title: RNA sequencing facilitates quantitative analysis of U118-NC and U118-SPNS2 transcriptomes

city: Guangzhou

first: Waiyip

last: Leung

state: Guangdong

address: Guangzhou Higher Education Mega Centre, Panyu District

institute: South China University of Technology

summary: To investigate the function of SPNS2 in GSCs progression, we established U118-SPNS2 cell lines with SPNS2 overexpressed. Then we performed gene expression profiling analysis using data obtained from RNA-seq of 2 cells (U118NC and U118-SPNS2)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  U118-NC and U118-SPNS2.

first: Weiye

last: Liang

first: Mingkai

first: Jian

last: Wang


title: The expression changes of small RNA during BMSCs proliferation

status: Public on Jun 01 2024

city: Shanghai

first: Chuandong

address: 320 Yueyang Road

country: China

institute: SJTU

type: Expression profiling by high throughput sequencing

summary: The proliferation, migration, and osteogenic differentiation of bone mesenchymal stem cells (BMSCs) play vital roles in maintaining bone mass and metabolism. BMSC base cell therapy has become a competitive treatment option for osteoporosis.Small  are critical regulators of cellular processes. Small RNA sequencing was used to detect piRNA expression during BMSC proliferation.

overall_design: The serum-free test (ST) group cells were cultured in a serum-free medium for 24 h, and the general medium (GM) group cells were cultured in a medium containing 10% fetal bovine serum for 24 h.  sequencing.

first: Chenglong


title: WT or Usp5 knockout (KO) PMs were infected with HSV-1 or not

city: Suzhou

first: Dapei

last: Li

address: NO100 Chongwen road

institute: Suzhou Institute of Systems Medicine,Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Transcriptome profiling analysis to study deubiquitinase gene expression levels in HSV-1 infected WT or Usp5 KO PMs

overall_design: Gene expression profiling analysis of RNA-seq data for HSV-1 infected WT or Usp5 KO PMs


title: PMs were infected with HSV-1 or not

summary: Transcriptome profiling analysis to study deubiquitinase gene expression levels in mock and HSV-1 infected PMs

overall_design: Gene expression profiling analysis of RNA-seq data for mock and HSV-1 infected PMs


title: The pluripotency state of human embryonic stem cells derived from single blastomeres of eight-cell embryos

city: Bellaterra

first: Ot

last: Massafret

state: Barcelona

address: carrer de la Vall Moronta, s/n

department: Departament de Biologia Cel·lular, Fisiologia i Immunologia

country: Spain

institute: Universitat Autònoma de Barcelona

overall_design: Three experimental groups were analysed: Blastomere-derived human embryonic stem cells (hESCs), blastocyst-derived hESCs and naïve hESCs, with 4, 4 and 1 biological replicate respectively. Blastocyst-derived hESCs are our primed control, and naïve hESCs are our naïve control

first: Montserrat

last: Barragán

first: Lucía

last: Álvarez-González

first: Begoña

last: Aran

first: Beatriz

last: Martín-Mur

first: Anna

last: Esteve-Codina

first: Aurora

last: Ruiz-Herrera

first: Rita

last: Vassena

first: Elena

last: Ibañez

first: Josep

last: Santaló


title: Effect of Palbociclib on gene expression of two gastric cancer cell lines(including AGS and SNU1)

first: Chunchao

last: Zhu

state: shanghai

address: Pujian road 160, shanghai

institute: Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

summary: Palbociclib, a kind of CDK4/6 inhibitor, was proved to be able to induce senescence in several cancer cell lines. After treated with Palbociclib, two GC cell lines (including AGS and SNU1) exhibited senescence-associated features, such as enlarged cell size, formation of heterochromatin foci in the nucleus, and increased activity of SA-β-Gal.Many senescence-related genes, such as CDKN1A, CDKN2A and TP53, were evaluated in the Palbociclib-treated GC cells, while proliferation-related genes, such as TOP2A and MKI67, were decreased. Moreover, GSEA demonstrated the senescence-related pathways, such as p53 and the nuclear factor-kappaB (NF-κB) pathways, were most significantly enriched in Palbociclib-treated group . In contrast, several cell cycle-related pathways were enriched in the control group. Together, these results indicated that Palbociclib could effectively induce senescence in GC cells and the senescent GC cells harbored higher GSSS.

overall_design: To investigate the effect of Palbociclib on gene expression of two gastric cancer (GC) cell lines(including AGS and SNU1),we treated AGS  and SNU1 for five days with Palbociclib. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 GC cells lines.Comparative gene expression profiling analysis of RNA-seq data for treated and untreated cells.


title: MicroRNA Expression Profiles in Follicular Fluid Exosomes of Women with Different Ovarian Reserve

city: Beijing

first: Qihui

last: Feng

address: Xizhimen South street

institute: Peking University People's Hospiotal

type: Non-coding RNA profiling by high throughput sequencing

summary: Limited research has explored the associations between microRNAs (miRNA) and diminished ovarian reserve (DOR). The study aimed to identify differentially expressed miRNAs in follicular fluid exosomes from women with DOR compared to normal ovarian reserve (NOR) and investigate their role in the proliferation and apoptosis of the human ovarian granulosa tumor cell line KGN.

overall_design: Follicular fluid exosomal miRNAs from women with DOR and NOR. All the participants were recruited from patients seeking fertility treatment at the Reproductive Medical Center of Peking University People’s Hospital between June 2020 and December 2020.

first: Yanbin

first: Huan

last: Shen


title: A enzymatic program that assembles amyloids

city: Miami

first: Stephen

last: Lee

state: FL

department: Biochemistry & Molecular Biology

country: USA

institute: University of Miami

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

overall_design: Refer to individual Series


title: Aberrant induction of the rare RNA binding protein PABPC4 in MYC-driven hepatocellular carcinoma [RNA-seq]

city: Jinan

first: Jinyuan

last: Liang

address: wenhua road

institute: Shandong university

summary: PABPC4 is a member of the poly(A)-binding protein (PABP) family, responsible for regulating post-transcriptional gene expression. While PABPC1 is widely expressed and has a general function in translation initiation and mRNA stability, PABPC4 shows lower expression levels and a more tissue-specific pattern. It plays a role in specific biological processes such as erythroid differentiation and oogenesis. The precise regulation and specific role of PABPC4 in hepatocellular carcinoma (HCC) have remained unclear despite previous studies highlighting its involvement in HCC cell lines. To uncover potential downstream targets of PABPC4 in HCC cells, we conducted RNA-seq and RIP-seq analyses to identify mRNAs that were both downregulated in PABPC4-deficient cells and bound by PABPC4.

overall_design: Two HepG2 PABPC4-KO clones, which lacked PABPC4 protein expression, were subjected to RNA-seq analysis, with HepG2 sgRen serving as the control.

first: Peng

last: Zhang

first: Shiyang

first: Detian

last: Yuan


title: Aberrant induction of the rare RNA binding protein PABPC4 in MYC-driven hepatocellular carcinoma [RIP-seq]

overall_design: RIP-seq for PABPC4 and PABPC1 in HepG2 cells.

first: Xiwei

last: Wang

first: Zhibiao

last: Mai

first: Xichen

last: Bao


title: Intravenous NeuroD1 Gene Therapy Rescues Neurovascular Impairment After Ischemic Stroke

first: He

last: Xiaosong

address: Xinzao Road

department: Department Of Anatomy

institute: Guangzhou Medical University

summary: To further  understand the impact of NeuroD1 on the endothelial cell gene expression profiles

overall_design: Comparative gene expression profiling analysis of RNA-seq data for isolated endothelial cells from GFP and NeuroD1 treated tie2-cre mice

first: Xiaosong

last: He


title: Aberrant induction of the rare RNA binding protein PABPC4 in MYC-driven hepatocellular carcinoma


title: Effect of GelMA and microfiber on gene expression in vivo

city: shanghai

first: Hai

last: Tang

address: zhengmin road

institute: Shanghai Pulmonary Hospital affiliated to Tongji University

summary: To investigate GelMA and microfiber on gene expression in vivo, We implanted GelMA and microfiber subcutaneously in rats.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq at two time points.


title: A bi-steric mTORC1-selective inhibitor overcomes drug resistance in breast cancer

city: San Francisco

first: Sourav

last: Bandyopadhyay

state: CA

address: 1450 3rd Street

department: Department of Bioengineering and Therapeutic Sciences

institute: University of California San Francisco

summary: Activation of the PI3K-mTOR pathway is central to breast cancer pathogenesis including resistance to many targeted therapies. The mTOR kinase forms two distinct complexes, mTORC1 and mTORC2, and understanding which is required for the survival of malignant cells has been limited by tools to selectively and completely impair either subcomplex. To address this, we used RMC-6272, a bi-steric molecule with a rapamycin-like moiety linked to an mTOR active-site inhibitor that displays >25-fold selectivity for mTORC1 over mTORC2 substrates. Complete suppression of mTORC1 by RMC-6272 causes apoptosis in ER+/HER2- breast cancer cell lines, particularly in those that harbor mutations in PIK3CA or PTEN, due to inhibition of the rapamycin resistant, mTORC1 substrate 4EBP1 and reduction of the pro-survival protein MCL1. RMC-6272 reduced translation of ribosomal mRNAs, MYC target genes, and components of the CDK4/6 pathway, suggesting enhanced impairment of oncogenic pathways compared to the partial mTORC1 inhibitor everolimus. RMC-6272 maintained efficacy in hormone therapy-resistant acquired cell lines and patient derived xenografts (PDX), showed increased efficacy in CDK4/6 inhibitor treated acquired resistant cell lines versus their parental counterparts, and was efficacious in a PDX from a patient experiencing resistance to CDK4/6 inhibition. Bi-steric mTORC1-selective inhibition may be effective in overcoming multiple forms of therapy-resistance in ER+ breast cancers.

overall_design: In this study, we investigated the effect and mechanism of RMC-6272, a potente and selective mTORC1 inhibitor, in breast cancer. Given that mTORC1 is a critical regulator of protein translation, to understand the global impact of complete and selective inhibition of mTORC1, we performed ribosomal profiling experiments in the breast cancer MCF-7 cells, comparing mRNA translation after RMC-6272 treatment with treatment of the DMSO vehicle or everolimus (rapamycin), a widely used mTORC1 inhibitor.

first: Delong

last: Meng

first: Xin

last: Zhao

first: Albertas

last: Navickas

first: Hani

last: Goodarzi


title: Kidney gene expression dynamics during torpor-arousal cycles in hibernating 13-lined ground squirrels

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: RNA-seq libraries were prepared from replicate samples (n=5-6) from six physiolocial groups to capture key changes in circannual hibernation.

overall_design: RNA-seq libraries were prepared from replicate samples (n=5-6) in the kidney from six physiological groups to capture key changes in circannual hibernation.

