine cerebellum analyzed by scRNAseq.


title: Tumour immune contexture is a determinant of anti-CD19 CAR T-cell efficacy in large B cell lymphoma

city: Foster City

first: Natahlie

last: Scholler

state: CA

address: 324 Likeside Drive FC324-1

department: Oncology Research Department

institute: Gilead

summary:
Axicabtagene ciloleucel (axi-cel), an anti-CD19 chimeric antigen receptor (CAR) T-cell therapy approved for treatment of relapsed/refractory large B-cell lymphoma (LBCL), has comparable efficacy across conventional LBCL markers. We analysed whether pre- and posttreatment  tumour immune contexture determines clinical outcomes for axi cel–treated patients in the ZUMA-1 pivotal study. Longitudinal evaluation of the tumour microenvironment (TME) uncovered dynamic patterns that occurred rapidly after axi-cel (within 2 weeks) in responders—pronounced enhancement of T- and myeloid cell signatures and diminution of B cell signature. Clinical response and overall survival associated with high CD8+ T-cell density (Immunoscore) and immune gene expression (Immunosign21) in TME pretreatment, which was paralleled by blood CAR T-cell levels posttreatment. High density of regulatory T cells in TME pretreatment associated with reduced axi-cel–related neurologic toxicity. At relapse, the TME evolved toward an immune-detrimental contexture with decreased T-cell–related and increased counterregulatory immune signatures and B cell lineage antigens. A TME rich in T-cell attractive chemokines (CCL5, CCL22), gamma-chain receptor cytokines (IL-15, IL-7, IL-21), and interferon regulated molecules associated with T-cell infiltration and markers of activity, a result validated in 2 independent datasets totalling ≈300 LBCL samples.
These findings advance mechanistic understanding of CAR T-cell therapy and foster biomarker development and treatment optimizations.

overall_design: 71 samples were analyzed for 65 patients with screening, baseline, DAY7-14, FCBWK4 and PROGFCB time points.

first: Nathalie

first: Regis

last: Perbost


title: Quantitative Analysis of transcriptome in organoids derived from TP190 wildtype(WT) and Williams Syndrome(NSUN-GTF2ird2+/-) human induced Pluripotent  Stem Cell

first: Stanislav

last: Zakharenko

state: Tennessee

address: 262 Danny Thomas Place

department: Developmental Neurobiology

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: mRNA profiles of 68-day old wild type (WT) and NSUN-GTF2ird2 +/- cortical organoids

first: Shibiao

last: Wan

first: Ti-Cheng

last: Chang

first: Yiping

last: Fan


title: Screening of differentially expressed circRNAs in renal cortex of mice with diabetic kidney injury

city: Fuzhou

first: Nanwen

last: Zhang

address: Fuzhou

institute: Fujian Medical University

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

summary: To determine the circRNA expression profile in DKI and  normal mice, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs in DKI and normal mice Kidney cortex tissues.

overall_design: normol tissue group and DKI tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Mingcai

last: Chen

first: Shijie

last: Luo


title: Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH


title: Distalised kidney organoids

city: Parkville

first: Sean

last: Wilson

state: Victoria

address: 50 Flemington Road

country: Australia

institute: MCRI

summary: Distalised organoid samples at Day 14 and Day 21 of culture. Day 21 cultures have RSPO1 addition either at Day 7 or Day 14 of culture.

overall_design: Single cell RNA-seq generated on a 10x Chromium genomics platform from iPSC-derived human kidney organoids. Each sample represents 6 pooled organoids derived from a single well of a transwell plate, generated from individual iPSC-derived reporter lines and harvested at either Day 14 (D14) or Day 21 (D21) of the differentiation protocol.

first: Pamela

last: Kairath

first: Melissa

last: Little


title: Effect of depletion of SEPT2 on gene expression during viral infection of peritoneal macrophages

city: Chongqing

first: Beibei

last: Fu

address: 174th, Shazheng Street, Shapingba District

institute: Chongqing University

summary: To investigate the immune function of SEPT2 in the regulation of viral infection, we obtained SEPT2-deficient PMs from SEPT2 conditional knockout mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of wild-type and SEPT2-deficient PMs with VSV or HSV-1 infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type and SEPT2-deficient PMs with VSV or HSV-1 infection.

