title: Integrated Whole Transcriptome Profiling and Bioinformatics Analysis for researching lychee downy blight (miRNA-Seq)

first: Liu

last: Hailun

address: Tianhe District

institute: Guangdong Academy of Agricultural Sciences

summary: Non coding RNA (ncRNA), such as miRNA, lncRNA and circRNA, has been found to play an important role in the mechanism of plant defense against pathogens. Lychee downy blingt is the main disease of litchi fruit, inflorescence and leaf, which seriously affects the yield of lychee. In this study, we carried out a P.litchii infection experiment on lychee fruits and leaves, and the mRNA and ncRNA in the treated fruits and leaves were analyzed by whole-transcriptome RNA sequencing technology. our work will Provide new insights for the resistance of lychee downy blight .

overall_design: The gene expression profiling analysis using data obtained from RNA-seq of 'Feizixiao'. The treated leaves and treated fruits were collected at 24 hpi. whole-transcriptome RNA sequencing was performed by Biomarker Technologies(Beijing, China) using an Illumina Nova platform.

first: Hailun

last: Liu

first: Mao

last: Yin


title: Integrated Whole Transcriptome Profiling and Bioinformatics Analysis for researching lychee downy blight (RNA-Seq)

status: Public on Feb 06 2023

city: Guangzhou

country: China

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing


title: Gene expression analysis of THP-1 cells (monocytic cell line) transfected with microRNA mimics: let-7d-3p, let-7e-5p,miR-146a-5p,miR-130a-3p, miR-151a-3p.

city: Kyoto City

first: Hiromi

last: Nishigaki

address: 465 Kajii-Cyo, Hirokouji, Kawaramachi doori, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

summary:
In our previous study,  hsa-let-7d-3p, hsa-let-7e-5p,hsa-miR-146a-5p,hsa-miR-130a-3p, hsa-miR-151a-3p,were significantly upregulated in the plasma of atopic patients.
To study the each function of let-7d-3p, let-7e-5p,miR-146a-5p,miR-130a-3p, miR-151a-3p which are significantly upregulated in the plasma of atopic patients, we performed mimic-transfected THP-1 cells, a mononuclear cell line, and performed comprehensive genetic analysis.

overall_design: THP-1 cells were transfected with let-7d-3p, let-7e-5p,miR-146a-5p,miR-130a-3p, miR-151a-3p mimics or negative controls, respectively, and RNA was extracted. This RNA was then used for hybridization on Affymetrix microarrays.

first: Mayumi

last: Ueta


title: Next Generation Sequencing of Transcriptomes from Murine Articular Chondrocytes Treated with IL-1𝝱 [Bulk RNA-seq]

city: St Louis

first: Jie

last: Shen

state: MO

address: 425 S. Euclid Ave

country: USA

institute: Washington University in St Louis

summary: Murine articular chondrocytes were isolated as previously described (Gosset et al., 2008) with modifications. Briefly, articular cartilages were dissected from femoral heads of 3-week-old wild-type C57/BL6J mice and digested for 4-6 hours in 0.5 mg/mL collagenase P (Roche, # 11249002001) in high-glucose DMEM (Thermo Fisher Scientific, #10569010) supplemented with 1% penicillin/streptomycin. Following digestion, cells were collected and seeded at a density of 50 x 104 cells/well in 12-well plates. The next day, cells were treated with IL-1𝝱 (1 ng/mL) (R&D Systems, #201-LB-005) for 24 hours.  Total RNA were then extracted from cell cultures and assayed for RNA sequencing.

overall_design: mRNA profiles of murine articular chondrocyte treated with IL-1𝝱


title: Expression data from  SQ-diEG treated B16F10 cells

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary:
Global gene expression profiling reveals a potential anti-melanoma effect of SQ-diEG in B16F10 cells. Squalene (SQ) was considered as a promising natural agent in anti-cancer treatment due to its strong antioxidant and anti-inflammatory activity; however, its pharmacological value has been largely underestimated because of its poor solubility and bioavailability. To adress this problem, a novel amphiphilic SQ derivative which bearing ethylene glycol oligomers was synthesized and was used as a permeation enhancer in this study to check its potential effect on anti-melanoma using B16F10 cells
B16F10 were murine melanoma cells line, treated with 2.5 µM and 40 µM with all samples for 48 h. Microarray gene expression profiling was conducted for two biological replicates

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). The mouse genome array strips were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Next Generation Sequencing of Transcriptomic microRNAs from Murine Articular Chondrocytes Treated with IL-1𝝱 [microRNA-seq]

summary: Murine articular chondrocytes were isolated as previously described (Gosset et al., 2008) with modifications. Briefly, articular cartilages were dissected from femoral heads of 3-week-old wild-type C57/BL6J mice and digested for 4-6 hours in 0.5 mg/mL collagenase P (Roche, # 11249002001) in high-glucose DMEM (Thermo Fisher Scientific, #10569010) supplemented with 1% penicillin/streptomycin. Following digestion, cells were collected and seeded at a density of 50 x 104 cells/well in 12-well plates. The next day, cells were treated with IL-1𝝱 (1 ng/mL) (R&D Systems, #201-LB-005) for 24 hours. Total RNA were then extracted from cell cultures and assayed for microRNA sequencing.

overall_design: microRNA profiles of murine articular chondrocyte treated with IL-1𝝱


title: Gene expression analysis of THP-1 cells (monocytic cell line) transfected with microRNA mimics: let-7d-5p, miR-27b-3p, miR-151a-5p.

summary:
In our previous study, hsa-let-7d-5p,hsa-miR-27b-3p,hsa-miR-151-5p were significantly upregulated in the plasma of atopic patients.
To study the each function of hsa-let-7d-5p,hsa-miR-27b-3p,hsa-miR-151-5p, which are significantly upregulated in the plasma of atopic patients, we performed mimic-transfected THP-1 cells, a mononuclear cell line, and performed comprehensive genetic analysis.

overall_design: THP-1 cells were transfected with let-7a-5p, miR-27b-3p, miR-151a-5p mimics or negative controls, respectively, and RNA was extracted. This RNA was then used for hybridization on Affymetrix microarrays.


title: Integrated Whole Transcriptome Profiling and Bioinformatics Analysis for researching lychee downy blight

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

overall_design: Refer to individual Series


title: High-throughput Identification of Novel Heat Tolerance Genes via Genome-wide Pooled Mutant Screens in the Model Green Alga Chlamydomonas reinhardtii

city: St. Louis

first: Ru

last: Zhang

state: Missouri

address: 95 N Warson Rd

institute: Donald Danforth Plant Science Center

summary: Different high temperatures adversely affect crop and algal yields with various responses in photosynthetic cells. The list of genes required for thermotolerance remains elusive. Additionally, it is unclear how carbon source availability affects heat responses in plants and algae. We utilized the insertional, indexed, genome-saturating mutant library of the unicellular, eukaryotic green alga Chlamydomonas reinhardtii to perform genome-wide, quantitative, pooled screens under moderate (35oC) or acute (40oC) high temperatures with or without organic carbon sources. We identified heat-sensitive mutants based on quantitative growth rates and identified putative heat tolerance genes (HTGs). By triangulating HTGs with heat-induced transcripts or proteins in wildtype cultures and MapMan functional annotations, we present a high/medium-confidence list of 933 Chlamydomonas genes with putative roles in heat tolerance. Triangulated HTGs include those with known thermotolerance roles and novel genes with little or no functional annotation. About 50% of these high-confidence HTGs in Chlamydomonas have orthologs in green lineage organisms, including crop species. Arabidopsis thaliana mutants deficient in the ortholog of a high-confidence Chlamydomonas HTG were also heat sensitive. This work expands our knowledge of heat responses in photosynthetic cells and provides engineering targets to improve thermotolerance in algae and crops.

overall_design: Pairwise genome-wide pooled mutant screens of Chlamydomonas reinhardtii comparing moderate (35oC) or acute (40oC) high temperature treated samples to control (25oC) in acetate-rich (TAP) or acetate-replete (TP) conditions

first: Erin

middle: M

last: Mattoon

first: William

middle: E

last: McHargue

first: Catherine

last: Bailey

first: Ningning

first: Chen

last: Chen

first: James

last: Eckhardt

first: Chris

middle: G

last: Daum

first: Matt

last: Zane

first: Christa

last: Pennachio

first: Jeremy

last: Schmutz

first: Ronan

middle: C

last: O'Malley

first: Jianlin

last: Cheng


title: Transcriptome sequencing (RNA-Seq) of liver tissues from LXRα-/- mices and wild type mices fed with a chow diet or a high fat diet (HFD).

first: Lan

last: Tang

state: Guangdong

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

institute: Southern Medical University

summary: Liver X receptor α (LXRα） is a key regulator of lipid homeostasis and effective inhibitors of inflammation. We used the second-generation transcriptome sequencing(RNA-seq) to determine the expression changes of each gene in  LXRα-/- mices and wild type mices fed with a chow diet or a high fat diet (HFD).We investigated  the downstream molecular mechanisms by which loss of LXRα regulates lipid synthesis and metabolism in HFD.

overall_design: mRNA profiles were obtained from mice livers which were divided into 4 group: WT Chow, LXRα-/- Chow, WT HFD and LXRα-/- HFD.