first: Sandra

middle: L

last: Martin


title: Clusterin is protective for liver fibrosis through mesothelial-specific LRP2 receptor mediated endocytosis

first: Minjun

address: xiangyin road

department: Cell biology

institute: Naval Medical University

summary: During liver fibosis, the CLU protein was overexpressed of hepatocytes. Loss of function perform showed that CLU is protective for liver fibrosis. Mechanismly, we found LRP2 postive cells were increased after hrCLU administration in fibrotic CLUKO mice. Then single cell analysis domenstrated that LRP2 positive cells were mesothelial cells, which play a critical role of endocytosis during fibrosis resolution. Taken together, we identify clusterin as a protective chaperone that can reverse liver fibrosis and clear extracellular matrix, which targets LRP2 signaling mediated endocytosis.

overall_design: The liver cells of three CLUKO mice administrated human recombinant clusterin during CCL4 injection and WT mice treated with CCL4 injection for 0, 2, 4 weeks were pooled and loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron)


title: RNA-Seq of gut of colorectal cancer mice fed black rice and control diets

city: WuHan

first: Yi-Xuan

last: Tu

state: HuBei

address: 1 Shizishan Rd

department: College of Life Science and Technology

institute: Huazhong agricultural university

summary: In order to explore the effect of black rice diet on the development of colorectal cancer in mice, we combined two types of colon cancer mouse models for intestinal transcriptome sequencing to explore the changes in host intestinal gene expression.

overall_design: We performed transcriptome sequencing by dissecting the intestinal tracts of colorectal cancer mice fed with black rice and control diet.

first: Zhen-Xia

last: Chen

first: Ling

first: Lu


title: ChIP-seq analysis of the TGF-b1-treated intestinal organoids with or without Smad4 loss

first: Ye-Guang

state: China

address: Haidian  District

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
The ChIP-seq analysis vilidated that Yap1/Smad2/3 signaling could regulate the transcriptional activity of key inflammasome genes upon TGF-b stimulation. In addition, TGF-b1 could be the downstream target gene of Yap.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Yap1, Smad2/3 as well as the Tead1 in indicated intestinal organoids.

first: Liansheng

last: Liu

first: Shan

last: Hua

first: Shicheng

last: Yu


first: He

summary: To further understand the impact of NeuroD1 on the global gene expression profile after MCAO

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cortex tissues from GFP and NeuroD1 treated MCAO mice

first: Xiaosong


title: The difference between neutrophils of HC, COVID-19 patients admitted in ICU and wards.

city: Edmonton

first: Shima

last: Shahbaz

state: Alberta

address: 7-096 Katz Group Center for Pharmacy and Health Research

country: Canada

institute: University of Alberta

summary:
We isolated neutrophils from 11 healthy controls, 12 COIVD-19 patients in ICU and 12 COVID-19 patients from ward and submitted the isolated RNA for RNA sequencing.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cohorts. .

overall_design: Comparative gene expression profiling analysis of RNA-seq data for neutrophils of HCs vs COVID-19 patients admitted in ICU and COVID-19 patients admitted in wards

first: Shokrollah

last: Elahi

first: Hussain

last: Syed

first: Eliana

last: Perez Rosero


title: Single-cell RNA sequencing of Drosophila wing discs harboring the scrib mutant clones in combination with RasV12, YkiS168A or NAct signals.

city: Hong Kong

first: Yan

last: Yan

address: Clear Water Bay

department: LIFS

institute: HKUST

summary: It has long been proposed that cell competition functions to remove precancerous clones. A classical model is the removal of polarity-deficient clones such as the scribble (scrib) mutant clones in Drosophila imaginal discs. The activation of Ras, Yki or Notch signaling robustly reverses the scrib mutant clonal fate from elimination to tumorous growth. Using single-cell transcriptomics techniques to profile wing imaginal discs harboring the scrib mutant clones in combination with different signals, we found that a critical converging point downstream of Ras, Yki and Notch signals is the upregulation of Upd2, which is necessary to promote tumorous growth. Unexpectedly, while Upd2 is not required for cell survival per se, Upd2-deficient clones are efficiently wiped out from epithelia, indicating that Upd2 is a previously unrecognized cell competition factor.

overall_design: We generate the scrib mutant clones with activated Ras, Yki or Notch signals using MARCM system in Drosophila wing imaginal discs. The control MARCM GFP+ clones occupy around 30% of the whole disc area at 36 hours after clone induction (ACI) and around 40% of the disc area at 60 hours ACI. In contrast, the scrib mutant clones occupy around 20% of the whole disc area at 36 hours ACI and 10% of the whole disc area at the 60 hours ACI. When RasV12, YkiS168A or NAct is co-expressed in the scrib mutant clones, the GFP+ clones occupy around 30% of the whole disc area at 36 hours ACI. By 60 hours ACI, the scrib mutant clones co-expressing RasV12, YkiS168A or NAct start to exhibit tumor-like morphology and occupy around 30%-40% of the whole disc area. The clone size and morphology are comparable across all five experimental groups at 36 hours ACI, and cell competition process is an on-going process at this early stage. Thus, we choose to generate single-cell RNA transcriptomics datasets of wing discs carrying GFP+ clones of these genotypes: control, scrib-/-, scrib-/- RasV12, scrib-/- YkiS168A and scrib-/- NAct at 36 hours ACI. To generate MARCM clones for each genotype, around 50 embryos were collected within 3 hours and raised until 60 hours after egg laying (AEL). The larvae were then placed in water bath for 1 hour at 37°C for heat shock and dissected at 36 hours to perform single cell experiment.

first: Wang

last: Ying

first: Deng

last: Mingxi

last: Jingjing


title: BCAS2 is involved in insulin synthesis and secretion by mRNA alternative splicing

city: BEIJING

address: Malianwa street

institute: China Agriculture University

summary:
Insulin secreted by pancreatic β cells is essential for maintaining the level of blood glucose. Diabetes is mainly caused by the loss of β cells or impaired β cell function. The previous study performed a whole transcriptome analysis on the islets of T2D and the control group, and the results showed that the splicing disorder of the splicing event was about 25%, breast carcinoma amplified sequence 2(BCAS2) is one of the components of the spliceosome, and its function in islet β cell is unclear. Here we report that knockdown of Bcas2 decreases in glucose and KCl-stimulated insulin secretion in the NIT-1 cell line. The pancreas weight, glucose tolerance and insulin sensitivity were detected in normal chow-fed and high-fat diet-fed Bcas2 f/f-βKO mice, and β cell mass and islet size was analyzed by immunohistochemistry. Glucose intolerance developed in Bcas2 f/f-βKO mice, but there were no significant differences in pancreas weight, insulin sensitivity, β cell mass and islet size. Further, GSIS and observation of insulin secretion granules were performed on normal chow-fed mice, and it was found that the insulin level in serum decreased and the number of insulin secretion granules decreased in Bcas2 f/f-βKO mice, which was related to the abnormal splicing of Syt7 and Tcf7l2 pre-mRNA. Taken together, these results demonstrate that BCAS2 is involved in alternative splicing during insulin synthesis and secretion.
Elisa,islet isolation,insulin secretion

overall_design: Knockdown of Bcas2 in β cells and control β cells.

first: Xuexue

first: Xiaomei

last: Xie

first: Jiahua

last: Li

first: Longjie

last: Sun


title: TRH regulates the synthesis and secretion of prolactin in rats with adenohypophysis through the differential expression of miR-126a-5p

city: Changchun

first: wenzhi

last: ren

state: Jilin

address: Linyuan street

department: Department of Laboratory Animals

institute: College of Animal Sciences, Jilin University

summary: Prolactin (PRL) is an important hormone that is secreted by the pituitary gland and plays an important role in the growth, development and reproduction of organisms. Thyrotropin-releasing hormone (TRH) is a common prolactin-releasing factor that regulates the synthesis and secretion of prolactin. In recent studies, microRNAs (miRNAs) have been found to play a key role in the regulation of pituitary hormones. However, there is a lack of systematic studies on the regulatory role that TRH plays on the pituitary transcriptome, and the role of miRNAs in the regulation of PRL synthesis and secretion by TRH lacks experimental evidence. In this study, we first investigated the changes in PRL synthesis and secretion in the rat pituitary gland after TRH administration. The results of transcriptomic analysis after TRH treatment showed that 102 genes, including those that encode Nppc, Fgf1, PRL, Cd63, Npw, and Il23a, were upregulated, and 488 genes, including those that encode Lats1, Cacna2d1, Top2a, and Tfap2a, were downregulated. These genes are all involved in the regulation of prolactin expression. The gene expression of miR-126a-5p, which regulates the level of PRL in the pituitary gland, was screened by analysis prediction software and by a dual luciferase reporter system. The data presented in this study demonstrate that TRH can regulate prolactin synthesis and secretion through miR-126a-5p, thereby improving our understanding of the molecular mechanism of TRH-mediated PRL secretion and providing a theoretical basis for the role of miRNAs in regulating the secretion of pituitary hormones.

overall_design:
To investigate the changes in mRNA in rat adenohypophysis before and after TRH treatment, we performed RNA-Seq.
After treating GH3 cells with TRH, we collected the cells from the control (N1, N2, N3) and treated groups (T1, T2, T3) for RNA-Seq.

first: Guokun

last: Zhao

first: Yi

last: Zheng


title: Effect of Lycium barbarum polysaccharide-glycoprotein(LBP) on irradiated HaCaT cells

city: Chendu

first: Si

middle: jing

last: Jiang

state: Sichuan

address: 32# W. Sec 2, 1st Ring Rd

department: Stomatology department

institute: Sichuan Provincial People's Hospital

summary: To investigate the protective effect of Lycium barbarum polysaccharide-glycoprotein (LBP) in the radiation-induced HaCaT cell injury, We performed gene expression profiling analysis using data obtained from RNA-seq of HaCaT cells at 3h after radiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for irradiated HaCaT cells with or without LBP pretreatemt.

first: Si-jing

first: Yandong

last: Mu


title: CDK7 kinase activity promotes RNA polymerase II promoter escape by facilitating initiation factor release

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

country: Germany

institute: Max-Planck-Institute for Multidisciplinary Scienes

summary: Cyclin-dependent kinase 7 (CDK7), part of general transcription factor TFIIH, promotes gene transcription by phosphorylating the C-terminal domain of RNA polymerase II (Pol II). Here, we combine rapid CDK7 kinase inhibition with multi-omics analysis to unravel the direct functions of CDK7 in human cells. CDK7 inhibition causes Pol II retention at promoters, leading to decreased Pol II initiation and immediate global downregulation of transcript synthesis. Elongation, termination, and recruitment of co-transcriptional factors are not directly affected. Although Pol II, initiation factors, and Mediator accumulate at promoters, Pol II complexes can also proceed into gene bodies without promoter-proximal pausing while retaining initiation factors and Mediator. Further downstream, Pol II phosphorylation increases, initiation factors and Mediator are released, allowing recruitment of elongation factors and increase in Pol II elongation velocity. Collectively, CDK7 kinase activity promotes the release of initiation factors and Mediator from Pol II, facilitating Pol II escape from the promoter.