first: Haibo

last: Wu

first: Xiaoyuan

last: Lin


title: Frequent low-dose THC in adolescence disrupts microglia homeostasis and disables response to microbial infection

status: Public on Sep 22 2022

city: Irvine

first: Daniele

last: Piomelli

address: 837 Health Sciences Road

institute: University of California, Irvine

summary: Adolescence is a time of experimentation with cannabis. We evaluated whether adolescent exposure to the drug's psychotropic consituent, delta-9-tetrahydrocannabidiol (THC), might persistently alter microglia function and brain immune responses to lipopolysaccaride administration.

overall_design: We administered THC (5 mg/kg, i.p.) once daily from postnatal day 30-44 and examined the brain transcriptome in adult animals (PND70) under basal or lipopolysaccharide (LPS, 0.33 mg/kg)-stimulated conditions.

first: Kwang-Mook

last: Jung

first: Hye-Lim

last: Lee

first: Erica

last: Squire


title: BAF60c Prevents Abdominal Aortic Aneurysms Formation through Maintaining Vascular Smooth Muscle Cell Homeostasis

city: Ann Arbor

first: Guizhen

last: Zhao

state: MI

address: 2800 Plymouth Rd

department: Cardiovascular Center

institute: University of Michigan


title: Unified rhombic lip origins of Group 3 and Group 4 medulloblastoma [atlas]

first: Kyle

last: Smith

first: Paul

last: Northcott


title: Wild-type and transgenic (TG) mice possessing G82R/L85P variant  mice by RNA sequencing

city: Guangzhou

first: Wenlong

last: Zhang

address: Yuexiu

institute: The First Affiliated Hospital of Guangzhou Medical University

summary: To explore effect of  variants (G82R and L85P ) in SLC1A2 (encoding GLT-1), we profiled hippocampal tissues from wild-type and transgenic (TG) mice possessing G82R/L85P variant  mice by RNA sequencing (RNA-seq).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and TG mice.

first: Qi

last: Qu

first: Shaogang

first: Yunlong


title: Impaired efferocytosis enables apoptotic osteoblasts to escape osteoimmune surveillance during aging (ChIP-seq)

city: Nanjing

first: Rongyao

last: Xu

address: 140 Hanzhong Road, Nanjing, Jiangsu Province 210029, China.

institute: Nanjing medical university

summary: Macrophages efferocytosis of apoptotic osteoblasts (apoOBs) is a key osteoimmune process for bone homeostasis that is highly regulated in osteoimmune surveillance. However, apoOBs accumulate in aged bone marrow, where they might mount proinflammatory responses and progressive bone loss. Why apoOBs were not cleared during aging remains unknown. Here, we show that apoOBs upregulate immune checkpoint molecule CD47 with age to evade macrophages clearance. Using osteoblast- and myeloid-specific gene knockout mice, we identify histone deacetylase SIRT6 as an essential regulator of the CD47–SIRPα checkpoint. Further, apoOBs that require SIRT6-mediated chemotaxis signals can recruit macrophages by releasing apoptotic extracellular vesicles. Therapeutically, we develop two targeting delivery strategies to enhance SIRT6 activity, showing increased apoOBs clearance and delayed age-related bone loss. Collectively, our data revealed a previously unknown linkage between immune surveillance and bone homeostasis and targeting the mechanism of SIRT6-regulated apoOBs clearance could be a promising therapeutic strategy for age-related bone diseases.

overall_design: Comparative gene expression profiling analysis of ChIP-seq data using Pol II  in the absence or presence of OSS_128167 treated osteoblasts


title: Unified rhombic lip origins of Group 3 and Group 4 medulloblastoma [methylation]

summary: Genome wide DNA methylation profiling of normal fetal Rhomic Lip and External Granule Layer.

overall_design: Bisulphite converted DNA from the 14 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip

first: Kye


title: Single-cell transcriptome analysis of the in-vivo response to viral infection in the cave nectar bat Eonycteris spelaea [scRNA-seq]

first: Wharton

last: Chan

summary: CD44+ sorted lung samples from 7 bats in two 10X 3’ v3 libraries and separately gated cells

overall_design: three bats at the baseline (0 dpi) and four bats post infection (4 dpi)

first: Akshamal

last: Gamage

first: Feng

last: Zhu

first: Linfa

last: Wang


title: Unified rhombic lip origins of Group 3 and Group 4 medulloblastoma [ATAC-seq]

summary: Genome wide ATAC-seq profiling of medulloblastoma subgroups.