first: Yulian


title: Ablation of CaMKIIδ oxidation by CRISPR-Cas9 base editing as a therapeutic approach for cardiac disease

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary:
To develop a new therapeutic strategy for cardiac ischemia/reperfusion injury, we ablated the oxidative activation site of CaMKIIδ in the heart using CRISPR-Cas9 adenine base editing technology.
Adult C57Bl6 mice were subjected to control surgery (IR-Sham, 3 biological replicates) or ischemia/reperfusion injury with either no injection (IR, 3 biological replicates), injection of a control virus (IR-Virus control, 3 biological replicates) or injection of a functional CaMKIIδ editing system (IR-Edit, 4 biological replicates).
Five weeks after the surgery, hearts were harvested for RNA isolation and subsequent bulk RNA sequencing and gene expression profiling analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for IR-Sham, IR, IR-Virus control, and IR-Edit.

first: Simon

last: Lebek

first: Francesco

last: Chemello

first: Xurde

last: Caravia

first: Wei

last: Tan

first: Hui

last: Li

first: Kenian

first: Lin

last: Xu

first: Ning

last: Liu

first: Rhonda

last: Bassel-Duby

first: Eric

middle: N

last: Olson


title: Identification of the Regulatory Roles of LncPLAAT3-AS in Porcine Adipocyte Differentiation and Lipogenesis

city: Chengdu

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

summary:
To investigate the role of lncPLAAT3-AS in adipocyte differentiation, we overexpressed and inhibited lncPLAAT3-AS in primary adipocytes from pigs.
We then performed gene expression profiling using data obtained from RNA-seq of a total of three different cells in two different treatments and a blank control.

overall_design: Three groups of samples, LncPLAAT3-AS overexpression group, LncPLAAT3-AS inhibition group and blank control group, three biological replicates per group

first: Zhiming

last: Wang

first: Jin

last: Chai

first: Yuhao

first: Yiren

last: Gu

first: Keren

last: Long

first: Mingzhou

first: Long

last: Jin


title: Cpeb1b-mediated cytoplasmic polyadenylation of shha mRNA modulates zebrafish definitive hematopoiesis

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: During vertebrate embryogenesis, hematopoietic stem and progenitor cell (HSPC) production through endothelial-to-hematopoietic transition requires suitable developmental signals, but how these signals are accurately regulated remains incompletely understood. Cytoplasmic polyadenylation, which is one of the posttranscriptional regulations, plays a crucial role in RNA metabolism. Here, we report that Cpeb1b-mediated cytoplasmic polyadenylation is important for HSPC specification by translational control of Hedgehog (Hh) signaling during zebrafish early development. Cpeb1b is highly expressed in notochord and its deficiency results in defective HSPC production. Mechanistically, Cpeb1b regulates hemogenic endothelium specification by the Hedgehog–Vegf–Notch axis. We demonstrate that the cytoplasmic polyadenylation element motif-dependent interaction between Cpeb1b and shha messenger RNA (mRNA) in the liquid-like condensates, which are induced by Pabpc1b phase separation, is required for cytoplasmic polyadenylation of shha mRNA. Intriguingly, the cytoplasmic polyadenylation regulates translation but not stability of shha mRNA, which further enhances the Shha protein level and Hh signal transduction. Taken together, our findings uncover the role of Cpeb1b-mediated cytoplasmic polyadenylation in HSPC development and provide insights into how posttranscriptional regulation can direct developmental signals with high fidelity to translate them into cell fate transition.


title: Effect of formate on LN229 cells

city: Esch-sur-Alzette

first: Rashi

last: Halder

address: 7, Avenue des Hauts-Fourneaux

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine

summary: We observed that high extracellular formate concentrations promote the in vitro invasiveness of glioblastoma (GBM) cells. To identify mechanistically, how formates promotes invasion we chose an unbiased approach of RNAseq.

overall_design: LN229 cells were treated for 8h or 24h with 500 uM Formate before RNA extraction.

first: Catherine

last: Delbrouck

first: Johannes

last: Meiser


title: CPEB4-mediated translational regulation in ex vivo activated CD8 Tcells [RIP-seq]

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: Here we show that CPEB4 preferably binds targets related to UPR and anaolic pathways in activated CD8 T cells

overall_design: RNA-immunoprecipitation sequencing of CPEB4-associated mRNAs in Wild type and CPEB4-KO activated CD8 T cells

first: Marcos

last: Fernández-Alfara

first: Raul

last: Mendez


title: CPEB4-mediated translational regulation in ex vivo activated CD8 Tcells [RNA-seq]

summary: Here we show the transcriptomic profile of resting and activated CD8 wild-type and KO for CPEB4

overall_design: RNA-seq in wild-type and CPEB4 KO CD8 T cells resting or activated ex vivo for 48h with CD3/CD28/IL2


title: CPEB4-mediated translational regulation in ex vivo activated CD8 Tcells


title: Dormant leukemia stem cells reinforced by chemotherapy drive early treatment failure in acute myeloid leukemia patients [scRNA_PT]

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

summary: Acute myeloid leukemia is characterized by a minor fraction of primitive leukemia stem cells (LSCs) that sustain disease propagation and may be at the origin of late relapse. Yet, LSC contribution to early therapy resistance and AML regeneration remains controversial. We prospectively identified LSCs in NPM1-mutated AML patients and xenografts by means of a microRNA-126 reporter and single cell RNA sequencing, precisely discriminating LSCs from regenerating hematopoiesis, and assessed their longitudinal response to chemotherapy. We here show that chemotherapy resulted in distinct outcomes within AML subpopulations: while the bulk leukemia proliferated and differentiated with expression of oxidative-phosphorylation signatures, persisting miR-126high LSCs enforced protective stemness and dormancy features, along with a generalized inflammatory and senescence-associated response. miR-126high LSCs were enriched at diagnosis in patients with chemotherapy-refractory AML. We derived a novel miR-126high LSC transcriptional signature, which robustly stratified patients for overall survival in large AML cohorts, shining the spotlight on LSCs as determinants of early therapy resistance.

overall_design: We undertook an extensive transcriptional characterization of diagnosis and matched early after treatment acute myeloid leukemia  blasts through bulk RNA sequencing of xenograft LSC enriched (GFPlow/miR-126high) and LSC depleted (GFPhigh/miR-126low) blast subpopulations coupled with unbiased single cell RNA sequencing of xenograft and patient samples. Longitudinal BM or PB samples for each patient were FACS sorted to purity for the population of interest and loaded on 10x genomics 3' GEX chip.

last: Naldini

first: Gabriele

last: Casirati

first: Ivan

last: Merelli

first: Bernhard

last: Gentner


title: Dormant leukemia stem cells reinforced by chemotherapy drive early treatment failure in acute myeloid leukemia patients [bulkRNA]

overall_design: We undertook an extensive transcriptional characterization of diagnosis and matched early after treatment acute myeloid leukemia  blasts through bulk RNA sequencing of xenograft LSC enriched (GFPlow/miR-126high) and LSC depleted (GFPhigh/miR-126low) blast subpopulations coupled with unbiased single cell RNA sequencing of xenograft and patient samples. Xenograft AML (n=4 AML, 5-12 mice each) from control or treated mice  were sorted for the top and bottom 20% GFP expressing blast subpopulations. GFPlow/miR-126high and GFPhigh/miR-126low blasts from each mouse were then processed for RNA extraction with the miRNEasy Micro Kit (Qiagen) and library production (SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA)) and sequenced on Illumina platforms.


title: CUT&Tag analysis of H3K36me3 and H3K27me3, in Setd2-WT and -KO murine PDAC cell line

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To gain mechanistic insight into how Setd2 loss promotes activation of AKT signaling, we performed CUT&Tag sequencing in PDAC cells (KPC1199) with Setd2-KO and Setd2-WT). Setd2-WT and -KO murine PDAC cells were cultured and freshly collected as soon as possible. Hyperactive pA-Tn5 Transposase for CUT&Tag kit from Vazyme (TD901), and antibodies against H3K36me3 and H3K27me3 were employed. Trueprep index kit v2 and v3 for illumina were used to establish DNA library.

overall_design: For library preparation, murine PDAC cell lines with Setd2-WT and -KO were first established. CUT&Tag and DNA library were prepared according to manufacturer’s instructions.

first: Niu

last: Ningning

first: Xue

last: Jing


title: Single-cell transcriptomic changes in sepsis patient

status: Public on Feb 05 2023

city: WuHan

first: Tang

last: ZhaoHui

state: HuBei

address: Qiaokou No.1095, Jiefang Avenue

department: Department of Emergency, Division of Surgical Critical Care

institute: TongJi hospital

summary: Sepsis is a syndromic response to infection and is frequently a final common pathway to death from many infectious diseases worldwide. The global burden of sepsis is difficult to ascertain, although a recent scientific publication estimated that there were 48.9 million cases and 11 million sepsis-related deaths worldwide, which accounted for almost 20% of all global deaths. Here we analyzed the whole blood transcriptome of 5 healthy controls and 5 patients with confirmed sepsis from the Department of Emergency, Division of Surgical critical care, Tongji Trauma Center, Tongji Hospital, Tongji Medical College. This research aims to understand the expression of immune cells in sepsis patients and to construct an immune cell landscape of sepsis.