overall_design: All samples were collected in biological duplicates, except MNase-ChIP-seq, for which three replicates were collected. Cells were treated for 15, 30, or 60 min with 7.5 μM of 1-NM-PP1 or an equal volume of DMSO (solvent control).

first: Taras

last: Velychko

first: Eusra

last: Mohammad

first: Ivan

last: Ferrer-Vicens

last: Parfentev

first: Marcel

last: Werner

first: Cecilia

last: Studniarek

first: Björn

last: Schwalb

first: Henning

last: Urlaub

first: Shona

last: Murphy

first: Patrick

last: Cramer


title: Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells [SLIM-seq]

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: The goal of this study is to determine the critical requirement of N6-Methyladenosine (m6A) methyltransferase Mettl3 during CD8+ T cell responses upon acute viral infection. We demonstrate that conditional ablation of Mettl3 in CD8+ T cells impairs effector expansion and terminal differentiation in an m6A-dependent manner, which in turn affects memory formation and secondary response. Mechanism analysis indicates that Mettl3 deficiency broadly affects expression of cell cycle and transcriptional regulators. Based on these findings, our study reveals the important role of m6A modification in CD8+ T cell responses.

overall_design: Wild-type naïve (CD44-CD62L+) CD8+ T cells (3 samples per group), effector  (CD44+CD62L-) CD8+ T cells (3 samples per group) and memory  (CD44+CD62L+) CD8+ T cells (3 samples per group) were sorted


title: Enrichment of sgRNA in a genome-wide CRISPR-cas9 knockout screening assay in HSV-1 infected the human amnionic WISH cells models.

first: Yang

state: Beijing

address: No.5, Dongdan Three Street, Dongcheng District, Beijing

department: Department of Immunology, Institute of Basic Medical Sciences

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

summary: The Human CRISPR Knockout Pooled Library (GeCKO v2, 1000000048, Addgene) was transferred into WISH cells. Then,half of  these cells were infected with HSV-1 for 30 hours, and  the remaining lived infected cells and uninfected cells  were collected for sgRNA sequencing and enrichment analysis.

overall_design: Comparative sgRNAs profiling analysis of RNA-seq data for HSV-1 infeccted cells and uninfected cells

first: Jiang

last: Yang

first: Fengjiao

last: Lu

first: Xuetao

last: Cao


title: Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells

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

overall_design: Refer to individual Series


title: Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells [RNA-seq]

overall_design: Naïve (CD44−CD62L+) CD8+ T cells were sorted from Mettl3ΔCd4 and control mice (3 samples per group), effector (CD44+CD62L−EYFP+) CD8+ T cells  (2 samples per group), and memory (CD44+EYFP+) CD8+ T cells (2 samples from control donors and 3 samples from Mettl3ΔGzmb donors ) were sorted from recipient mice in adoptive transfer experiments


title: TGF-β promotes colitis and cancer development in Smad4-deficient intestinal epithelium in a Yap-dependent manner

first: Ye-Guang

last: Chen


title: TGF-β promotes colitis and cancer development in Smad4-deficient intestinal epithelium in a Yap-dependent manner (DSS)

summary: TO highlight an integral role of the TGF-β/Smad4 axis in restraining intestinal inflammation and suggest TGF-β or Yap signaling as potential therapeutic targets in inflammatory bowel disease patients with decreased Smad4 expression. We then performed gene expression profiling analysis using data obtained from RNA-seq of colonic epithelia cells derived from DSS treatment.

first: Liansheng

last: Liu

first: Shicheng


title: Genome-wide map of TRIM33 binding sites in primary dendritic cells

first: Xiangyi

last: Shen

address: D303 Zhengyutong Medical Building, Tsinghua University

department: The Institute for Immunology, School of Medicine

summary: The homeostatic control of dendritic cells (DCs) is critical for appropriate immune responses, yet the regulatory mechanisms are not fully elucidated. Genome-wide mapping of TRIM33 binding sites in primary DCs revealed a role of this molecule in DC transcription regulation, and therefore homeostasis.

overall_design: Chromatin immunoprecipitation-sequencing (ChIP-seq) was performed to determine genome-wide binding sites of TRIM33 in plasmacytoid dendritic cells (pDCs) as well as type 1 and 2 conventional dendritic cells (cDC1s, cDC2s). Primary DCs were sorted from wildtype C57BL/6 mice, and 2 biological repeats were prepared for each subset and subjected to ChIP assays with anti-TRIM33 antibody. Immunoprecipitated DNA was sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

first: Li

last: Wu


title: Analysis of lncRNA-mRNA co-expression profiles in CD133 positive cancer stem-like cells from osteosarcoma cell line Saos-2

city: beijing

first: Xiong

last: Shu

address: No.31, Xinjiekou East Street, Xicheng District, Beijing

institute: Beijing Research Institute of Traumatology and Orthopaedics, Beijing JiShuiTan Hospital

summary: Osteosarcoma (OS) is an essential threatening tumor of bone in young adults. OS stem cells (OSCs) act a significant role in the occurrence, metastasis, drug resistance and recurrence of OS. CD133 is an integral membrane glycoprotein, which has been identified as an OSCs marker. However, the mechanisms of metastasis, chemoresistance and progression in CD133(+) OSCs need to be further explored. We aim to detect the lncRNA and mRNA profiles in CD133(+) cells compared with CD133(-) cells from the Saos-2 cell line in the present study.

overall_design:
The expression of lncRNAs and mRNAs in CD133(+) cells compared with CD133(-) cells from the Saos-2 cell line was explored by high-throughput sequencing and differentially expressed (DE) lncRNAs and DEmRNAs were obtained.
Comparative The expression of lncRNAs and mRNAs in CD133(+) cells compared with CD133(-) cells from the Saos-2 cell line.

first: Chengai

first: Yuliang

last: Ran


title: The underlying mechanism by which NAT10 exerted carcinogenesis and its potential targets in MM

city: Nanjing

first: Yuanjiao

last: Zhang

address: Xianlin Road

institute: nanjing university of chinese medicine

summary: An acRIP experiment was performed in KMS28-PE WT and KMS28-PE NAT10-OE cells. We compared the peak summit of  KMS28-PE WT and KMS28-PE NAT10 OE cells to find the differences between KMS28-PE WT and KMS28-PE NAT10 OE cells.

overall_design: Examination  in K28MS-PE cells.

first: YuanJiao

first: Ye

first: Chunyang

last: Gu


title: Transcriptomic analysis of the effect of cytoplasmic Rat1 (cRat1)

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: The main decay pathway of yeast mRNAs in the cytoplasm uses the 5’-3’ exonuclease Xrn1. This protein shuttles from the cytoplasm to the nucleus, where it has a role as transcription factor. We have recently demonstrated that importing depends on two nuclear localization sequences (NLS 1 & NLS2) and that exporting depends on its binding (presumably co-transcriptional) to mRNAs. It is also known that Xrn1 is able to degrade decapped mRNAs that are still being translated by ribosomes. In this work, we analyze the pleiotropic functions of Xrn1 by comparing the phenotypes of yeast strains lacking Xrn1 or its capacity to be imported into the nucleus with those of the substitution of Xrn1 by a cytoplasmic version of the paralogous 5’-3’ exonuclease Rat1 (cRat1). We find that most of the global phenotypes of an xrn1 mutant are partially complemented by cRat1 indicating that this 5’-3’ exonuclease has a similar enzymatic capacity as Xrn1 and that the lack of a cytoplasmic 5’-3’-exoribonuclease is the cause of the physiological defects of an xrn1 mutant. The capacity of cRat1 to perform co-translational decay is, however, very limited. The comparison with the strain carrying Xrn1 with non-functional NLSs (Xrn1ΔNLS1/2) shows that it is slightly deficient in 5’→3’-co-translational decay but much more efficient than cRat1. In both strains, cRat1 and Xrn1ΔNLS1/2, the lack of nuclear Xrn1 has a very minor influence on cell growth experiment in wild type and xrn1 mutant strains.

overall_design: Cells were grown in YPD at 30 ºC to 0.4-0.5 OD600. Cells were spun-down and collected. Note that each sample record represents two (cDNA) or three (GRO) replicates.

first: José

last: Pérez-Ortín

last: García-Martínez

first: Jorge

last: Moreno-García


title: Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells [miCLIP]

first: Shuyang

overall_design: Control and Mettl3ΔGzmb effector (CD44+CD62L-EYFP+) CD8+ T cells  (2 samples per group)  were sorted


title: H2BFWT nucleosome structure reveals its nucleosome-destabilizing mechanisms through reductions of specific DNA-histone interactions and explains the mechanistic impact of its infertility-related H100R SNP during early spermatogenesis in humans

first: Toyotaka

last: Ishibashi

address: Rm6260, Academic Building, HKUST, Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: Spermatogenesis is the process by which spermatogonial stem cells differentiate into haploid spermatozoa. During this process, multiple testis-specific histone variants are involved in the dynamic chromatin transitions. H2BFWT is a testis-specific H2B variant only found in primates, and several reports showed that single-nucleotide polymorphisms (SNPs) of H2BFWT are associated with male non-obstructive infertility. Different from another testis-specific variant TH2B, H2BFWT is preferentially localized in sub-telomeric regions and the promoter regions of testicular high expression genes during the transition from differentiated spermatogonia to early spermatocytesspermatogenesis. Cryo-EM structural analysis shows that the H2BFWT nucleosome is defined by weakened interactions between H2A-H2BFWT dimer and H4, and between the histone octamer and DNA. WIn addition, we found that the shape of the H2A L1 loops was also changed by the presence of H2BFWT. Furthermore, our structural model shows that H2BFWTH100R, which is one of the SNPs associated with infertility, further destabilizes the nucleosome and increases the nucleosome unwrapping rate by interfering with the interaction with H4K91. Taken together, our results suggest that H2BFWT may be necessary for the regulation of spermatogenesis-related genes transcription in spermatogonia by decreasing RNA polymerase II transcription barriers, and that the H100R mutation overdrives its nucleosome-destabilizing effects which likely explain how it causes infertility.

overall_design: Explore the distribution of H2BFWT in the genome within the human testis from two donors.