overall_design: ATAC sequencing from medulloblastoma samples


title: Unified rhombic lip origins of Group 3 and Group 4 medulloblastoma

overall_design: Multi-omics from medulloblastoma samples


title: Single-cell transcriptome analysis of the in-vivo response to viral infection in the cave nectar bat Eonycteris spelaea [Bulk RNA-seq]


title: HOXB13 lysine 13 acetylation regulated transcriptional targets in castration-resistant prostate cancer

city: St. Louis

first: Kiran

last: Mahajan

state: Missouri

address: CB 8242 600 South Euclid Ave

department: Surgery

institute: Washington University

summary: To understand the mechanistic role of HOXB13 lysine acetylation in CRPC development andd progression, differential gene expression analysis  was performed following RNA-sequencing  of the HOXB13K13A mutant versus the isogenic parental C4-2B to identify bonafide transcriptional targets of acetylated HOXB13.  Chromatin remodeling and self-renewal genes were significantly impacted as a result of HOXB13-K13 mutation. These results suggested that single-site acetylation in HOXB13 is critical and may even be sufficient to promote cellular reprogramming associated with PC pathogenesis.

overall_design: Total RNA was isolated from C4-2B parental and HOXB13K13A mutant clones  and subjected to RNA -sequencing.


title: Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina [CUT&RUN]

first: Matthew

last: Brooks

summary: The basic motif-leucine zipper (bZIP) transcription factor NRL determines rod photoreceptor cell fate during retinal development, and its loss leads to cone-only retina in mice. NRL works synergistically with homeodomain protein Cone-Rod Homeobox and other regulatory factors to control the transcription of most genes associated with rod morphogenesis and functional maturation, which span over a period of several weeks in the mammalian retina. We predicted that NRL gradually establishes rod cell identity and function by temporal and dynamic regulation of stage-specific transcriptional targets. Therefore, we mapped the genomic occupancy of NRL at four stages of mouse photoreceptor differentiation by CUT&RUN analysis. Dynamics of NRL binding revealed concordance with the corresponding changes in transcriptome of the developing rods. Notably, we identified c-Jun proto-oncogene as one of the targets of NRL, which could bind to specific cis-elements in the c-Jun promoter and modulate its activity in HEK293 cells. Coimmunoprecipitation studies showed the association of NRL with c-Jun, also a bZIP protein, in transfected cells as well as in developing mouse retina. Additionally, shRNA-mediated knockdown of c-Jun in the mouse retina in vivo resulted in altered expression of almost 1000 genes, with reduced expression of phototransduction genes and many direct targets of NRL in rod photoreceptors. We propose that c-Jun-NRL heterodimers prime the NRL-directed transcriptional program in neonatal rod photoreceptors before high NRL expression suppresses c-Jun at later stages. Our study highlights a broader cooperation among cell-type restricted and widely expressed bZIP proteins, such as c-Jun, in specific spatiotemporal contexts during cellular differentiation.

overall_design: CUT&RUN protocol (Skene, Henikoff et al. 2018) was performed using anti-Nrl antibody on 250,000 retinal cells per experiment at postnatal day P2, P4, P10, and P28. Experiments were performed in quadruplicate and were paried-end sequenced on an Illumina HiSeq 2500.

first: Xulong

last: Liang

first: Anand

last: Swaroop


title: Acute alcohol produces epigenomic and transcriptomic changes in the amygdala to elicit anxiolysis

city: Chicago

first: Subhash

middle: C

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

overall_design: Refer to individual Series


title: Hypoxia-inducible factor 2α attenuates renal ischemia-reperfusion injury by suppressing CD36-mediated lipid accumulation in dendritic cells

city: Shanghai

first: Junwen

address: No.639 Zhizaoju Road

institute: 9th people's hospital

summary: Hypoxia is a hallmark of renal ischemia reperfusion injury (IRI) and serves as an essential regulator of innate immune responses during this process, although the mechanisms of this regulation remain unclear. Here, we show that dendritic cell (DC)-specific genetic ablation of hypoxia-inducible factor (HIF) 2α, a transcription factor induced by oxygen shortage, leads to hyperactivation of natural killer T cells (NKTs), ultimately exacerbating renal IRI in mice. HIF-2α deficiency in DCs triggers IFN-γ and IL-4 production in NKTs, along with upregulation of type I interferon (IFN) and chemokine responses critical for NKT activation. Mechanistically, loss of HIF-2α in DCs promotes their expression of CD36, a scavenger receptor for lipid uptake, resulting in increased lipid accumulation. Furthermore, HIF-2α binds directly to a reverse hypoxia-responsive element (rHRE) in the CD36 promoter, supporting its transcriptional regulation of CD36. Importantly, CD36 blockade by sulfo-N-succinimidyl oleate (SSO), reduces NKT activation and abolishes the exacerbation of renal IRI in mice with DC-specific HIF-2α knockout. Taken together, our study reveals a previously unrecognized role of a HIF-2α-CD36 regulatory axis in rewiring DC lipid metabolism under IRI-associated hypoxia, and suggests a potential therapeutic target to resolve long-standing obstacles in clinical treatment of this severe complication.