overall_design:
To identify patients meeting sepsis-3 criteria, patients had to have met the following criteria within 6 hours of arrival at the emergency department:
1) Evidence of suspected infection which is identified as the combination of administration of antibiotics (oral or parenteral) and a body fluid culture specimen obtained.
2) Presence of organ dysfunction which is identified as a Sequential Organ Failure Assessment (SOFA) score of 2 or higher.
3) No blood transfusion and no hormonal therapy prior to specimen collection.
Each sample represents mixed sample of healthy controls and patients with confirmed sepsis.

first: ZhaoHui

last: Tang

first: TeDing

last: Chang

first: Shunyao

last: Chen

first: Hai

last: Deng

first: Deng

first: JiaLiu

last: Luo

first: Cong

last: Zhang

first: ZhenWen

last: Li

first: Han

last: Wu

first: TingXuan

first: LiMing

last: Dong


title: Dormant leukemia stem cells reinforced by chemotherapy drive early treatment failure in acute myeloid leukemia patients [scRNA_PDX]

first: Matteo

last: Barcella

overall_design: We undertook an extensive transcriptional characterization of diagnosis and matched early after treatment acute myeloid leukemia  blasts through bulk RNA sequencing of xenograft LSC enriched (GFPlow/miR-126high) and LSC depleted (GFPhigh/miR-126low) blast subpopulations coupled with unbiased single cell RNA sequencing of xenograft and patient samples. Xenograft AML (n=4) from control or treated mice (2 replicates each encompassing 5-7 mice each stained with surface Hashtag antibodies - biolegend TotalSeq B chemistry -) were loaded on 10x genomics 3' Gene expression chips and libraries produced with the corresponding kit following manufacturer's instructions. Representative xenografts were sorted for the bottom 20% GFP expressing AML blast population which was marked with an indipendent hashtag and pooled with the corresponding Live human AML blasts for chip loading and library prepration.

last: Naldini

first: Gabriele

first: Ivan


title: Comparison of STAMP and TRIBE for identifying the targets of RNA-binding proteins in human and Drosophila cells [human]

city: Waltham

first: Katharine

last: Abruzzi

state: MA

address: 415 South St.

department: Biology

institute: HHMI; Brandeis University

summary: RNA binding proteins (RBPs) perform a myriad of functions and are implicated in numerous neurological diseases. To identify the targets of RBPs in small numbers of cells, we developed TRIBE, in which the catalytic domain of the RNA editing enzyme ADAR (ADARcd) is fused to a RBP. In STAMP, the ADARcd is replaced by the RNA editing enzyme Apobec (REF). Here we compared the two enzymes fused to the RBP TDP43 in human cells. Although they both identified TDP43 target mRNAs, combining the two methods more successfully identified high confidence targets. We also assayed the two enzymes in Drosophila cells in which RBP-Apobec fusions generated only low numbers of editing sites comparable to the level of control editing. This was true for two different RBPs, Hrp48 and Thor (Drosophila EIF4E-BP), and contrasted with successful RBP-ADARcd fusions. The results indicate that TRIBE is the method of choice in Drosophila.

overall_design: Comparing TRIBE and STAMP in HEK-293 cells and Drosophila S2 cells.  2 biological replicates for each experiment.  Smartseq2 sequencing libraries from cell lines used to identify TRIBE and STAMP induced editing sites.

first: Corrie

last: Ratner

first: Michael

last: Rosbash


title: Comparison of STAMP and TRIBE for identifying the targets of RNA-binding proteins in human and Drosophila cells [Drosophila]


title: Identify VDR targets within the proximal and distal intestine using a genome-wide method.

city: Piscataway

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: The object of this aim is to understand the mechanism by which vitamin D mediates calcium absorption. Our working hypothesis is that VDR has distinct sets of binding sites: proximal versus distal intestine. Thus, to accomplish the goals, we will 1) determine whether 1,25(OH)2D3/VDR regulates specific target genes in proximal and distal intestine, 2) identify the locations of genomic binding sites for VDR in proximal and distal intestine.

overall_design: Mouse data comprising RNA-Seq from 24 samples was obtained: 8 samples from the colon (4 vitamin D treated replicates, 4 vitamin D-deficient replicates), 8 samples from the duodenum (4 vitamin D treated replicates, 4 vitamin D-deficient replicates), and 8 samples from the ileum (4 vitamin D treated replicates , 4 vitamin D-deficient replicates).

first: Puneet

last: Dhawan

first: Rohit

last: Aita

first: Shanshan

first: Sylvia

last: Christakos


title: Transcriptome, Small RNA, and Degradome Sequencing Reveals the Roles of MicroRNAs in Response to High Night Temperature Stress at the Filling Stage of Rice (degradome)

status: Public on Feb 04 2023

city: nanchang

first: zhao

middle: hai

last: wang

state: jaingxi

address: zhimin dadao 1101

institute: jiangxi agricultural university

summary: we utilized microRNA sequencing to identify differentially expressed miRNAs in rice heat-tolerant line and heat-sensitive line under high night temperature stress .

overall_design: the treatment and control of the heat-sensitive and -tolerant lines of near-isogenic lines with significant differences in heat tolerance at filling stage

first: Jiangmin

last: Fan

first: Hongyu

first: Yan

last: Shi

first: Yuewu

first: Yuxiang

last: He

first: Qiang

last: Wang

first: Siyi

last: Liu

first: Youmin

last: Yao

first: Jianglin

last: Liao

first: Yingjin

last: Huang

first: Zhaohai


title: Subgenome-dominant expression and alternative splicing in response to pathogen stress in polyploid Brassica napus and progenitors

city: Vancouver

first: Keith

middle: L.

last: Adams

state: BC

address: 3156-6270 University Blvd.

department: Botany

country: Canada

institute: The University of British Columbia

summary: Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both natural and resynthesized lines of polyploid Brassica napus, along with the progenitors B. rapa and B. oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-seq analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12,709 DAS events) and lower in resynthesized Brassica napus (8,863 DAS events). Natural B. napus had more up-regulated events and fewer down-regulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus specifically, this resulted a disproportionate C subgenome contribution to pathogen defense response,  characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in natural and resynthesized B. napus, and indicate that abiotic stress can influence the evolution of homeologous genes in polyploids.

sample_organism:
Brassica napus
Brassica rapa
Brassica oleracea

overall_design: Comparative gene expression profiling and alternative splicing analyses in Sclerotinium sclerotiorum-infected and control mock-infected leaves of Brassica napus (natural and resynthesized polyploids) and progenitors Brassica rapa and Brassica oleracea.

first: Grant

last: de Jong

middle: L


title: Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [RNA-Seq]

city: washington dc

first: Shaoqi

last: Zhu

state: District of Columbia

address: 725 21st st nw

institute: The George Washington University

summary: CTCF is known to mediate long range chromatin intearction and 3D genome organization. In CD8+ T cells responding to actue infection, CTCF is redistributed to induce the the cytotoxic program while using its insulation function to suppresss memory precursor fate.

overall_design: Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Ctcf wild-type or floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4  post infection, P14 cells were sort purified and used for RNAseq analysis.

first: Hai-Hui

last: Xue

first: Weiqun

last: Peng


title: Transcriptomics analysis of heart, kidney, and liver tissues from 58 Collaborative Cross strains

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: We report transcriptomic profiling from bulk heart, kidney, and liver tissues for 58 strains of the inbred mouse Collaborative Cross (CC). Each strain is represented by a male/female pair. Reads were first aligned to the pooled transcriptomes of the eight founder strains of the CC and then total gene counts were quantified using the EMASE and GBRS software tools. Total read counts can be further normalized for use in differential gene expression analysis, expression quantitative trait locus (eQTL) analysis, and integrative analyses with other -omic data sets measured on the same samples, including proteomics and phosphoproteomics.

overall_design: RNA profiling of heart, kidney, and liver bulk tissues of male/female pairs from 58 Collaborative Cross (CC) mouse strains

first: Gregory

middle: R

last: Keele

first: Tian

last: Zhang

first: Steven

last: Munger

first: Fernando

last: Pardo-Manuel de Villena

first: Martin

last: Ferris

first: Joao

middle: A

last: Paulo

last: Gygi

first: Gary

last: Churchill


title: Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [Cut & Run]

overall_design: Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Ctcf wild-type or floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4 or day 8 post infection, P14 cells were sort purified and used for CTCF CUT&RUN analysis in live cells along with naive cells.


title: Analysis of the transcriptome, proteome, histological, and biochemical profiles of oriental river prawn Macrobrachium nipponense under long-term salinity exposure

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

summary: the transcriptome changes in long-term different salinity gradients were determined to investigate the related gene responsible for the molecular involvements to M. nipponense after long-term salinity exposure.

overall_design: The gills, hepatopancreas and muscle of 30 M. nipponense were used for transcriptome analysis underlying the long term salinity exposure

first: Yaoran

last: Fan

first: Xiao

last: Wu

first: Jianbin

last: Feng

first: Jiale

last: Li


title: Transcriptome, Small RNA, and Degradome Sequencing Reveals the Roles of MicroRNAs in Response to High Night Temperature Stress at the Filling Stage of Rice

first: zhao

last: wang

first: Jiangmin

first: Hongyu

first: Yan

last: Shi

first: Yuewu

first: Yuxiang

last: He

first: Qiang

last: Wang

first: Siyi

last: Liu

first: Youmin

last: Yao

first: Jianglin

last: Liao

first: Yingjin

last: Huang

first: Zhaohai


title: RNA sequencing of blood from sex- and age-matched discordant siblings supports immune and transcriptional dysregulation in Autism Spectrum Disorder.