first: Dongbo

last: Ding

first: Mingxi

last: Deng


title: Circulating exosomal microRNAs are indicative of patients with biliary colic

city: Chengdu

first: Wenchuan

last: Qi

address: 37,12th Bridge Road, Jinniu District

institute: Chengdu University of Traditional Chinese Medicine

summary: Background: Gallstone disease (GSD) is one of the most prevalent and costly digestive system diseases in the world and can lead to pancreatitis, severe biliary tract infection and malignant biliary tract tumors. Gallstones can induce biliary colic, and the pain radiates to the shoulder and back. Severe attacks cause nausea and vomiting, which seriously affect the patient's work and life. Exosomes are important extracellular vesicles, and exosomal microRNAs (miRNAs) can be used as biomarkers and therapeutic targets for a variety of diseases. To the best of our knowledge, exosomal miRNA has not been well evaluated as a biomarker of the progression of cholelithiasis or the onset of biliary colic. Methods: Plasma samples from 10 patients with biliary colic attack were collected for exosome extraction, identification and miRNA sequencing. The exosome miRNA sequencing data of 10 healthy people in the GEO database were used as controls for data analysis. Results: Comparison of the plasma exosomal miRNAs of patients with biliary colic to those of healthy controls showed that 35 exosomal miRNAs were upregulated and 9 miRNAs were downregulated. GO and KEGG analyses showed that differential miRNAs are involved in the inflammatory response. The analysis of the subject operation characteristic curve shows that the expression of plasma exosomal miR-1268a can better reflect the attack characteristics of biliary colic than other miRNAs. miR-146a-3p participates in body inflammation and lipid metabolism processes and can be used as a potential therapeutic target. Conclusion: Plasma exosomal miRNAs can be used as biomarkers during the onset of biliary colic and can also be used as potential molecular targets to inhibit inflammation and analgesia.

first: Xiangying

last: Ye

first: Yuangfang

last: Zhou

first: Ning

last: Sun

first: Jian

last: Xiong

first: Xiaodong

last: Zheng

first: Ruirui

first: Fanrong

last: Liang


title: Counting abortive transcription by Flux-seq

city: Guangzhou

first: Jie

address: ShiLouGang Road 10

institute: Institute of Biological and Medical Engineering， Guangdong Academy of Science

summary: To analyze abortive transcription rate close to TSS, we developed a new method called Flux-seq

overall_design: All sample have been labelled by 4sU run-on and followed with biotin replace and enrichment. The original RNA have been fragmented for sequencing through. 3 run-on length: 5, 15,45mins have been designed and each time points have 3 replicates.

first: Philip

last: Davies

first: Daniel

last: Hebenstreit


title: TGF-β promotes colitis and cancer development in Smad4-deficient intestinal epithelium in a Yap-dependent manner (organoids)

city: Beijing

first: Ye-Guang

last: Chen

summary: TO highlight an integral role of the TGF-β/Smad4 axis in restraining intestinal inflammation and suggest TGF-β or Yap signaling as potential therapeutic targets in inflammatory bowel disease patients with decreased Smad4 expression. We then performed gene expression profiling analysis using data obtained from RNA-seq of indicated intestinal organoids.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for indicated intestinal organoids.

first: Liansheng

last: Liu

first: Shicheng

last: Yu


title: Discovery of neuro- and vascular-associated periosteum-resident macrophages essential for cortical bone regeneration scRNA

city: 市辖区

first: zaiqi

last: xie

state: 徐汇区

address: 上海市徐汇区岳阳路320号

institute: chinese academy of science

summary: The periosteum contains a highly osteogenic and neuro-vascular microenvironment that is essential for cortical bone formation and regeneration. Resident tissue macrophages (RTMs) are critical for maintaining tissue-specific niches and participating in tissue regeneration. However, the characteristics, origin and functions of periosteum-resident macrophages (PRMs) remain largely unknown. In this study, we demonstrated that PRMs are generated during embryonic hematopoiesis and are self-maintained locally during regeneration. Furthermore, by single-cell RNA sequencing analysis of periosteum myeloid cells, CX3CR1+CD45+ACE+ and CX3CR1+CD45+CD74+ cells were identified as vascular-associated and neuro-associated PRMs, respectively. Both cell types were found to arise from CX3CR1+CD168+CD45+ PRMs and shown to play critical roles in maintaining the periosteum neuro-vascular niche and promoting early-stage cortical bone regeneration. Importantly, the neuro-vascular characteristic of PRMs are directly modulated via Periostin, the essential ECM distributed in periosteum. These findings elucidate the characteristics and origins of PRMs and reveal their essential roles in maintaining the local niche and cortical bone regeneration as well as highlighting the potential value of PRMs as a therapeutic target in bone regeneration.

overall_design: To conduct a more comprehensive characterization of periosteum resident macropahges by single-cell RNA sequencing analysis.

first: Jiping

first: Wenhui

last: Xing


title: Discovery of neuro- and vascular-associated periosteum-resident macrophages essential for cortical bone regeneration [neg vs pos]

address: 上海市徐汇区岳阳路320号

overall_design: Examination of different gene expression in different subsets of CX3CR1+ periosteum resident macrophages.


title: Discovery of neuro- and vascular-associated periosteum-resident macrophages essential for cortical bone regeneration

address: 上海市徐汇区岳阳路320号


title: Mice melanoma treated by anti-PD1 and intra-tumor microbiome

city: Shanghai

first: Zhao

last: Zhang

state: SHANGHAI

address: 130 Dongan Rd

institute: FUDAN UNIVERSITY

summary:
To investigate the contribution of intratumor microbiome in cancer immunotherapy, we applied microbiome Eudoraea in combination with anti-PD-1 antibody in mouse model of B16F10 melanoma.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different treatments .

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mice with lgG+PBS, anti-PD-1 + PBS, lgG + Eudoraea,and anti-PD-1+Eudoraea treatments.

first: Leng

last: Han

first: Hong


title: RNA-seq profiling of wild type and Trim33-/- dendritic cell-related progenitors

first: Xiangyi

last: Shen

institute: Tsinghua University

summary: The development of dendritic cells (DCs) is regulated by complex transcriptional networks. DCs originate from the multipotent progenitors (MPPs) in the bone marrow, which could further give rise to common lymphoid progenitors (CLPs) and common dendritic cell progenitors (CDPs). Whereas CDPs, which could be further divided into CD115+ and CD115- populations, give rise to both conventional (cDC) and plasmacytoid DCs (pDCs), CLP is an addtional source of pDCs. Transcriptome profiling of wild type and Trim33-/- MPPs, CD115- CDPs, and CLPs revealed a critical role of TRIM33 in the development of DCs.

overall_design: Wild type (Trim33fl/fl) or Trim33-/- MPPs (Lin- Sca-1+ CD117+ CD34+ FLT3+), CD115- CDPs (Lin- CD11c- FLT3+ CD117int CD115- CD127-), and CLPs (Lin- CD11c- Sca-1+ CD117+ CD127+ FLT3+) were sorted from 6~8-week-old mice bone marrow and subjected to RNA extraction. Trim33 knockout in vivo relied on Cre recombinase-dependent exicision of Trim33 exon2-4, which would result in frameshift and premature translational stop. Three biological repeats were prepared for individual cell types of each genotype. Transcriptome was profiled by RNA-seq at the Beijing Genomics Institution (BGI) on the BGISEQ-500 platform to generate 50 base-pair single end reads.

first: Xiaoguang

last: Li

first: Tao

last: Wu

first: Li


title: Transcriptomic analysis of the spiral ganglion from hearing and aminoglycoside deafened rats

city: Iowa City

first: Steven

middle: Haym

last: Green

state: Iowa

address: 143 Biology Building

department: Biology

institute: University of Iowa

summary: We used RNAseq to assess transcriptomic changes in the spiral ganglion of rats deafened with kanamycin compared to hearing control rats to gain a better understanding of the deafening-induced changes that occur in the spiral ganglion. Transcriptomic profiles were obtained from whole spiral ganglion from hearing and deafened rats at P32 and P60. We observed significant changes in gene expression in not only deafened compared to hearing ganglia, but also from P32 to P60 in normal hearing animals. The most prominent change after deafening was an increase in immune response-related gene expression, indicating that immune response activation occurs in the deafened spiral ganglion.

overall_design: RNA profiles of the spiral ganglion from hearing and aminogycoside deafened rats at P32 or P60. There were 3 biological replicates of each condition (P32 Hearing, P32 Deaf, P60 Hearing, P60 Deaf), with each biological replicate being sequences in technical triplicate (each replicate was sequenced on 3 different lanes)

first: Benjamin

middle: M

last: Gansemer

middle: H


title: Discovery of neuro- and vascular-associated periosteum-resident macrophages essential for cortical bone regeneration [veh vs pos]

address: 上海市徐汇区岳阳路320号

overall_design: Examination of different gene expression in CX3CR1+ACE+ and CX3CR1+CD74+ PRMs after treated by rmPeriostin or PBS.


title: Genome-wide map of TRIM33 binding sites in the dendritic cell line Mutu DC1940

summary: Transcriptional control of dendritic cell (DC) homeostasis has not been fully understood. Genome-wide binding analysis of TRIM33 in dendritic cells revealed a critical role in gene regulation for DC differentiation.

overall_design: To determine the genome-wide binding sites of TRIM33 in DCs, chromatin immunoprecipitation-sequencing (ChIP-seq) assays were performed. An immortalized cell line named Mutu DC1940 (Marraco et al., 2012) was found to harbor much primary DC features, and is therefore suitable for sampling. 2 biological repeats of TRIM33-immunoprecipitated chromatin and the corresponding input and IgG controls were prepared from wildtype Mutu DC1940 cells. The Illumina NovaSeq 6000 platform was used to generate PE150 reads.

first: Tingting

last: Guo


title: RNA-seq profiling of wild type and Trim33-/- splenic dendritic cells

summary: The homeostatic control mechanism of dendritic cells (DCs), including pDCs, cDC1s and cDC2s, is not fully elucidated. Transcriptome profiling of wildtype and TRIM33 conditional knockout mice revealed a key role of TRIM33 in maintaining the homeostasis of all DC subsets.

overall_design: Splenic pDCs (CD11c+ SiglecH+), cDC1s (CD11c+ SiglecH- MHC II+ CD24+ CD172a-) and cDC2s (CD11c+ SiglecH- MHC II+ CD24- CD172a+) of 6 to 8-week old Trim33fl/fl (WT) or Trim33fl/fl Itgax-Cre (KO) mice were isolated from spleen by depleting non-DC lineage with a homemade antibody cocktail and  fluorescent activated cell sorting. Total RNA was extracted with the TRIzol reagent. 2 - 3 biological replicates were prepared for each cell subset of each genotype. Transcriptome was profiled by RNA-seq at the Beijing Genomics Institution (BGI) on the BGISEQ-500 platform to generate 50 base-pair single end reads.