overall_design: To investigate how HIF-2α affected glycolipid priming by DCs at a molecular level, we used RNA sequencing to examine transcriptomic differences between BMDCs isolated from Hif2αfl/fl (WT) and CD11c-Cre;Hif2αfl/fl (KO) mice, which were cultured for 4 hours with α-GalCer following 24 hour-dimethyloxalylglycine (DMOG, a HIF-2α stabilizer) incubation.


title: Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina [RNA-seq]

overall_design: shRNA-mediated knockdown of mouse Jun was performed using electroporation with shRNA-expressing vector or control pLKO.1-Scrambled vector co-transfected with Nrlp-EGFP vector in neonatal mice at P0. EGFP positive rod photoreceptors electroporated with control or Jun shRNA constructs were purified by flow-sorting at P10. Experiments were performed in triplicate.


title: Quantitative Analysis of transcriptome in Gad2+ neurons isolated from Wild Type and GTF2ird1-/-

city: Memphis

first: Stanislav

last: Zakharenko

institute: St. Jude Children's Research Hospital

summary:
The goals of this study are to compare transcriptome of Gad2 + inhibitory neurons, isolated from cerebral cortex of wild type and GTF2ird1-/- mice
Wild type or GTF2ird1-/- were crossed with Gad2-Cre/Ai14, and total RNA was isolated from flow cytometry-sorted TdTomato positive cells

overall_design: mRNA profiles of adult wild type (W) and GTF2ird1-/- (K) mice

first: Seung

last: Han

first: Shibiao

last: Wan

first: Ti-Cheng

last: Chang

first: Yiping

last: Fan


title: Periostin may act on monocytes and monocyte-derived macrophages with a pro-fibrotic phenotype in patients with systemic sclerosis (SSc)

city: Yokohama-shi

first: Yukie

last: Yamaguchi

state: Kanagawa-Ken

address: 3-9 Fukuura Kanazawa-ku

institute: Yokohama City University Graduate School of Medicine

summary:
Background: Circulating periostin levels are increased in systemic sclerosis (SSc) patients and correlates positively with disease severity. Additionally, monocytes/macrophages are one of the key cells in SSc pathogenesis. However, the effect of periostin on immune cells, particularly monocytes and macrophages, has not been well investigated.
Objectives: To examine the effect of periostin on monocytes and monocyte-derived macrophages (MDMs) in SSc.
Methods: Monocytes were purified from blood samples of nine diffuse cutaneous SSc patients and five healthy controls (HCs) and were differentiated into macrophages. Cell surface markers were assessed by flow cytometry. RNA sequencing analysis was performed on recombinant periostin-stimulated monocytes from three HCs. Cytokine/chemokine and extracellular matrix (ECM) protein expressions in MDMs differentiated supplemented with recombinant periostin were assessed by quantitative real-time polymerase chain reaction and bead-based immunoassays in six HCs. Moreover, we evaluated whether periostin was involved in monocyte migration by Transwell assay.
Results: The modified Rodnan total skin thickness score correlated positively with the proportion of CD80-CD206+ M2 cells. The M2 macrophage proportion was reduced in rPn-stimulated MDMs in HCs, but not in SSc patients. mRNA expression levels of pro-fibrotic cytokine, chemokine, and ECM protein genes were significantly upregulated in recombinant periostin-stimulated monocytes and MDMs as compared to those from control monocytes and MDMs. Similar trends for their protein levels were also observed in MDMs. Moreover, the ratio of migrated cells in recombinant periostin-stimulated monocytes was significantly higher than that in control monocytes.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of recombinant periostin-stimulated monocytes from three healthy controls.

first: Mao

last: Suzuki

first: Yasushi

last: Ototake

first: Miho

last: Asami

first: Noriko

last: Ikeda

first: Tomoya

last: Watanabe

first: Miwa

last: Kanaoka


title: Acute alcohol produces transcriptomic changes in the amygdala

summary: RNA-sequencing of adult rat amygdala tissue following acute ethanol treatment, compared to saline-treated controls.