city: Milan

first: Pasquale

last: Tomaiuolo

state: Milan

address: via Balzaretti n.9

department: Department of Pharmacologic Sciences

institute: University of Milan

summary:
The present study uses an intra-familial design, matching affected and unaffected sibling pairs by sex and age and controlling for pharmacological treatment in the autistic sibling.
The aim of this study is to find ASD blood biomarkers possibly applicable within “high risk” families, where one child has already received an ASD diagnosis.

overall_design: We conducted RNA sequencing (RNA-Seq) in a sample of ASD unaffected siblings (SIB) matched by sex and age

first: Ignazio

middle: S

last: Piras

first: Simona

last: Baghai Sain

first: Chiara

last: Picinelli

first: Marco

last: Baccarin

first: Paola

last: Castronovo

middle: J

last: Morelli

first: Dejan

last: Lazarevic

first: Maria

last: Scattoni

first: Giovanni

last: Tonon

first: Antonio

last: Persico


title: RNA-seq Analysis on the Renal Tissue Injury in the Development of Goslings Gout

city: Nanjing

first: Yumeng

last: Xi

address: 50 Zhongling Street

institute: Jiangsu Academy of Agricultural Sciences

summary: The transcription expressions of gout goslings in renal tissues was significantly different from that of healthy goslings. With P <0.05 and |log2(fold change)| >1 as the selection standards, 1749 differential expression genes were found. Among these, 501 genes were up-regulated and 1248 genes were down-regulated in the gout group. The gene ontology (GO) search revealed many significant terms, including chemokine activity, T cell receptor binding, antigen binding, immune response, G-protein coupled receptor signaling pathway, chemokine-mediated signaling pathway, inflammatory response and so on. The Kyoto Encyclopedia of Genes and Genomes (KEGG) selected the cytokine-cytokine receptor interaction, intestinal immune network for IgA production, cell adhesion molecules. In conclusion, the kidney injuries in gout goslings is closely related to immune response, inflammatory response and cell adhesion processes.

overall_design: We used RNA-seq to measure the transcription differences in renal tissues between gout and healthy goslings during their disease period. Five goslings with typical visceral gout characteristics and serum manifestations were selected as “gout group”, and six healthy goslings were also selected as the “control group”. RNA-seq was used to test the transcription differences in renal tissues between gout and control groups.

first: YuMeng

first: ZhenDan

last: Shi


title: genes deregulated by LMP2A in nasopharyngeal cancer

city: Kuala Lumpur

first: Lu Ping

last: Tan

address: Jalan Pahang

department: Molecular Pathology Unit

country: Malaysia

institute: Institute for Medical Research

summary: Our data shows that LMP2A promotes a more aggressive tumor phenotype. To evaluate the gene expression deregulated by LMP2A, RNA from the LMP2A cells and xenografted tumors were subjected to gene expression array.

overall_design: RNA from LMP2A overexpressed cells and negative control were isolated for gene expression array. The same RNA samples were also used for miRNA microarray.

first: L

first: S

middle: H

last: Chew

first: T

last: Chu

first: Ashikin

last: Nurul

first: Syazwani

last: Nur

last: Hoe

first: A

last: Munirah

last: Khoo


title: Impact of chronic low dose dioxin exposure during pregnancy on the mouse pancreas from both dams and their male and female offspring

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: Purpose: to determine whether exposure to chronic low dose dioxin impacts pancreas physiology during pregnancy (dams) and/or pancreas development (offspring)

overall_design: Female C57Bl/6 mice were injected s.c. 2x/week with either corn oil (control) or 20 ng/kg/d TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) starting prior to mating and continuing throughout pregnancy until birth. Whole pancreas tissue was extracted from both dams and their offspring on the day of birth. One male and one female pup was used from each litter.

first: Jennifer

last: Bruin


title: LMP2A promotes aggressive nasopharyngeal carcinoma tumor growth

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

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

overall_design: Refer to individual Series


title: Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [ATAC-Seq]

first: Shaoqi

last: Zhu

overall_design: Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Ctcf wild-type or floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4 post infection, P14 cells were sort purified and used for ATAC-seq analysis along with naive cells.

first: Hai-Hui

last: Xue

first: Weiqun

last: Peng


title: miRNAs deregulated by LMP2A in nasopharyngeal cancer

summary: Our data shows that LMP2A promotes a more aggressive tumor phenotype. To evaluate the miRNAs deregulated by LMP2A, RNA from the LMP2A cells and xenografted tumors were subjected to miRNA microarray.

overall_design: LMP2A overexpressed cells and negative control were isolated for miRNA microarray. The same RNA samples were also used for gene expression array.


title: NPC stem-like cells


title: NPC stem-like cells [Agilent]

summary: Stem-like cells of nasopharyngeal cancer were enriched by 3 different methods: 1) Side population (SP) assay, 2) LMP2A over-expression and 3) spheroid culture. SP cells and LMP2A over-expressed cells were inoculated into immunocompromised mice for xenograft tumors. Transcriptomes of all 5 of these in vitro and in vivo generated NPC stem-like cells were then analyzed and compared to their counterparts by microarray. All samples were analyzed in the Agilent platform except the SP cells and their counterpart (analyzed in the Affymetrix platform).

overall_design: Two to three RNA sample replicates were prepared from each type of the NPC stem-like cells and their counterpart. Dye swap was performed to avoid bias. Each Agilent array was loaded with equal amount of 2 differentially labeled c-RNAs for hybridization. After conversion of scanned microarray images into signal intensities and dye differences corrected in Feature extraction, all analysis was performed in the single color analysis module in GeneSpring.

first: SL

first: R

last: Fazlyn

middle: K

last: Ahmad

first: AM

first: AS

middle: B


title: NPC stem-like cells [Affymetrix]

overall_design: Three RNA sample replicates were prepared from each type of the NPC stem-like cells and their counterpart.


title: SIRT6 is a key regulator of mitochondrial function in the brain

status: Public on Feb 03 2023

city: Beersheba

first: Dmitrii

middle: Nikolaevich

last: Smirnov

address: David Ben Gurion Blvd 1

department: Department of Life Sciences

country: Israel

institute: Ben-Gurion University of the Negev

summary: The SIRT6 deacetylase has been implicated in DNA repair, telomere maintenance, glucose and lipid metabolism and, importantly, it has critical roles in the brain ranging from its development to neurodegeneration. Here, we combined transcriptomics and metabolomics approaches to characterize the functions of SIRT6 in mouse brains. Unexpectedly, our analysis reveals that SIRT6 is a central regulator of mitochondrial activity in the brain. SIRT6 deficiency in the brain leads to mitochondrial deficiency with a global downregulation of mitochondria-related genes and pronounced changes in metabolite content. We suggest that SIRT6 affects mitochondrial functions through its interaction with the transcription factor YY1 that, together, regulate mitochondrial gene expression. Moreover, SIRT6 target genes include SIRT3 and SIRT4, which are significantly downregulated in SIRT6-deficient brains. Our results demonstrate that the lack of SIRT6 leads to decreased mitochondrial gene expression and metabolomic changes of TCA cycle byproducts, including increased ROS production, reduced mitochondrial number, and impaired membrane potential that can be partially rescued by restoring SIRT3 and 4 levels. Importantly, the changes we observed in SIRT6 deficient brains are also occurring in aging human brains and particularly in patients with Alzheimer's, Parkinson's, Huntington's, and Amyotrophic lateral sclerosis disease. Overall, our results suggest that the reduced levels of SIRT6 in the aging brain and neurodegeneration initiate mitochondrial dysfunction by altering gene expression, ROS production and mitochondrial decay.

overall_design: We performed comparative transcriptomic analysis of 4 WT and 4 brain-specific SIRT6-KO mouse brain profiles.

first: Ekaterina

last: Eremenko

first: Daniel

last: Stein

first: Shai

last: Kaluski

first: Weronika

last: Jasinska

first: Claudia

last: Consetino

first: Barbara

last: Martinez-Pastor

first: Yariv

last: Brotman

first: Raul

last: Mostoslavsky

first: Debra

last: Toiber

last: Khrameeva


title: High-throughput discovery and characterization of viral transcriptional effectors in human cells

city: Stanford

first: Connor

middle: Hayakawa

last: Ludwig

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

summary: Viruses encode transcriptional regulatory proteins critical for controlling viral and host gene expression. Given their multifunctional nature and high sequence divergence, it is unclear which viral proteins can affect transcription and which specific sequences contribute to this function. Using a high-throughput assay, we measured the transcriptional regulatory potential of over 60,000 protein tiles across ~1,500 proteins from 11 coronaviruses and all nine human herpesviruses. We discovered hundreds of new transcriptional effector domains, including a conserved repression domain in all coronavirus Spike homologs, dual activation-repression domains in VIRFs, and an activation domain in six herpesvirus homologs of the single-stranded DNA-binding protein that we show is important for viral replication and late gene expression in KSHV. For the effector domains we identified, we investigated their mechanisms via high-throughput sequence and chemical perturbations, pinpointing sequence motifs essential for function. This work massively expands viral protein annotations, serving as a springboard for studying their biological and health implications and providing new candidates for compact gene regulation tools.