title: Transcriptomic analysis of resistant (BR2655) and susceptible (HR12) rice cultivars after infection with rice blast fungus M. Oryzae (M036)

city: Mysuru

first: Chandrakanth

last: R

state: Karantaka

address: JLB Road

department: Molecular Biology

country: India

institute: Yuvaraja's College, University of Mysore

summary:
Purpose: To study the differential gene expression by comparing resistant and susceptible rice cultivars against the rice blast fungus M. Oryzae.
Methods: Rice leaves were collected after M. Oryzae (MO36) infection from resistant and susceptible cultivars, preserved on deep freezer on -80O C frozen on liquid nitrogen, Total RNA from rice plant tissues was extracted using RNeasy Plant Mini Kit (Qiagen) by following manufacturer protocol. RNA libraries were prepared for sequencing using standard Illumina protocols.
Results: Around 35 million pairs of filtered 150 base paired reads were obtained for each biological sample. These reads were mapped against RGAP7 using reference assembly tool of CLC Genomics Workbench. The mapped read data was summarised in to a matrix for each sample. count data was compared between the samples to identify the differentially expressed genes. genes were further filtered based on fold change, p value and FDR p value. The count data was further statistically analysed using Kal's Z test integrated into CGWB. Genes exhibiting 3 fold change and FDR p value <0.05 were filtered as either up regulated or down regulated gene. we obtained 7577 and 4290 significant (FDR adjusted p value ≤0.05) differentially expressed locus id in the resistant and susceptible rice cultivars, respectively . The number of significant DEL with fold change value greater and less than 3 were 3523 upregulated 4054 downregulated and 2190 upregulated & 2100 downregulated in resistance and susceptible cultivars, respectively. 2-way and and 4-way upregulated and downregulated gene comparisions was carried out. To identify the changes in biological process and molecular function the pathway and gene set enrichment analysis was performed in resistant BR2655 and susceptible HR12 rice cultivars.
Conclusions: This study represents the first transcriptome analysis of resistant BR2655 and susceptible HR12 upon M.oryzae infection, generated by RNA-seq technology. This transcriptome analysis further helps to understand the differential gene expression analysis response to the M.oryzae. And candidate genes which are involved in triggering defense mechanism in rice plants. Further it helps to understand the mechanism of activating a cascade of defense responses in resistant and susceptible plants.

overall_design: Transcriptome profiling of rice resistant BR2655 cultivar and susceptible HR12 cultivar, leaves after mock and M.oryzae infection

first: R

last: Chandrakanth

first: N

middle: S

last: Devaki


title: Regulated intramembrane proteolysis dependent TYRO3 signaling in melanoma cells

city: Turku

first: Katri

middle: Mataleena

last: Vaparanta

address: Vanha Hämeentie 82 as 2

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: Multi-omics examination of regulated intramembrane proteolysis (RIP) dependent TYRO3 signaling in melanoma cells.

overall_design: Transcriptome of melanoma cells rescued with the wild-type or RIP resistant variants of TYRO3 or GFP as control. Three replicate experiments.

first: Johannes

middle: A

last: Merilahti

first: Veera

last: Ojala

first: Klaus

last: Elenius


title: ECM Culture of Normal Breast Lines

city: Baltimore

first: Daniele

middle: Marie

last: Gilkes

state: MD

address: 1650 N Orleans St, CRB1 128, None

department: Oncology

institute: Johns Hopkins

summary: We cultured htertHME, HME2, PCS600010, and MCF10A cells in decellularized ECM scaffolds generated by BJ fibroblasts or on an uncoated, plastic cell culture dish (Unc) to analyze the potential effects of ECM signalling breast cancer development. Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment. After RNA purification, samples were confirmed to have a RIN value > 9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 3000/4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

overall_design: Three replicate sets were generated by culturing htertHME, MCF10A, HME2, and PCS600010 cells in ECM scaffolds or on an uncoated surface in 6 cm dishes for 24 hours.


title: Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

institute: Johns Hopkins University

summary: Single cell RNA-Seq time-course analysis revealed in vivo mouse gastrulation and in vitro directed differentiation

overall_design: Investigation of transcriptome dynamics of hematopoietic stem cell formation using a combinatorial Runx1/Ly6a reporter system

first: Yuqi

last: Tan

first: Abby

last: Spangler

first: Michael

last: Farid

first: Da

last: Peng


title: Transcriptome of hematopoietic stem cells from wild-type and Eumyc transgenic mice on wild-type or caspase-1/11 double knockout backgrounds

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: To determine the transcriptional effects of caspase 1 and caspase 11 deficiency as well as Emu-myc, we performed RNA sequencing (RNAseq) on sorted HSCs from four groups of mice (wild type, Emu-myc, Casp1−⁄−Casp11−⁄−, and Casp1−⁄−Casp11−⁄−Emu-myc).

overall_design: Three mice of each genotype were used.

first: Julie

last: Blander


title: RNA-seq time series of adventitious root development in Populus ussuriensis

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

summary: For the RNA-seq experiments, two-week-old seedlings were cutting and harvested the basal ends of stem cuttings (0.5 cm). Samples were collected from two biological replicates (40 cuttings each).

overall_design: RNA-seq of the basal ends of stem cuttings (0.5 cm).

first: Hairong

last: Wei

first: Quangang

last: Liu

first: Wenlong


title: Systematic metabolome analysis of hematopoietic cells identified uridine as a vital anti-aging factor in hematopoiesis

city: Hangzhou

first: Xiangjun

last: Zeng

address: Zhejiang univerisity

institute: Zhejiang univerisity

summary: In this study, we employed immunomagnetic enrichment and fluorescence-activated cell sorting (FACS) to isolate 15 hematopoietic cell types, over 9×108 hematopoietic cells from 200 young and 150 aged mice, ranging from HSPCs to mature blood cells. UPLC-MS/MS untargeted analysis identified about 2000 metabolites in each cell population, which contributed to define cell-specific signatures and depict aging landscape of blood cells. We further validated our findings by experimentally screening metabolites delaying senescence and identified uridine as potential regulator to rejuvenate aged HSPCs. To enable public access to our dataset, we have constructed an open-source platform (MetaB, www.XXX.com) for easy data browsing and analysis. Collectively, our study developed a solid reference benchmark for metabolic studies in hematopoietic system and provided additional clarity to the mechanisms underlying hematopoietic aging.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for uncultured aged HSPCs, uncultured young HSPCs, aged HSPCs cultured with vehicle and aged HSPCs cultured with uridine.

first: Ce

last: Shi

first: Pengxu

last: Qian

first: He

last: Huang


title: Transcriptome sequencing and bioinformatics analysis of gastrocnemius muscle in type 2 diabetes mellitus rats

status: Public on May 31 2024

city: Qingdao

first: Kuishuai

last: Xu

state: --- Select One ---

institute: the affiliated hospital of qingdao university

summary:
Objective Type 2 diabetes mellitus (T2DM) is one of the high risk factors for sarcopenia. However, the pathogenesis of diabetic sarcopenia has not been fully elucidated. This study obtained transcriptome profiles of gastrocnemius muscle in normal and T2DM rats based on high-throughput sequencing technology, which may provide new ideas for exploring the pathogenesis of diabetic sarcopenia.
Methods Twelve adult male Sprague-Dawley rats were randomly divided into Control group and T2DM group, and gastrocnemius muscle tissue was retained for transcriptome sequencing and real-time quantitative polymerase chain reaction (qRT-PCR) 6 months later. Screening differentially expressed genes (DEGs), Cluster analysis, gene ontology (GO) functional annotation analysis and Kyoto Encyclopedia of Genes and Gnomes (KEGG) functional annotation and enrichment analysis were performed for DEGs. Six DEGs related to apoptosis were selected for qTR-PCR verification.

overall_design: This study was divided into 2 groups, control group and T2DM group, with 3 samples in each group. The samples were gastrocnemius tissue from rats


city: Strasbourg

first: Isabelle

last: Caldelari

address: rue René Descartes

country: France

institute: CNRS

summary: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaG sRNA targetome. Affinity purification of in vivo regulatory complexes coupled with high throughput RNA sequencing methodology or MAPS standing for “MS2 affinity purification coupled to RNA".

first: Stefano

last: Marzi

first: Pascale

last: Romby


title: The Central Role of Gasdermin D in Asthmatic Airway Inflammation and Remodeling

city: Jinan

first: Pin

last: Wang

address: 107 Wenhuaxi Street

institute: Shandong University

summary: Emerging evidence demonstrates that pyroptosis has been implicated in the pathogenesis of asthma. GSDMD is the pyroptosis executioner. The mechanism of GSDMD in asthma remains unclear. The aim of this study was to elucidate the potential role of GSDMD in asthmatic airway inflammation and remodeling. First, we performed immunofluorescent staining and ELISA to detect the protein levels of N-GSDMD in the airway epithelium and IL-18, IL-1β in serum of both asthma patients and the healthy individuals. We demonstrated that N-GSDMD, IL-18, and IL-1β were significantly increased in mild asthma compared with that from the controls. Then, wild type and Gsdmd-knock out (Gsdmd-/-) mice were used to establish asthma model. We isolated primary macrophages and performed histopathological staining, ELISA, flow cytometry to define the roles of GSDMD in allergic airway inflammation and tissue remodeling in vivo. We observed that the production of N-GSDMD, IL-18, and IL-1β were enhanced in OVA-induced asthma mice model. The knockout of Gsdmd resulted in attenuated N-GSDMD, IL-18, and IL-1β production in both bronchoalveolar lavage fluid (BALF) and lung tissue in asthmatic mice. In addition, Gsdmd-deficiency mice exhibit a significantly reduction in airway inflammation and remodeling, which might be associated with reduced Th17 type inflammation response and M2 polarization. Third, we explored the underlying mechanism of GSDMD in asthma by bulk RNA-sequencing. We found GSDMD may improve asthmatic airway inflammation and remodeling through regulating macrophage adhesion and migration, and then lead to M2 polarization by targeting Notch signaling pathway. These findings demonstrated that GSDMD plays a critical role in the pathogenesis of allergic inflammation and tissue remodeling.

overall_design: Macrophages were obtained from bone marrow of Gsdmd-/- and wildtype mice, and differentiated for 6 days before sent for sequencing.


title: Whole Transcriptome analysis to identify non-coding RNA regulators and hub genes in Sperm of non-obstructive azoospermia by microarray

city: Amol

first: Hossein

last: Azizi

address: Taleghani str, Abouzar

country: Iran

institute: Amol University of Special Modern Technologies

summary: Our study utilizes whole transcriptome analysis via microarray technology to uncover non-coding RNA regulators and hub genes within sperm samples afflicted by non-obstructive azoospermia. This comprehensive approach offers insight into the intricate molecular landscape underlying this condition, shedding light on potential regulatory mechanisms and key genetic players implicated in its pathogenesis.