overall_design: RNA-seq (n=3 each for Acute Ethanol and Control)

first: Harish

last: Krishnan

first: Huaibo

last: Zhang

first: Ying

last: Chen

first: Jenny

last: Drnevich

first: Dennis

last: Grayson


title: Analysis of N1-methyladenosine methylome (m1A) enrichment level in ocular melanoma.

first: Xiang

last: Gu

address: Zhizaoju Road

institute: shanghai ninth people hospital

summary: To investigate the function of N1-methyladenosine methylome (m1A) in ocular melanoma, we analyzed m1A enrichment level in ocular melanoma and melanocyte cell lines and established ALKBH3 knock down cell lines in 92.1.

overall_design: meRIP-seq

first: X

first: P

last: Chai


title: Targeted Escalation of Acetylated HOXB13 Regulated Super-Enhancers Promotes Prostate Tumor Autonomy

first: Kiran

last: Mahajan

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


title: Integrating transcriptome, proteome, and phosphoproteome analysis reveals loss function of IQGAP2 promotes cell proliferation through the mTOR pathway

first: Guibin

last: Li

address: No. 10 Luoxuan 3rd Road, Guangzhou International Biotech Island

institute: KingMed Diagnostics

summary: Tuberous sclerosis complex (TSC) is a rare genetic disease caused by abnormal of TSC1 or TSC2 gene. Our previous data deduced that IQGAP2 can be one of the genes potentially responsible for non-TSC1 or TSC2 mutation TSC patients. To investigate the pathogenesis of IQGAP2 in TSC, we performed global transcriptome, proteome, and phosphoproteome analyses and found the alter of genes related to mTOR signaling pathway in IQGAP2 knockdown cells. In addition, we found that knockdown of IQGAP2 resulted in increased cell proliferation and enhanced the phosphorylation level of AKT and S6K by functional analysis, meanwhile, the AKT and mTOR inhibitors can partially rescue cell abnormal proliferation by decreasing hyperphosphorylation. Our data revealed a potential connection between mTOR signaling pathway and aberrant cell proliferation in IQGAP2 knockdown cells, and provide a new latent therapeutic strategy for non-TSC1 or TSC2 mutation patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HaCaT cells and its KD derivatives (shIQGAP2).

first: Yuhuan

last: Meng

first: Tao


title: A resource for integrated genomic analysis of the human liver

city: Chapel Hill

first: Federico

last: Innocenti

state: North Carolina

address: 120 Mason Farm  Road, CB7361

department: Eshelman School of Pharmacy

institute: University of North Carolina at Chapel Hill

summary: In this study, we generated whole-transcriptome RNA-Seq from n=192 genotyped liver samples and used these data with existing data from the GTEx Project (RNA-Seq; PMID: 32913098) and previous liver eQTL (microarray; GSE32504, GSE25935, GSE9588, and GSE24293) studies to create an enhanced transcriptomic sequence resource in the human liver. Analyses of genotype-expression associations show pronounced enrichment of associations with genes of drug response.  The associations are primarily consistent across the two RNA-Seq datasets, with some modest variation, indicating the importance of obtaining multiple datasets to produce a robust resource. We further used an empirical Bayesian model to compare eQTL patterns in liver and an additional 20 GTEx tissues, finding that MHC genes, and especially class II genes, are enriched for liver-specific eQTL patterns. To illustrate the utility of the resource to augment GWAS analysis with small sample sizes, we developed a novel meta-analysis technique to combine several liver eQTL data sources. We also illustrate its application using a transcriptome-enhanced re-analysis of a study of neutropenia in pancreatic cancer patients. The associations of genotype with liver expression, including splice variation and its genetic associations, are made available in a searchable genome browser.

overall_design: RNA-seq of 192 human liver tissue samples

first: Yi-Hui

last: Zhou

first: Paul

last: Gallins

first: Amy

middle: S

last: Etheridge

first: Dereje

last: Jima

first: Elizabeth

last: Scholl

first: Fred

last: Wright


title: Impaired efferocytosis enables apoptotic osteoblasts to escape osteoimmune surveillance during aging (mRNA)

first: Rongyao

last: Xu

overall_design: Comparative gene expression profiling analysis of RNA-seq data for apoptotic osteoblasts (apoOBs)  from young and old mice


title: Genes regulated by Hfq

city: Miami

first: Chaitanya

last: Jain

state: FL

address: 1011 NW 15th St

department: Biochemistry and Molecular Biology

institute: University Of Miami

summary: The effect of Hfq inactivation on RNA abundance was measured

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: To identify RNAs regulated by Hfq, we created a Hfq-deletion mutant strain and isolated RNA from wild-type and the mutant strains. The abundance of different RNAs in the wild-type and mutant strains was determined using RNA-Seq.