overall_design: RNA-seq for 13 different K562 cell lines that can each inducibly express a different full-length viral protein (or mCitrine as a negative control) upon doxycycline treatment, with two replicates per cell line. Some samples are also treated with interferon (IFN) beta to investigate how viral protein expression affects type I IFN signaling.

first: Abby

last: Thurm

first: Lacramioara

last: Bintu


title: Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs

first: Shaoqi

last: Zhu


title: PA-seq of retinoblastoma and retina

city: shanghai

first: xiaomeng

last: cheng

state: Shanghai

address: Jiangwan Campus of Fudan University, 2205 Songhu Road, Yangpu District, Shanghai, China

institute: Fudan University

summary: To obtain a global view of APA during the development of retinoblastoma, we subjected total RNAs from five retina sample and five retinoblastoma samples to PA-seq, which precisely identify poly(A) sites at the genome scale.

overall_design: Examination of dynamics of alternative polyadenylation in retinoblastoma (RB) patients.Five retina samples and five retinoblastoma samples were subjected to PA-seq.The RNA-seq data of corresponding samples from PRJNA752257.

first: Zhaozhao

last: Zhao

first: Ting

last: Ni


title: Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress [RNA-seq]

city: Safed

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

institute: Bar-Ilan University

summary: To determine how constitutively active autophagy in Becn1F121A mice affects the colonic tissue, we performed a transcriptional analysis.

overall_design: Distal colon secretions from naïve 8-week-old mice were collected and RNA extracted.


title: Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress [16S]

summary: To determine how constitutively active autophagy in Becn1F121A mice affects the fecal microbiota, we performed a 16s analysis.

sample_organism:
synthetic construct
mouse gut metagenome

overall_design: Fecal pelletes from WT and Becn1F121A mice were collected and bacteria DNA extracted.

first: Bel

last: Shai


title: Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress super

sample_organism:
Mus musculus
synthetic construct
mouse gut metagenome


title: Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [CUT&Run 2]

state: WASHINGTON

institute: the george washington university

overall_design: Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Tbet/Runx3 wild-type or double floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4 post infection, P14 cells were sort purified and used for CTCF CUT&RUN analysis in live cells. As negative controls, IgG CUT&RUN was perfomed on CTCF-deficient naive CD8 T cells.

first: Hai-Hui

last: Xue

first: Weiqun

last: Peng


title: Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [Hi-C]

overall_design: Naive P14 TCR transgenic CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 8 post infection, KLRG1+IL-7Ra- P14 cells were sort purified as effector CD8 T cells and used for in situ HiC analysis.


title: Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [CUT&Run 3]

overall_design: Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Ctcf wild-type or floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4 post infection, P14 cells were sort purified and used for Tcf1 CUT&RUN analysis in fixed cells along with naive CD8 T cells as positive control.


title: Molecular characterisation of a mutant kras-driven zebrafish model of hepatocellular carcinoma

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: We used doxycycline (dox) treatment to generate a larval model of hepatocellular carcinoma (HCC)22. In this model, we induced the expression of a single EGFP-krasG12V transgene, denoted TO(krasG12V)T/+ in developing livers by treating with doxycycline between 2-7 days post-fertilisation (dpf). This led to the accumulation of a constitutively active, EGFP-tagged, potently oncogenic form of Kras specifically in hepatocytes, causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype (WT) livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox-treated TO(krasG12V)T/+ livers compared WT livers, and a further 6000+ genes were significantly downregulated. Of the upregulated genes, many were significantly enriched in KEGG pathways associated with highly proliferative cancers, including DNA replication, cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox-treated TO(krasG12V)T/+ versus WT livers and the differential gene expression data for the HCC (LIHC) and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox-treated TO(krasG12V)T/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox-treated TO(krasG12V)T/+ zebrafish provide an authentic model of human HCC.

overall_design: Paired-end RNA-sequencing data was generated for 8 samples of zebrafish liver. Of these samples, 3 are wild type (WT) and 5 are kras mutants. Differential analyses were performed, identifying differentially expressed genes between the kras mutant and wild type groups. Please note, all WT and 2 of the mutant samples are sequenced over 2 runs.

first: Joan

last: Heath

first: Karen

last: Doggett

first: Kimberly

last: Morgan


title: Chemical reprogramming of melanocytes to skeletal muscle cells

city: Beijing

first: Yaqi

last: Wang

state: Beijing

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: We identify a combination of small molecules to be able to transdifferentiate dermal cells  to muscle cells. To characterize the cellular diversity of the neonatal dermal we performed scRNA-seq on mononuclear cell suspensions obtained from the neonatal dermal. Following normalization and quality control of scRNA-seq data, we captured 40537 cells with an average of 5755 genes expressed per cell. We charted the entire course of skin-to-muscle chemical reprogramming by single cell RNA-sequencing to determine the source cells in CD73- cells from skin with the potential to be transdifferentiated to muscle cells .We found that melanocytes could be chemically reprogrammed to myogenic lineage cells.

overall_design: Single cell RNA profiles from neonatal CD73- dermal cells treated by small molecules

first: Ping

last: Hu

first: Wenjun

last: Yang

first: Cheng

last: Li


title: The role of MEF2A in iPSC-CMs maturation

first: Zhang

last: Jing

address: Nanjing University

institute: Nanjing University

summary: To understand the role of MEF2A in iPSC-CMs maturation, we used MEF2A-siRNA to reduce MEF2A transcription in iPSC-CMs and then examined the changes in transcription levels

overall_design: Gene expression profiles were obtained through RNA-sequencing of samples obtained from iPSC-CMs treated with scramble siRNA or si-MEF2A

first: Jing

last: Zhang

first: Jingping

first: Zhaohui

last: Ouyang


title: Chromatin landscape in perinatal cardiomyocytes

summary: In order to understand the transcriptional regulatory program of cardiomyocytes perinatal transition, we mapped chromatin accessibility, transcription-centered long-range chromatin interactions as well as gene expression in cardiomyocyte undergoing perinatal transition.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Gene expression profiles, chromatin accessibility genome-wide maps and chromatin interactions were obtained through RNA-sequencing, ATAC-sequencing and HiChIP sequencing of samples obtained from late fetal and neonatal cardiomyocytes.


title: Proteomics coupled transcriptomics reveals lipopolysaccharide inhibiting peroxisome proliferator-activated receptors signalling pathway to reduce lipid droplets accumulation in mouse liver

status: Public on Feb 02 2023

city: Chongqing

first: Qihuan

last: Fu

state: Chongqing

address: 181 Hanyu Road, Shapingba District

department: Chongqing University Cancer Hospital

institute: Chongqing University

summary: Lipid droplets (LDs) are multifunctional organelles consisting of a central compartment of non-polar lipids shielded from the cytoplasm by a phospholipid monolayer. The excessive accumulation of lipid droplets in cells is closely related to the development and progression of many diseases in humans and animals, such as liver-related and cardiovascular diseases. Thus, regulating the LDs size and abundance is necessary to maintain metabolic homeostasis. In this study, we found that LPS stimulation reduced the LDs content in the mouse liver. We tried to explain the possible molecular mechanisms at the broad protein and mRNA levels, finding that inhibition of the peroxisome proliferator-activated receptors (PPAR) signalling pathway by LPS may be a critical factor in reducing LDs content.

overall_design: Transcriptome sequencing analysis of livers from LPS-treated and untreated mice.

first: Haiying

last: Ran

first: Ying

last: Wan

first: Jiangbei

last: Yuan


title: Control of Th17 Cell Development Through Cooperative Transcriptional Activities of Class IIa HDAC4 and HDAC7

city: New York

first: Rajal

last: Sharma

state: NY

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

summary: Histone deacetylases (HDACs) are long recognized for important functions in regulating gene transcription in biology and diseases. However, unlike for ubiquitously expressed class I HDACs, we have little mechanistic understanding of class II HDACs that have postulated tissue specific functions. Here we report that class IIa Hdac4 and Hdac7 are up-regulated in transcription through IL-6-Stat3 signaling selectively in mouse T-helper 17 (Th17) cells during lineage-specific differentiation, but not in Th1, Th2, and Treg subtypes. Genetic knockout of Hdac4 or Hdac7 established their importance for Th17 differentiation with different functional mechanisms. Hdac4 works with Th17 transcription factors JunB-Irf4-Batf for transcriptional activation of Th17 signature genes Il17a/f, whereas Hdac7 acts distinctively in concert with Aiolos/Ncor1/Hdac3 co-repressor complex for transcriptional repression of Th17 negative regulators including Il2. Pharmacological inhibition or gene knockout of Hdac4 and Hdac7 ameliorates development of T-cell transfer induced colitis and experimental autoimmune encephalomyelitis (EAE) in mice through blockage of Th17 cell development in colon and central nervous system that recapitulate inflammatory bowel diseases and multiple sclerosis in humans, respectively. Our study highlights a previously unknown distinct mechanisms of Hdac4 and Hdac7 in transcriptional control of Th17 cell development, and rationalizes a new therapeutic strategy of targeting class IIa HDAC4/7 for the treatment of Th17-related inflammatory and autoimmune diseases.