overall_design: We evaluate RNA transcripts to identify hub gene and non-coding RNA regulators in sperm of three cases of non-obstructive azoospermia and 3 controls by  microarray

first: Danial

last: Hashemi Karoii

first: Thomas

last: Skutella


title: RNA sequencing analyses reveal the potential anti-inflammatory mechanisms of acacetin against ODG/R injuries in microglia

city: Urumqi

first: juan

last: Bu

address: 29 Tianchi Road

institute: People's Hospital of Xinjiang Uygur Autonomous Region

summary:
Background: Acacetin is a natural flavonoid known for its anti-tumor, antioxidant, and anti-inflammatory properties. Our previous studies have shown its protective effects against cerebral ischemia-reperfusion injury (IRI), but the underlying molecular mechanisms remain unclear.
Purpose: The study delves into acacetin's mechanism in mitigating cerebral IRI, with a focus on transcriptomic insights.
Methods: We established the oxygen-glucose deprivation/re-oxygenation (OGD/R) model in BV2 microglia, treating them with 10μM acacetin. Then we assessed cell proliferation using CCK-8 and measured Lactate Dehydrogenase (LDH) release. High-throughput RNA sequencing (RNA-seq) underpinned the analysis of differentially expressed genes (DEGs) and long non-coding RNAs (lncRNAs), functional enrichment, and alternative splicing events (ASEs), validated by reverse transcription–quantitative polymerase chain reaction (RT-qPCR).
Results: OGD/R injury significantly impaired cell proliferation and increased LDH release, effects mitigated by acacetin. RNA-seq identified 2,148 upregulated and 2,135 downregulated DEGs post-OGD/R. In contrast, the acacetin-treated group showed 248 upregulated and 240 downregulated DEGs compared to the OGD/R group. All DEGs were enriched in both Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Overlapping analysis indicated that acacetin treatment reversed the expression of 203 genes affected by OGD/R, including inflammation-related genes such as Isg15, Fcgr1, Il1b, and Parp12. Moreover, the oxidative stress-related gene, Mt2, was downregulated post-OGD/R but upregulated following acacetin treatment. We further found that OGD/R and acacetin treatment could modulate gene splicing events, impacting cell apoptosis or inflammatory responses, such as the A3SS splicing event in the Trim47 gene. RNA-seq	 also highlighted differential expression of numerous lncRNAs, particularly the upregulation of lncRNA Rmrp and Terc post-OGD/R and their subsequent downregulation post-acacetin treatment. These lncRNAs might regulate cell proliferation through mediating target gene expressions. RT-qPCR validation confirmed these findings.
Conclusion: Significant upregulation of genes and ASEs linked to oxidative stress and inflammatory response is observed in cerebral IRI. Acacetin intervention reverses these effects, highlighting its mechanism in alleviating the injury by modulating gene expression and splicing events.

overall_design: Cultured BV2 microglia were used to establish the oxygen glucose deprivation/re-oxygenation (OGD/R) model, subsequently intervened with 10μM acacetin. Cell proliferation was assessed using the CCK-8 assay, and LDH release was evaluated by the LDH assay. High-throughput RNA sequencing (RNA-seq) was used in alternative splicing events (ASEs) analysis and differentially expressed genes (DEGs) analyses of mRNA and lncRNA, with validation achieved using reverse transcription–quantitative polymerase chain reaction (RT-qPCR).

first: Juan

first: Yeledan

last: Mahan

first: Yanmin

last: Zhang

first: Shengnan

first: Xuanxia

last: Wu

first: Xiaoling

first: Ling

last: Zhou


title: Myelin oligodendrocyte glycoprotein reactive Th17 cells drive Janus Kinase 1 dependent transcriptional reprogramming in astrocytes and alter cell surface cytokine receptor profiles during experimental autoimmune encephalomyelitis.

city: Columbus

first: Gordon

middle: P

last: Meares

state: OH

address: 460 Medical Center Dr.

department: Neurology

institute: The Ohio State University

summary: Multiple sclerosis (MS) is an autoimmune demyelinating disease affecting the central nervous system (CNS). T helper (Th) 17 cells are involved in the pathogenesis of MS and its animal model of experimental autoimmune encephalomyelitis (EAE) by infiltrating the CNS and producing effector molecules that engage resident glial cells. Among these glial cells, astrocytes have a central role in coordinating inflammatory processes by responding to cytokines and chemokines released by Th17 cells. In this study, we examined the impact of pathogenic Th17 cells on astrocytes in vitro and in vivo. We identified that Th17 cells reprogram astrocytes by driving transcriptomic changes partly through a Janus Kinase (JAK)1-dependent mechanism, which included increased chemokines, interferon-inducible genes, and cytokine receptors. In vivo, we observed a region-specific heterogeneity in the expression of cell surface cytokine receptors on astrocytes, including those for TGFβ, IL-10, IL-1, IL-17, IFN-γ, and TNF-α. Additionally, these receptors were dynamically regulated during EAE induced by adoptive transfer of myelin-reactive Th17 cells. This study overall provides evidence of Th17 cell reprogramming of astrocytes, which may drive changes in the astrocytic responsiveness to cytokines during autoimmune neuroinflammation.

overall_design: To test if Th17 cells were activating JAK1-dependent signaling in astrocytes, we knocked down JAK1 in the astrocytes and cultured the astrocytes with and without pathogenic Th17 cells. Following co-culture with Th17 cells, T cells were removed, and astrocyte RNA isolated for analysis. The experimental groups are 1) Astrocytes non-targeting siRNA, no Th17 cells; 2) Astrocytes non-targeting siRNA with Th17 cells; 3) Astrocytes JAK1 siRNA, no Th17 cells; 4) Astrocytes JAK1 siRNA with Th17 cells. Three biological replicates of astrocytes were analyzed for each condition.

first: Sarah

last: Milne

first: Anirudhya

last: Lahiri

first: Cristina

last: Sanchez


city: Epalinges

first: Laura

last: Yerly

address: Chemin de Boveresses 155

country: Switzerland

institute: CHUV

summary: Investigating transcriptional programs regulating invasion in basal cell carcinoma through scRNAseq analysis

overall_design:
Biopsy of basal cell carcinoma processed for scRNAseq analysis; B=baseline, W=wounded, UW=unwounded

**Submitter states that the raw data will be deposited in dbGaP due to patient privacy concerns**

first: Massimo

last: Andreatta

first: Josep

last: Garnica

first: Jeremy

last: Di Domizio

first: Michel

last: Gilliet

first: Santiago

last: Carmona

first: François

last: Kuonen


title: Gene expression analysis of mouse F1 hybrids to study cis regulatory variations

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary: To analyze the difference in gene expression between alleles of F1 hybrids of mouse C57BL6/J (B6) and MSM/Ms (MSM) strains, we sequenced these F1 hybrids of reciprocal crosses. While most genes did show allelic bias, a small number of genes showed either B6- or MSM-biaed expression in both crosses. These allelic differences were associated with the allelic differences in histone acetylation in promoter regions determined by another experiments.

overall_design: Using F1 hybrids between B6 and MSM of reciprocal crosses, RNA was extracted  from  female liver, and sequenced with the 150-bp paired-end mode. Alleles were determined for each read, and the allele frequencies were calculated for each gene. For each crosses, two biological replicates were analyzed.

first: Beverly

last: Boyboy


title: Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement

city: Melbourne

first: Zhoujie

last: Ding

state: VIC

address: 89 Commercial Road

country: Australia

institute: Monash University

summary: B and T cells can recognise and respond to a vast array of foreign pathogens by virtue of the diverse antigen-receptor repertoire generated by gene rearrangement during development. Here, we show that deficiency in Ki67, a nuclear protein ubiquitously expressed throughout the cell cycle, impairs B-cell development at specific, early stages. We identified that Ki67 maintains global chromatin accessibility in lymphocyte progenitors at stages where antigen-receptor gene rearrangements occur and that gene rearrangement is less efficient in the absence of Ki67. That the defects in B cell development are caused by disrupted antigen-receptor gene rearrangement is shown by pre-rearranged antigen-receptor genes fully compensating for loss of Ki67. Collectively, these results identify a unique contribution from Ki67 to somatic antigen-receptor gene rearrangement.

overall_design: B cell progenitors(pre-pro-B, pro-B and small pre-B)  were sorted and ATAC-sequencing were performed on these cell populations from WT or Mki67-/- mice

first: Maree

last: Hagan

first: Feng

last: Yan

first: David

last: Tarlinton


title: Single cell transcriptomic profiling of murine adult healthy gingiva

city: London

first: Inês

last: Sequeira

address: Institute of Dentistry, 4 Newark street

country: United Kingdom

institute: Queen Mary University of London

summary: scRNA-seq performed on gingival tissue isolated from healthy mice at postnatal day 28 (P28).

overall_design: scRNA-seq of one biological replicate of healthy mouse gingiva at P28. 3 animals were pooled.

first: Ines

first: Diana

last: Pereira


title: The PCNA-Pol d complex couples lagging strand DNA synthesis to parental histone transfer

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: How parental histone H3-H4 tetramers, the primary carrier of epigenetic modifications, are transferred to leading and lagging strands of DNA replication forks following DNA replication is an important question that remains not well understood. Here we show that DNA polymerase clamp PCNA and its partner involved in lagging strand DNA synthesis, Pol d, regulate parental histone transfer to lagging strands. Mutations at PCNA as well as at subunits of Pol d that impair the PCNA-Pol d interaction affect parental histone transfer to lagging strands, and this defect unlikely arises from their impacts on DNA synthesis. Moreover, Pol d interacts with H3-H4 in vitro. We suggest that the PCNA-Pol d complex, best known for its role in lagging strand DNA synthesis and DNA repair, couples lagging strand DNA synthesis to the transfer of the parental histones H3-H4 for the inheritance of chromatin structures following DNA replication and possibly DNA repair.

overall_design: ChIP-Seq and eSPAN for H3K4me3 and H3K56ac and BrdU-Seq in WT and mutant yeast cells

first: Albert

last: Serra-Cardona

first: Xu

last: Hua

first: Hui

last: Zhou

first: Zhiguo

last: Zhang


title: Glucose deprivation regulates the expression of BACH1-upregulated pro-metastatic genes

first: Wei

last: Gu

address: 1130 St. Nicholas Ave.

summary: Since the primary effect of the ketogenic diet is to establish a glucose-deprived condition in vivo, we, therefore, used glucose starvation in vitro to mimic the effects of the keto diet. In our endeavor to comprehend the influence of glucose starvation on pro-metastatic genes associated with BACH1, we performed RNA-Seq analysis on MDA-MB-231 ctrl cells and BACH1 knockout cells.

overall_design: MDA-MB-231 Ctrl cells (2 individual clones) and BACH1 knockout cells (3 individual clones) were incubated in DMEM medium with either 4.5g/L or 0g/L glucose for 40h. Subsequently, the cells were collected for RNA sequencing.

first: Su

last: Zhenyi

first: Gu

last: Wei


title: Crosstalk between Regnase-1 and -3 shapes mast cell survival and cytokine expression