first: Sandeep

last: Ojha


title: Transcriptome of EpoR-/- CFU-E cells

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: During erythropoiesis, erythroid progenitor cells proliferate in response to erythropoietin (Epo) and progressively differentiate, which encompasses an increasing accumulation of iron-bound hemoglobin. The impact of Epo on these dynamic processes remained to be resolved. By combining the development of a time-collapsed super SILAC method with transcriptome analysis we examined Epo-induced alterations in the proteome of erythroid progenitor cells at the colony-forming unit erythroid stage (CFU E). We showed that the timing of a major increase in the transcription factors GATA1 and TAL1 precedes the cessation of cell cycle progression but coincides with a massive upregulation of enzymes of the heme biosynthetic pathway. A failure of this upregulation due to the absence of the Epo receptor resulted in massive iron accumulation in the fetal liver and dilation of the maternal vasculature in the placenta. Thus, Epo-induced dynamic proteome adaptations in CFU E cells not only prevent anemia but also severe iron-intoxication in embryos.

overall_design: Heterozygous erythropoietin receptor null (EpoR+/-) BALB/c mice were obtained from Harvey F. Lodish (Whitehead institute for Biomedical Research Cambridge, Massachusetts). To obtain EpoR-/- embryos EpoR+/- mice were breed and the embryos were genotyped by using gene-specific primers (5'-GCACTGAGTGTGTTCTG-3', 5'-GCCTCA CACTCT TCACC-3' and 5'-GCTGCTAAAGCGCATGC-3'). Fetal livers from EpoR-/- BALB/c mice embryos at 13.5 gestational day were dissected from the uteri of the sacrificed mice. Fetal liver cells were re-suspended in 500 μl 0.3% BSA/PBS, passed through 40 μm cell strainers (BD Biosciences) and subsequently treated with 10 ml Red Blood Cell Lysis Buffer (Sigma-Aldrich) to remove erythrocytes. To isolate CFU E cells, a negative selection was performed, in which the fetal liver cells of 40 - 50 livers were incubated for 30 min at 4°C with 10 μl rat antibodies against the following murine surface markers: GR1, CD41, CD11b, CD14, CD45, CD45R/B220, CD4, CD8 (all BD Biosciences), TER-119 (from A. Müller, Würzburg, Germany) and with the rat monoclonal antibody YBM/42 (from S. M. Watt, Oxford, UK). Cells were washed three times in 0.3% BSA/PBS and incubated for 30 min at 4°C with anti-rat antibody-coupled magnetic beads (BD Biosciences). MACS columns (Miltenyi Biotech) were applied for sorting according to the manufacturer’s instructions. Sorted immediately used for microarray analysis.

first: Sajib

last: Chakraborty

first: Hauke

last: Busch

first: Melanie

last: Boerries

first: Ursula

last: Klingmüller

first: Marcel

last: Schilling

first: Lorenz

last: Adlung


title: Analysis of differential genes in the intestinal epithelial cell from M. tuberculosis-treated mice

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

institute: Catholic University of Korea

summary:
The pathogenic organism Mycobacterium tuberculosis could act as a strong nonspecific immunopotentiator, generating beneficial effects on some disease pathogeneses.
We used DNA microarrays to analyze gene expression profiles in the intestinal epithelial cells from M. tuberculosis-treated mice and identified distinct classes of 124 upregulated genes and 107 downregulated genes.

overall_design: A pooled sample was prepared for each group by mixing equal quantities of total RNA from individuals (n=5) in each group in order to have the same amount of biological diversity within each pooled RNA sample.

first: Yu-Mi

last: Kim

first: Wan-Uk

first: Donghyun


title: Acute alcohol produces epigenomic changes in the amygdala

first: Subhash

last: Pandey

summary: ATAC-sequencing of adult rat amygdala tissue following acute ethanol treatment, compared to saline-treated controls.

overall_design: ATAC-seq (n=6 each for Acute Ethanol and Control)

first: Harish

middle: R

last: Krishnan

first: Huaibo

last: Zhang

first: Ying

last: Chen

first: Jenny

last: Drnevich

first: Dennis

last: Grayson