overall_design: Murine Th17 cells were treated with TMP269 and collected for RNA-seq along with non-treatment controls. Genome-wide occupancy of Hdac proteins was assessed in Th17 cells using specific antibodies.

first: M

middle: M

last: Zhou


title: Adverse effects of SYP-3343 on zebrafish development via ROS-mediated mitochondrial dysfunction

first: Guoliang

last: Chen

address: No. 174, Shazheng Street

department: Bioengineering College

summary: As a newly-invented and highly-efficiency strobilurin fungicide, pyraoxystrobin (SYP-3343) has been recognized as a highly poisonous toxin for a variety of aquatic organisms. Nevertheless, the developmental toxicity and potential mechanism of SYP-3343 have not been well-documented. The results showed that SYP-3343 was relatively stable and maintained within the range of 20 % in 24 h, and the LC50 value to embryos at 72 hpf was 17.13 μg/L. The zebrafish embryotoxicity induced by 1, 2, 4, and 8 μg/L SYP-3343 is demonstrated by repressive embryo incubation, enhancive mortality rate, abnormal heart rate, malformed morphological characteristic, and impaired spontaneous coiling, indicating SYP-3343 mostly exerted its toxicity in a dose- and time-dependent manner. Besides SYP-3343 was critically involved in regulating cell cycle, mitochondrial membrane potential, and reactive oxygen species production as well as zebrafish primary cells apoptosis, which can be mitigated using antioxidant N-acetyl-L-cysteine. A significant change occurred in total protein content, the biochemical indices, and antioxidant capacities owing to SYP-3343 exposure. Additionally, SYP-3343 altered the mRNA levels of heart development-, mitochondrial function-, and apoptosis-related genes in zebrafish embryos. These results indicated that SYP-3343 induced apoptosis accompanying reactive oxygen species-initiated mitochondrial dysfunction in zebrafish embryos.

overall_design: Forty embryos exposed to control and 8 μg/L SYP-3343 from 3 hpf to 24 hpf were collected. Thereafter, the embryos were shock-frozen in liquid nitrogen and stored at − 80 ◦C. Twol replicates were performed for each group.

first: Mingxing

first: Panpan

last: Zhu

first: Guixue

first: Tingzhang


title: GZ21T inhibits the growth of actinic keratoses in a UVB induced model of skin carcinogenesis

city: Baltimore

first: Zachary

last: Bordeaux

state: MD

address: 206 1550 Orleans Street

department: Dermatology

institute: Johns Hopkins

summary: To investigate the mechanism behind GZ21T's ability to inhibit actinic keratoses growth in an ultra-violet B induced model of skin carcinogenisis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lesional, peri-lesional, non-lesional, and non-UV exposed skin of control and GZ21T treated SKH1 mice

first: Shawn

middle: G

last: Kwatra

first: Madan


title: Lifelong tissue memory relies on spatially organized dedicated progenitors located distally from the injury [ATAC-Seq]

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

institute: University of Turin

summary: It is believed epithelial cells that have participated in a wound repair elicit a more efficient but locally  restricted response to future injuries. However here we show that the cell adaptation resulting from a localised tissue damage has a wide spatial impact at a scale not previously noticed. We demonstrate that away from injured site, after a first injury a specific epithelial stem cell population gives rise to long term wound-memory progenitors residing in their own niche of origin. Notably these progenitors have not taken part in the first wound healing but become pre-activated through priming. This adaptation differs from classical features of trained immunity previously shown to be adopted by other epithelial stem cells. Our newly identified wound-distal memory cells display an intrinsic pre-activated state, maintained at chromatin and transcriptional level, leading to an enhanced wound repair ability that can be partially recapitulated through epigenetic perturbation even in absence of an injury. Importantly, the harmful consequences of wound repair, such as exacerbated tumorigenesis, occur within these primed cells and follow their spatial distribution. Overall, we show that sub-organ scale adaptation of an injury relies on spatially organized and memory-dedicated progenitors, characterized by a chromatin actionable cell state, that establishes an epigenetic field cancerization and predisposes to tumour onset.

overall_design: Lrig1 GL cells were  isolated  from tail epidermis from the indicated time point and/or treatment. Sca1+ cells were sorted to enrich for upper-HF cells and accessible chromatin regions were profiled using ATAC-seq, as described in Buenrostro et al., Nat Methods, 2013

first: Chiara

last: Levron

first: Mika

last: Watanabe

first: Valenitna

last: Proserpio

first: Gabriele

last: Piacenti

first: Stefan

last: Kaltenbach

first: Annalaura

last: Tamburrini

first: Takuma

last: Nohara

first: Francesca

last: Anselmi

first: Carlotta

last: Duval

first: Luca

last: Elettrico

first: Daniela

last: Donna

first: Laura

last: Conti

first: Denis

last: Baev

first: Ken

last: Natsuga

first: Tzachi

last: Hagai

first: Salvatore

last: Oliviero

first: Giacomo

last: Donati


title: Lifelong tissue memory relies on spatially organized dedicated progenitors located distally from the injury [bulkRNAseq]

first: Andrea

last: Lauria

overall_design: Lrig1 GL cells were isolated from tail epidermis at 8w pw1 from Distal memory or Ctrl region and FACS sorted to enrich for upper-HF cells (Sca1+). Cells were then plated and cultured for 1 week before  transcriptome was assessed by bulk RNA-Seq

first: Chiara

last: Levron


title: Differentiation of Peritubular Myoid-Like Cells from Human Induced Pluripotent Stem Cells

city: Vancouver

first: Ryan

last: Flannigan

address: 2660 Oak St, Vancouver, BC V6H 3Z6

institute: University of British Columbia

summary: Infertility affects approximately 15% of couples, and in couples where a male factor is present 15% of these males lack production of any sperm. In order to derive novel regenerative therapies, we must first have an improved understanding of the cell-type-specific function in normal and infertile human testes that regulate spermatogenesis must be achieved. This understanding requires the ability to isolate and functionally characterize each human testis cell type in isolation and in combination within the spermatogenic niche. Similar to other human organ systems, lack of availability to obtain biopsies with viable cells to subsequently, isolate and propagate specific cell types, has stifled human spermatogenesis research. Previous researchers have utilized engineering human induced pluripotent stem cells (hiPSCs) to generate various organ specific cell types for use as in vitro models. In the human testis, previous groups have derived Leydig cells, Sertoli cells, spermatogonial stem cells (SSCs), macrophages and endothelial cells via this method. However, peritubular myoid cells (PTMs)  which serve critical roles in human testis cytoarchitecture and spermatogenic regulation, remain to be  derived.  Therefore, this study set forth to generate hiPSC-derived PTMs to serve as a tool to model and study human PTM function and in vitro spermatogenic modelling by deriving the final missing somatic cell type ofin the human testis. PTMs and Leydig cells arise from a common progenitor, so it was hypothesized that PTMs could be derived by modifying an existing differentiation protocol for Leydig cell differentiation from hiPSCs. These hiPSC-derived cells, or hPTMs, were characterized and compared to hiPSC-derived Leydig cells (hLCs) and primary PTMs. Results show that the substitution of the molecular patterning factor Platelet-Derived Growth Factor Subunit B (PDGFBB) for Platelet-Derived Growth Factor Subunit A (PDGFAA) in a molecule-based differentiation protocol for deriving Leydig-like cells is sufficient to derive cells with peritubular myoid-like transcriptomes and smooth muscle protein expression in an hiPSC line primed for a mesoderm lineage. Results also indicate that maturation of differentiated PTMs between hiPSC lines is variable. Comparison of lineage affiliated gene expression suggests that hiPSC lines with gene expression reflecting a primed state for mesoderm lineage can more efficiently and consistently derive hPTM-like cells. Overall, these hPTMs will allow for in  vitro study of their phenotypes and functional role in spermatogenesis.

overall_design: We conducted RNAseq experiments on hiPSC-derived peritubular myoid cells. Two hiPSC lines were used: iPS11-10 (Cell Applications) and DL01 (WiCell). Both were differentiated into peritubular myoid cells, and undifferentiated hiPSCs from both were used as negative controls. As a postive control, primary peritubular myoid cells were isolated by magnetic activated sorting and expanded in vitro from testicular tissue obtained from a human patient ("PDGFRA"). In total 5 samples were analyzed: 11-10 hiPSCs, DL01 hiPSCs, 11-10  myoids, DL01 myoids, and PDGFRA+ primaries. Each was completed in technical triplicates.

first: Faraz

last: Hach

first: Meghan

last: Robinson

first: Anne

last: Haegert

first: Yen-yi

last: Li

first: Tunc

last: Morova


title: Single cell assessment of trophoblast stem cell and primary cytotrophoblast derived organoids as placenta models

first: Alexander

last: Beristain

address: 950 West 28th Ave

department: Obstetrics & Gynecology

institute: The University of British Columbia

summary: The establishment and function of the human placenta is dependent on specialized cells called trophoblasts. We here report transcriptomic data from n=3 pooled human first trimester patient-derived regenerative and n=3 pooled EVT differentiated trophoblast organoids (PD-TOrg) at single-cell resolution. This study sought to compare the undifferentiated and EVT-differentiated PD-TOrg molecular programs and cell states to those found in vivo and in hTSC-TOrgs previously published in Shannon et al., 2022. Placental tissues were collected following elective termination at the British Columbia Women’s Hospital CARE clinic for PD-TOrg establishment. PD-TOrg cultures were established and differentiated as described and sequenced on either day 0 of culture (for regenerative organoid colonies), or day 7 of culture (for EVT-differentiated organoid colonies).