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

institute: Institute for Research in Biomedicine

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

overall_design: Refer to individual Series


title: Developmental origins of Parkinson’s disease risk: developmental exposure to the organochlorine pesticide dieldrin leads to sex-specific DNA modifications in critical neurodevelopmental pathways in the mouse midbrain

city: Piscataway

first: Alison

middle: I

last: Bernstein

state: NJ

address: 170 Freylinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

type: Methylation profiling by high throughput sequencing

summary: Epidemiological studies show that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson’s disease (PD). Animal studies support a link between developmental dieldrin exposure and increased neuronal susceptibility in the α-synuclein preformed fibril (α-syn PFF) and MPTP models in adult male C57BL/6 mice. In a previous study, we showed that developmental dieldrin exposure was associated with sex-specific changes in DNA modifications within genes related to dopaminergic neuron development and maintenance at 12 weeks of age. Here, we used capture hybridization-sequencing with custom baits to interrogate DNA modifications across the entire genetic loci of the previously identified genes at multiple time points – birth, 6 weeks, 12 weeks, and 36 weeks old. We identified largely sex-specific dieldrin-induced changes in DNA modifications at each time point that annotated to pathways important for neurodevelopment, potentially related to critical steps in early neurodevelopment, dopaminergic neuron differentiation, synaptogenesis, synaptic plasticity, and glial-neuron interactions. Despite large numbers of age-specific DNA modifications, longitudinal analysis identified a small number of DMCs with dieldrin-induced deflection of epigenetic aging. The sex-specificity of these results adds to evidence that sex-specific responses to PD-related exposures may underly sex-specific differences in disease. Overall, these data support the idea that developmental dieldrin exposure leads to changes in epigenetic patterns that persist after the exposure period has ended and disrupt critical neurodevelopmental pathways and that developmental exposures can impact risk of late life diseases, including PD.

overall_design: Capture hybridization data for developmental dieldrin exposure study with 4 follow-up timepoints in exposed offspring: birth, 6 weeks old, 12 weeks old, and 36 weeks old. At each timepoint (and across the later 3 timepoints), we compared control (n=8-10 per sex) vs. dieldrin treatment (0.3 mg/kg) (n=8-10 per sex) using the DSS R package.

first: Joseph

last: Kochmanski

first: Mahek

last: Virani

first: Nathan

middle: C

last: Kuhn

first: Sierra

last: Boyd

first: Marie

last: Adams

first: Katelyn

last: Becker


title: Molecular insights into female hybrid sterility in interspecific crosses between Drosophila melanogaster and Drosophila simulans (small RNA-Seq)

status: Public on May 30 2024

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

summary: Species of the genus Drosophila have served as favorite models in speciation studies, however genetic factors of the interspecific hybrid sterility are underinvestigated to date. Here we performed the analysis of reproductive incompatibilities of hybrid females in crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis, molecular, cellular and genetic approaches we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis and functional defects of oogenesis in hybrids. A premature GSC loss was a most prominent defect of oogenesis in hybrid ovaries. Owing differential expression of genes encoding components of the piRNA pathway rhino and deadlock, functional RDCmel complex in hybrid ovaries was not assembled. At the same time the activity of RDCsim complex was maintained in hybrids, independently from the genomic origin of piRNA clusters. Despite identification of a cohort of overexpressed TEs in hybrid ovaries we found no evidences that their activity can be considered as the main cause of hybrid sterility. We revealed complex pattern of Vasa protein expression in hybrid germline, including partial AT-chX piRNA targeting of vasasim allele and significant developmental delay of vasamel expression. We came to the conclusions that complex multi-locus genetic changes between the species were responsible for hybrid sterility phenotype.

sample_organism: Drosophila melanogaster x Drosophila simulans

overall_design: To evaluate piRNA clusters activity and TE-related piRNA level in ovaries of interspecific hybrids and parental species small RNA libraries were created.


title: Molecular insights into female hybrid sterility in interspecific crosses between Drosophila melanogaster and Drosophila simulans

platform_organism: Drosophila melanogaster x Drosophila simulans


title: Gene expression profiles in poh1-deficient murine pancreas

city: Shanghai

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

summary: To investigate the molecular events essentifal for POH1-mediated ADM and PDAC development, we performed RNA-seq assays to detect transcriptome changes in POH1-deficient pancreas.

overall_design: The pancreatic tissues depleted of poh1 gene were obtained from Pdx1-Cre+, poh1f/f mice. The pancreas from Pdx1-Cre+, poh1f/+ mice were used as control.

first: Tiantian

last: Jing

first: Yizhen

last: Liu


title: Capturing totipotency in human cells through spliceosomal repression [ChIP-seq]

city: Beijing

first: Li

last: Ding

address: No.5, Yiheyuan Road

institute: Peking University

summary:
Supplemented with splicing inhibitor PlaB, we realize in vitro culturing of human totipotent stem cells comparable to 2-4-cell blastomeres
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for h3k4me3 and h3k27me3 in hESC sand hTBLCs

overall_design: Comparative epigenetic profiling analysis of h3k4me3 and h3k27me3 data for hESCs and hTBLCs

first: Shiyu

last: Li

first: Min

last: Yang

first: Hui

last: Shen


title: Capturing totipotency in human cells through spliceosomal repression


title: Molecular insights into female hybrid sterility in interspecific crosses between Drosophila melanogaster and Drosophila simulans (RNA-Seq)

overall_design: To analyze the nature of hybrid sterility in crossings between D. Melanogaster (hmr2) and D. Simulans (w501) flies we prepared, sequenced, and analyzed whole-transcriptome libraries of mRNA isolated from the ovaries of interspecific hybrids and parental species.


title: Capturing totipotency in human cells through spliceosomal repression [ATAC-seq]

summary:
Supplemented with splicing inhibitor PlaB, we realize in vitro culturing of human totipotent stem cells comparable to 2-4-cell blastomeres
Assay for transposase accessible chromatin with high-throughput sequencing in hESC sand hTBLCs

overall_design: Comparative chromatin accessibility analysis of more open and closed signals in ATAC-seq for hESCs and hTBLCs


title: Distinct SIV-specific lymphoid tissue CD8 T cells exhibit simultaneous effector and stem-like profiles and associate with limited SIV persistence

status: Public on May 29 2024

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: HIV cure efforts are increasingly focused on harnessing CD8 T cell functions; however, a deeper understanding of CD8 T cells promoting HIV control is necessary to properly inform therapeutic approaches. Here, we identified a novel TOX-expressing CD8 T cell population associated with control of SIV infection in lymphoid tissue of rhesus macaques defined as an antigen-responsive TCF1+ CD39+ subset expressing high levels of TOX and inhibitory receptors but lower levels of canonical cytolytic molecules such as granzyme B, granzyme A, and perforin. Transcriptional analysis of SIV-specific CD8 T cells, as well as proteomic analysis of purified CD8 T cell subsets, revealed these TCF1+ CD39+ cells as an intermediate effector population retaining stem-like features while maintaining a lineage relationship with terminal effector cells. TCF1+ CD39+ CD8 T cells expressed higher levels of CXCR5 than terminally differentiated cells, were found at higher frequency in follicular micro-environments, and were preferentially located in the proximity of SIV-RNA+ cells both in lymph node T cell zone and B cell follicles. Their frequency was strongly associated with reduced plasma viremia and, importantly, lower size of the intact reservoir. Finally, we confirmed the presence of a highly similar TOX-enriched TCF1+ CD39+ cell population in lymph node biopsies from ART-naïve and ART-treated people living with HIV. Collectively, these data identify a unique population of lymphoid CD8 T cells possessing both stem-like and effector properties that contribute to limiting HIV/SIV persistence.

overall_design: Cryopreserved LN samples from 5 A*01+ animals at D42 p.i. were thawed and minimum of 10,000 SIV-specific CD8 from each animal was sorted by FACS, loaded onto 10X Chromium Controller, and analyzed by scRNASeq.

first: Zachary

last: Strongin

first: Laurence

middle: R

last: Marchand

first: Claire

last: Deleage

first: Maria

middle: B

last: Pampena

last: Cardenas

first: Christian

last: Beusch

first: Timothy

middle: N

last: Hoang

first: Elizabeth

last: Urban

first: Mael

last: Gourves

first: Kevin

last: Nguyen

first: Stacey

last: Lapp

first: Andrew

last: Rahmberg

first: Justin

last: Harper

first: Perla

last: del Rio Estrada

first: Mauricio

last: Gonzalez-Navarro

first: Yara

last: Luna-Villalobos

first: Santiago

last: Avila-Rios

first: Gustavo

last: Reyes-Teran

first: Rafick

last: Sekaly

first: Guido

last: Silvestri

first: Deanna

last: Kulpa

first: Asier

last: Saez-Cirion

first: Jason

last: Brenchley

first: Steven

last: Bosinger

first: David

last: Gordon

first: Michael

last: Betts

first: Haydn

middle: T

last: Kissick

first: Mirko

last: Paiardini


title: Capturing totipotency in human cells through spliceosomal repression [scRNA-seq]

first: Li

last: Ding

summary: Supplemented with splicing inhibitor PlaB, we realize in vitro culturing of human totipotent stem cells comparable to 2-4-cell blastomeres

overall_design: teratomas derived from hESCs and hTBLCs are dissociated and performed single cell RNA sequencing. hTBLC and naïve hESCs cultured in E8 medium are collected at different time points and performed single cell RNA sequencing.

first: Shiyu

last: Li

first: Min

last: Yang

first: Hui

last: Shen


title: Analysis of human liver transcriptome after exposure to okadaic acid

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

summary:
Purpose: Not much research has been done on the effects of okadaic acid on the liver, but it has been shown, that it not only reaches the liver, but has an especially long retention time in it. In this study, differentiated HepaRG cells were incubated bith different, non-cytotoxic okadaic acid concentrations for 24h and the total RNA was used for sequencing.
Method: Transcriptomic responses were analyzed using RNA sequencing technology

overall_design:
Examination with a total of 12 samples, thereof 3 negative control samples and 9 samples in 3 treatment groups in triplicates
Comparative gene expression profiling analysis by RNA sequencing regarding the effect of okadaic acid relative to the non-treated cells.

first: Leonie

last: Wuerger

first: Albert

last: Braeuning


title: A hybrid single cell demultiplexing strategy that increases both cell recovery rate and calling accuracy

city: New York

first: Patrick

last: Wilson

address: 413 E. 69th Street

department: gale and Ira Drukier Institute for Children's Health

institute: Weill Cornell Medicine

summary: Recent advances in single cell RNA sequencing allow users to pool multiple samples into one run and demultiplex in downstream analysis, greatly increasing the experimental efficiency and cost-effectiveness. However, the expensive reagents for cell labeling, limited pooling capacity, non-ideal cell recovery rate and calling accuracy remain great challenges for this approach. To date, there are two major demultiplexing methods, antibody-based cell hashing and Single Nucleotide Polymorphism (SNP)-based genomic signature profiling, and each method has advantages and limitations.  Here, we propose a hybrid demultiplexing strategy that increases calling accuracy and cell recovery at the same time. We first develop a computational algorithm that significantly increases calling accuracy of cell hashing. Next, we cluster all single cells based on their SNP profiles. Finally, we integrate results from both methods to make corrections and retrieve cells that are only identifiable in one method but not the other. By testing on several real-world datasets, we demonstrate that this hybrid strategy combines advantages of both methods, resulting in increased cell recovery and calling accuracy at lower cost.