overall_design: PD-TOrgs were established from 3 independent placental tissues using a modified version of previously described protocols and differentiated into EVT-trophoblast organoids by removal of WNT signaling components. Live trophoblasts were purified for mRNA sequencing from n=3 pooled regenerative organoid cultures on culture day 0 and from n=3 pooled EVT-differentiated organoid cultureds on culture day 7 in EVT-differentiation media using the 10X Genomics chromium single cell 3’ reagent v3 chemistry kit.

first: Matthew

last: Shannon

first: Gina

last: McNeil

first: Jasmin

last: Wächter

first: Burak

last: Koksal

first: Barbara

last: Castellana

first: Jennet

last: Baltayeva

first: Peter

middle: C

last: Leung


title: Effect of the CTG repeat expansion on RNA splicing in children with congenital myotonic dystrophy

city: Salt Lake City

first: Robert

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

summary: Congenital myotonic dystrophy (CDM) is the most severe form of myotonic dystrophy type-1 (DM1).  In adult DM1, dysregulation of alternative splicing of many transcripts results in the disease pathology.  In CDM, the degree of aberrant splicing is not known, nor is it understood which transcripts are altered.  Muscle biopsies were obtained from children with CDM, adults with DM1, healthy adult controls, and pathologically normal pediatric muscle.  RNA was isolated and paired-end RNA-Seq was performed.  Analysis used MAJIQ to generate percent spliced in (PSI) values.  Sample sets were analyzed with Weighted Gene Co-expression Network Analysis (WGCNA) to identify splicing patterns. 11 muscle biopsies from children with CDM (age 2 month-16 years), 9 pediatric controls (age 1 month-13 years), 16 adult DM1 patients (ages 29-57), and 6 adult healthy controls (ages 19-28) were used for analysis.  MAJIQ identified 2266 splicing events with adequate read depth and a PSI>0.15.  WGCNA identified 4 patterns of splicing.  The majority of the splicing events were the same in cases of CDM and DM1, while a subset of splicing changes were unique to CDM, many (e.g., PALLD) specific to development.  The relative expression of RNA splicing factors with age may account for differences in the splicing patterns in CDM and DM1.  Children with CDM have the RNA splicing events previously identified in adults with DM1, despite a divergent phenotype.  There are also a minority of splicing events that are specific to CDM, largely related to transcripts regulating development.

overall_design: 42 skeletal muscle biopsy samples: 11 congenital myotonic dystrophy (CDM), 16 adult myotonic dystrophy, 9 pediatric controls, 6 adult controls


title: Regulation of Immunological Tolerance by the p53-Inhibitor iASPP

city: Boston

first: Elliot

last: Akama-Garren

state: MA

address: 200 Longwood Ave

institute: Harvard Medical School

summary: Maintenance of immunological homeostasis between tolerance and autoimmunity is essential for the prevention of human diseases ranging from autoimmune disease to cancer. Accumulating evidence suggests that p53 can mitigate phagocytosis-induced adjuvanticity thereby promoting immunological tolerance following programmed cell death. Here we identify Inhibitor of Apoptosis Stimulating p53 Protein (iASPP), a negative regulator of p53 transcriptional activity, as a regulator of immunological tolerance.  iASPP-deficiency promoted lung adenocarcinoma and pancreatic cancer tumorigenesis, while iASPP-deficient mice were less susceptible to autoimmune disease.  Immune responses to iASPP-deficient tumors exhibited hallmarks of immunosuppression, including activated regulatory T cells and exhausted CD8+ T cells. Interestingly, iASPP-deficient tumor cells and tumor-infiltrating myeloid cells, CD4+, and gd T cells expressed elevated levels of PD-1H, a recently identified transcriptional target of p53 that promotes tolerogenic phagocytosis.  Identification of an iASPP/p53 axis of immune homeostasis provides a therapeutic opportunity for both autoimmune disease and cancer.

overall_design: RNA-seq was performed on pancreatic tissue lysates from genetically modified mice (4 WT, 3 iC, 7 KC, 4 KPC, 8 KiC)

first: Xin

last: Lu

first: Thomas

last: Carroll

first: Paul

last: Miller


title: Lifelong tissue memory relies on spatially organized dedicated progenitors located distally from the injury [scRNAseq_gradient]

first: Andrea

last: Lauria

overall_design: Lrig1 GL cells were  isolated  from tail epidermis at 8w pw1  time point. Sca1+ cells were sorted to enrich for upper-HF cells into lysis buffer and processed for scRNA-seq, using the Smart-Seq2 protocol

first: Chiara

last: Levron

first: Mika

last: Watanabe

first: Valenitna

last: Proserpio

first: Gabriele

last: Piacenti

first: Stefan

last: Kaltenbach

first: Annalaura

last: Tamburrini

first: Takuma

last: Nohara

first: Francesca

last: Anselmi

first: Carlotta

last: Duval

first: Luca

last: Elettrico

first: Daniela

last: Donna

first: Laura

last: Conti

first: Denis

last: Baev

first: Ken

last: Natsuga

first: Tzachi

last: Hagai

first: Salvatore

last: Oliviero

first: Giacomo

last: Donati


title: Three-dimensional chromatin re-organization during muscle stem cell aging [scATAC-seq]

city: San Francisco

first: Susanna

last: Rosi

address: 2200 Island Dr

institute: Altos labs

summary: Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world’s population continues to increase. A critical contributor to sarcopenia is the loss in the number and function of muscle stem cells, which maintain tissue homeostasis and regenerate damage. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.

overall_design: Age-matched Hi-C and single-cell ATAC-seq (scATAC-seq) datasets from young (3 months) and aged (24-29 months) mice. Hi-C datasets were generated from muscle stem cells that were FACS-isolated from skeletal hindlimb muscles. scATAC-seq datasets were generated from single nuclei collected from skeletal hindlimb muscles.

first: Benjamin

last: Yang

first: Carlos

last: Aguilar


title: Three-dimensional chromatin re-organization during muscle stem cell aging

overall_design: Refer to individual Series


title: The SET Oncoprotein Promotes Estrogen-Induced Transcription by Facilitating Establishment of Active Chromatin

city: Nanjing

first: Changying

last: Guo

state: Jiangsu

address: Longmian Avenue, No. 639

department: School of Life Science and Technology

institute: China Pharmaceutical university

summary: SET is a multifunctional histone-binding oncoprotein that regulates transcription by an unclear mechanism. Here, we show that SET enhances estrogen-dependent transcription. SET knockdown abrogates transcription of estrogen-responsive genes and their enhancer RNAs (eRNAs). In response to 17β-estradiol (E2), SET binds to the estrogen receptor α (ERα) and is recruited to estrogen receptor α (ERα)-bound enhancers and promoters at estrogen response elements (EREs). SET functions as a histone H2 chaperone that dynamically associates with H2A.Z via its acidic C-terminal domain and promotes H2A.Z incorporation, ERα, MLL1 and KDM3A loading and modulates histone methylation at EREs. SET depletion diminishes recruitment of condensin complexes to EREs and impairs E2-dependent enhancer-promoter looping. Thus, SET boosts E2-induced gene expression by establishing an active chromatin structure at ERα-bound enhancers and promoters, which is essential for transcriptional activation.

overall_design: CUT&Tag sequencing for SET and ERα in T47D cells with or without estradiol treatment

first: Karla

middle: F

last: Meza-Sosa

first: David

last: Valle-Garcia

first: Guomeng

last: Zhao

first: Kun

last: Gao

first: Lieberman

last: Judy


title: Three-dimensional chromatin re-organization during muscle stem cell aging [Hi-C]


title: PbAP2-FG2 and AP2R-2 function together as a transcriptional repressor complex essential for Plasmodium female development [ChIP-seq]

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

summary: To investigate the genome-wide binding sites of the transcriptional regulators, PbAP2-FG2 and AP2R-2 in female gametocytes of Plasmodium berghei, the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) analyses were performed. Parasites expressing GFP-fused PbAP2-FG2 (PbAP2-FG2::GFP) or GFP-fused AP2R-2 (AP2R-2::GFP) were harvested after treating the infected mice with sulfadiazine and subjected to ChIP-seq experiments using anti-GFP antibody. Binding sites of PbAP2-FG2 and AP2R-2 were determined from the sequence data.

overall_design: Mice were infected with PbAP2-FG2::GFP or AP2R-2::GFP and treated with sulfadiazine in their drinking water. Chromatins associated with GFP-tagged PbAP2-FG2 or AP2R-2 were IPed with anti-GFP antibody, and DNA fragments purified from the IPed chromoatins were sequenced by the Next Generation Sequencing. Using non-IPed samples as a control (INPUT), binding sites of PbAP2-FG2 and AP2R-2 were determined from the sequence data.

first: Tsubasa

last: Nishi

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Masao

last: Yuda


title: PbAP2-FG2 and AP2R-2 function together as a transcriptional repressor complex essential for Plasmodium female development