overall_design: MBCs specifically reactive against a panel of influenza antigens including hemagglutinin, neurminidase and neucleoprotein were baited along with T cell as carrier cells from cohort of seasonal influenza vaccinees for characterization of anti-influenza humoral immunity.

first: Jiayi

last: Sun

first: Yanbin

last: Fu

first: Lei


title: Capturing totipotency in human cells through spliceosomal repression [RNA-Seq]

summary:
Supplemented with splicing inhibitor PlaB, we realize in vitro culturing of human totipotent stem cells comparable to 2-4-cellb blastomeres
Poly(A) RNA-seq is performed on hESCs cultured in MYCP medium

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hESCs and hTBLCs


title: Arginine impacts aggregation, biofilm formation, and antibiotic susceptibility in Enterococcus faecalis

status: Public on May 28 2024

city: Minneapolis

first: Julia

last: Willett

state: Minnesota

address: 689 23rd Avenue SE, 4-149 Micro Research Facility

institute: University of Minnesota

summary: Enterococcus faecalis is a commensal bacterium in the gastrointestinal tract (GIT) of humans and other organisms. Outside of the GIT, E. faecalis can cause infections in root canals, wounds, surgical sites, the urinary tract, and on heart valves. Many of these infections can be polymicrobial, and a variety of toxins and nutritional signals influence interactions between E. faecalis and other microbes. Like other bacteria, E. faecalis metabolizes arginine through the arginine deiminase (ADI) pathway, which converts arginine to ornithine and releases ATP, ammonia, and CO2.  E. faecalis arginine metabolism also affects virulence of other pathogens, such as Clostridioides difficile and Escherichia coli, during co-culture.  E. faecalis may encounter elevated levels of arginine in the GIT or the oral cavity, where arginine is used as an additive in dental therapeutics to disrupt plaque formation and biofilm growth by oral streptococci.  However, little is known about how E. faecalis responds to growth in arginine.  To address this gap, we used RNAseq and additional in vitro assays to measure changes in growth, gene expression, and biofilm formation in arginine relative to control conditions.  Here, we demonstrate that arginine decreases E. faecalis biofilm production and causes widespread differential expression of genes related to metabolism, nutrient transport, quorum sensing, and polysaccharide synthesis. Growth in arginine also increases aggregation of E. faecalis cultures and promotes decreased susceptibility to the antibiotics ampicillin and ceftriaxone. Together, this shows that E. faecalis undergoes global transcriptional changes during growth in arginine and provides a platform for better understanding of how the presence of arginine in the niches colonized by E. faecalis affects the physiology of this organism in addition to the virulence of surrounding microbes.

overall_design: Planktonic and biofilm cultures of E. faecalis OG1RF were grown with and without arginine.  Total RNA was extracted for sequencing.


title: Single cell RNA sequencing of primary breast cancer

city: Seoul

first: Kyung Yeon

last: Han

address: 81, Irwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Genome Institute, Samsung Medical Center

summary: A total of 9 patients diagnosed with HR+/HER2- breast cancer  were recruited for this study. Tissue specimens were obtained by surgical excision without prior treatment. Tumor tissues were mechanically dissociated and enzymatically digested on the day of surgery. We profiled transcriptomic characteristics using single cell RNA-seq to  investigate the relationship between migratory tumor subtypes and cancer-associated fibroblasts (CAFs) in tumor progression.

overall_design: Library preparation was performed using the Chromium Single cell 3’ gene expression system (version 2) and processed following the manufacturer’s protocol (10x Genomics, USA). The library was sequenced on a HiSeq 2500 system using 100-bp paired-end sequencing, and raw sequencing data were processed using Cell Ranger.

first: Eun Hye

last: Joo

first: Woong-Yang

last: Park


title: Transcriptome Analysis Reveals Potential Protective Effects and Biomarkers of Pien Tze Huang on CCl4-induced Liver Cancer (circRNA)

status: Public on May 26 2024

first: Yongzhi

last: Wang

state: Shanghai

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

summary: Pien Tze Huang (PZH) is a traditional Chinese medicine which was widely utilized in Asia for hepatic diseases. We construct two groups liver cancer mice model using CCl4, one group using PZH treatment and another group didn?t treatment. We found that the liver functional indices including ALB, ALT and AST were significantly increased in non-PZH treatment group. HE staining showed that inflammation was emerged surrounding the hepatic vein in the non-PZH treatment group, Masson staining revealed that there are blue collagenous fibre surrounding hepatic vein in the non-PZH treatment group, this result indicated that PZH cured the hepatic inflammation and cancer. We performed the mRNA,LncRNA,ciecRNA and miRNA sequencing aim to explore the drug target using PZH treatment on transcriptome level. 478 protein coding transcripts and 68 lncRNA transcripts were differentially expressed. Our research provided potential transcriptional therapeutic target for the clinical treatment using PZH.

overall_design: We constructed two groups liver cancer mice model using CCl4, one group used PZH treatment, another group did not receive treatment. We also did a blank experiment with normal mice using water. In the 22nd week, we selected six mice from each group for RNA sequencing.

first: Hao

last: Wu

first: Shengying

last: Qin


title: Research on Differences and Immune Infiltration-Related Macrophages Between Non-Small Cell Lung Cancer and Adjacent Tissues

city: Suzhou

first: Junhong

last: Jiang

address: No.1 Songtao Street

institute: Dushu Lake Hospital Affiliated to Soochow University

summary: Non-Small Cell Lung Cancer (NSCLC) is a highly lethal respiratory tumor with unclear molecular mechanisms. RNA-seq data from 34 early-stage samples and adjacent non-cancerous tissues identified 1088 differentially expressed genes using Deseq2. Mendelian randomization (MR) analysis of 26,153 genes and 63,053 LUSC patients, including 7,838,805 SNPs, identified 213 potential exposure factors. Five differentially expressed genes (GYPE, PODXL2, RNF182, SIRPG, WNT7A) were identified, with PODXL2 as a risk factor. GO and KEGG analyses highlighted the mTOR and Wnt signaling pathways. Immune infiltration analysis showed decreased Plasma cells, Tregs, and activated Dendritic cells, but increased Macrophages M1. External validation using TCGA and 11 GEO datasets confirmed SIRPG's role in LUSC. SIRPG is a significant exposure risk factor for LUSC, with Macrophages M1 and the mTOR signaling pathway playing crucial roles.

overall_design: To study the differentially expressed genes between NSCLC tumor tissues and adjacent non-cancerous tissues.

first: Jing

first: Haitao

last: Ma

first: Daxiong

last: Zeng


title: Senescent glia link neuronal mitochondrial dysfunction and lipid droplet accumulation with age

status: Public on May 24 2024

city: Philadelphia

first: Nancy

last: Bonini

state: PA

address: 433 S University Ave

institute: University of Pennsylvania

summary: Senescence is a cellular state linked to aging and age-onset disease across many mammalian species. Acutely, senescent cells promote wound healing and prevent tumor formation; but they are also pro-inflammatory, thus chronically exacerbate tissue decline. While senescent cells are active targets for anti-aging therapy, why these cells form in vivo, how they affect tissue aging, and the impact of their elimination remain unclear. Here we identify naturally-occurring senescent glia in aged Drosophila brains and decipher their origin and influence. Using AP1 activity to screen for senescence, we determine that senescent glia can appear in response to neuronal mitochondrial dysfunction. In turn, senescent glia promote lipid accumulation in non-senescent glia; similar effects are seen in senescent human fibroblasts in culture. Targeting AP1 activity in senescent glia mitigates senescence biomarkers, extends fly life and health span, and prevents lipid accumulation. However, these benefits come at the cost of increased oxidative damage in the brain, and neuronal mitochondrial function remains poor. Altogether, our results map the trajectory of naturally-occurring senescent glia in vivo and indicate that these cells link key aging phenomena: mitochondrial dysfunction and lipid accumulation.

overall_design: In mice, eliminating senescent cells one day per week is sufficient to extend life and health span. Similarly in flies, we found that blocking AP1 activity in glia for 1 d/wk extends fly life and health span. To understand what changes in the brain when we target senescent glia and extend animal life and health, we performed bulk-RNA-seq on brains with (repoGS>UAS-puckered or repoGS>UAS-dsFosDN) or without (repoGS>UAS-GFP) glial AP1 activity blocked for 1 d/wk. Whole brains (n=20) were dissected from young (7d) or aged (42d) flies and used for bulk-RNA-sequencing and downstream gene expression analysis.

first: China

last: Byrns

first: Alexandra

middle: E

last: Perlegos


title: Red2Flpe-SCON: A Versatile, Multicolor Strategy for Generating Mosaic Conditional Knockout Mice

status: Public on May 25 2024

city: Pohang

first: Somi

last: Kim

address: 47, Jigok-ro

department: Life Sciences

institute: POSTECH

summary: Image-based lineage tracing enables tissue turnover kinetics and lineage potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco, which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion kinetics and neighboring effects of oncogenic clones to be dissected. We now report Red2Flpe-SCON: a new mosaic knockout system that uses multicolor reporters to label both mutant and wild-type cells. We have developed the Red2Flpe mouse line for red clone-specific Flpe expression, as well as the FRT-based SCON (Short Conditional IntrON) method to facilitate tunable conditional mosaic knockouts in mice. We used the Red2Flpe-SCON method to study Sox2 mutant clonal analysis in the esophageal epithelium of adult mice which revealed that the stem cell gene, Sox2, is not essential for adult stem cell maintenance itself, but rather for stem cell proliferation and differentiation.

overall_design: We isolated wild-type and mutant esophageal cells from Rosa-CreERT2; Confetti-Red2Flpe; Sox2scon/scon mice 4 weeks after induction and performed scRNA-seq using the SORT-seq method.

first: Szu-Hsien

first: Jong

first: Gabriele

last: Colozza

first: Bon-Kyoung

last: Koo


title: Senescent glia link neuronal mitochondrial dysfunction and lipid droplet accumulation with age [19082-12_MASTER]

overall_design: To determine if fly AP1+ glia have features of senescent mammalian cells, we FACS-sorted and bulk-RNA-sequenced three distinct cell populations from aged fly brains (40 d): neurons, AP1+ glia, and AP1neg glia. For this, glia were labelled with GFP expressed under a constitutive pan-glial driver (repo-GAL4) while cells with AP1 activity were identified using a genomic dsRed fluorescent reporter under the control of an AP1 binding motif. Whole brains were dissected from aged flies (40 d) and dissociated into a cell suspension. Neurons (dsRednegGFPneg), AP1neg glia (dsRednegGFP+) and AP1+ glia (dsRed+GFP+) were then FACS-isolated and bulk RNA-sequenced for downstream gene expression analysis (n=500 cells per biological replicate, 4 replicates). Using the same approach described above, we also isolated and sequenced neurons from 5 d fly brains for comparison to aged neurons.