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


title: N6-adenine DNA-immunoprecipitation-based genomic profiling in eukaryotes

city: Seattle

first: Andrew

middle: Ben

last: Stergachis

state: WA

address: 1959 NE Pacific St

department: Medical Genetics

institute: University of Washington

type: Methylation profiling by high throughput sequencing

summary: The detection of low-abundance DNA N6-methyladenine (DNA-m6A) remains challenging, limiting our understanding of this novel base in eukaryotes. To address this, we introduce an approach for systematically validating the selectivity and sensitivity of antibody-based DNA-m6A methods, revealing most commercial antibodies as poorly selective towards DNA-m6A. Finally, we validate selective anti-DNA-m6A antibodies with sensitivity <2 ppm, and expose distinct pathways mediating endogenous DNA-m6A in C. reinhardtii, A. thaliana, and D. melanogaster.

sample_organism:
Chlamydomonas reinhardtii
Arabidopsis thaliana
Drosophila melanogaster

overall_design: The first part of this series is the evaluation of antibody-based DNA-m6A methods for identifying endogenous DNA-m6A-modified genomic loci using exogenously methylated control samples. Specifically, we applied DNA-m6A immunoprecipitation followed by massively parallel sequencing (m6A-IP-seq) to gDNA isolated from Drosophila S2 cell nuclei treated with 0.6 units, 0.075 units or no non-specific N6-adenine methyltransferase. For the second part of this series, we applied m6A-IP-seq to gDNA derived from three organisms with previously reported endogenous DNA-m6A (C. reinhardtii A. thaliana cauline leaves, and dechorionated D. melanogaster 45-minute embryos).

first: Brian

last: Debo

first: Ben

last: Mallory


title: Wound memory of epidermal stem cells [scRNAseq L1 PRT]

first: Andrea

last: Lauria

summary: Wound priming in epidermal Lrig1 stem cell progeny  leads to a more efficient response to future injuries. To identify a key epigenetic factor of this cellular adaptation, we performed an epigenetic drug screening in Lrig1 genetically labled mice.  Pre-treatment with PRT4165 lead to a more efficient wound closure. To understand if PRT4165 was able to recapitulate wound priming, we performed single cell RNA-seq transcriptome profiling of epidermal Lrig1 stem cell progenies from PRT4165-treated or untreated murine skin.    [PRT4165is  an inhibitor of the enzymatic activity of Ring1a/Ring1b, component of the Polycomb repressive complexes 1 (PRC1), responsible for the monoubiquitination of lysin 119 on histone H2A (H2AK119ub)]

overall_design: Single cell RNA-seq transcriptome profiling of epidermal Lrig1 stem cell progenies. After genetical labeling through tamoxifen application, tomato positive epidermal cells were sorted from  treated with PRT4165 or vehicle  treated tail skin.

first: Chiara

last: Levra Levron

first: Mika

last: Watanabe

first: Valenitna

last: Proserpio

first: Gabriele

last: Piacenti

first: Stefan

last: Kaltenbach

first: Takuma

last: Nohara

first: Francesca

last: Anselmi

first: Carlotta

last: Duval

first: Daniela

last: Donna

first: Denis

last: Baev

first: Ken

last: Natsuga

first: Tzachi

last: Hagai

first: Salvatore

last: Oliviero

first: Donati

last: Giacomo


title: Wound memory of epidermal stem cells [bulk RNA-seq]

summary: Trained wound-memory in epidermal cells elicits a more efficient response to future injuries, but the full spectrum of their adaptive responses and the contribution of cell lineage subsets is unknown. We performed  mini bulk RNA-Seq of Lrig1 and Lgr5 stem cell progenies in the context of two consecutive skin injuries to deeply characterise lineage specific adaptation mecanisms.

overall_design: RNA-seq transcriptome profiling of epidermal Lrig1 and Lgr5 stem cell progenies in the context of two consecutive skin injuries. After genetical labeling through tamoxifen application, tomato positive epidermal cells were sorted from tail skin at different time points: homeostasis (0w), one week post first wound (1w); two weeks post first wound (2w); four weeks post first wound (4w); eight weeks post first wound when a new homeostasis is re-established complete re-epithelialization (8w), one week post secon wound (9w).


title: PbAP2-FG2 and AP2R-2 function together as a transcriptional repressor complex essential for Plasmodium female development [RNA-seq]

first: masao

last: yuda

summary: Plasmodium berghei transcriptomes of pbap2-fg2 and ap2r-2 knockout parasites [pbap2-fg2(-) and ap2r-2(-), respectively] were analyzed at the gametocyte stage.

overall_design: pbap2-fg2(-) and ap2r-2(-) were harvested after sulfadiazine treatment, and total RNA was extracted from the parasites. Libraries were constructed from the total RNA and then sequenced by the Next Generation Sequencing.

first: Tsubasa

last: Nishi

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Masao

last: Yuda


title: Wound memory of epidermal stem cells [scRNAseq L1-aged]

first: Andrea

last: Lauria

summary: Wound priming in epidermal Lrig1 stem cell progeny  leads to a more efficient response to future injuries. To understand if primed progenitors maintain during aging the transcriptional program acquired during wound healing in young age, we performed single cell RNA-Seq of Lrig1 stem cell progeny 40 weeks after injury.

overall_design: Single cell RNA-seq transcriptome profiling of epidermal Lrig1 stem cell progenies.  After genetical labelling through tamoxifen application, tomato positive epidermal cells were sorted from repaired and age control skin.

first: Chiara

last: Levra Levron

first: Mika

last: Watanabe

first: Valenitna

last: Proserpio


title: Wound memory of epidermal stem cells [scRNAseq_L5]

summary: Trained wound-memory in epidermal cells elicits a more efficient response to future injuries, but the full spectrum of their adaptive responses and the contribution of cell lineage subsets is unknown. We performed single cell RNA-Seq of Lrig1 and Lgr5 stem cell progenies in the context of two consecutive skin injuries to deeply characterise lineage specific adaptation mecanisms.

overall_design: Single cell RNA-seq transcriptome profiling of epidermal Lgr5 stem cell progenies in the context of two consecutive skin injuries. After genetical labeling through tamoxifen application, tomato positive epidermal cells were sorted from tail skin at different time points: homeostasis (0w), one week post first wound (1w); eight weeks post first wound  when a new homeostasis is re-established complete re-epithelialization (8w), one week post secon wound (9w).

first: Gabriele

last: Piacenti

first: Stefan

last: Kaltenbach

first: Takuma

last: Nohara

first: Francesca

last: Anselmi


title: Microenvironment analysis of mouse and human neuroblastoma reveals shared populations and unmasks various subsets of immunosuppressive cells

city: Paris

first: Isabelle

last: Janoueix-Lerosey

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

summary: High-risk neuroblastoma is a pediatric cancer with dismal prognosis. In this study, we have used various approaches including single-cell RNA sequencing to dissect the tumor microenvironment of both a transgenic mouse neuroblastoma model and a cohort of biopsies from neuroblastoma patients. From the diverse cell populations identified, our data document a striking correspondence of the microenvironment populations between tumors from both species and unravel a complex content in myeloid cells and cancer-associated fibroblasts. Within the myeloid compartment we have characterized a population of cells exhibiting features of tumor-associated neutrophils and demonstrate that these cells obtained from the mouse model have immunosuppressive properties. Altogether, our study shows that neuroblastoma tumors have an immunocompromised microenvironment characterized by dysfunctional T-cells and accumulation of immunosuppressive cells. Our data provide the rationale for novel immunotherapeutic strategies in neuroblastoma, targeting both tumor cells and components of its microenvironment.

overall_design: Single-Cell RNA-seq data for MYCN-driven mouse neuroblastoma

first: Ana

last: Costa

first: Cécile

last: Thirant

first: Amira

last: Kramdi


title: Effects of miR-4707-3p expression on differentiation of primary human neural progenitor cells

status: Public on Feb 01 2023

city: Chapel Hill

first: Jason

last: Stein

state: NC

address: Neuroscience Research Building 8109C, 115 Mason Farm Rd

institute: UNC Chapel Hill

summary: To test the effects of miR-4707-3p expression on gene expression and differentiation of primary human neural progenitor cells (phNPCs), we produced two doxycycline inducible stable cell lines using lentiviral transduction. Lines expressed either mir-4707 and GFP or only GFP using the pTRIPZ expression vector. Stable lines were grown in differentiation media with doxycycline for one or two weeks before RNA was extracted and assayed on a Clariom S Pico Microarray Assay.

overall_design: 24 total samples of primary human neural progenitor cells were assayed at either one or two weeks in differentation media. Six replicates in each category: control cells at week 1, control cells at week 2, mir4707 cells at week 1, and mir4707 cells at week 2.


title: Wound memory of epidermal stem cells [scRNAseq_L1]

summary: Trained wound-memory in epidermal cells elicits a more efficient response to future injuries, but the full spectrum of their adaptive responses and the contribution of cell lineage subsets is unknown. We performed  single cell RNA-Seq of Lrig1 and Lgr5 stem cell progenies in the context of two consecutive skin injuries to deeply characterise lineage specific adaptation mecanisms.

overall_design: Single cell RNA-seq transcriptome profiling of epidermal Lrig1 stem cell progenies in the context of two consecutive skin injuries. After genetical labeling through tamoxifen application, tomato positive epidermal cells were sorted from tail skin at different time points: homeostasis (0w), one week post first wound (1w); eight weeks post first wound  when a new homeostasis is re-established complete re-epithelialization (8w), one week post secon wound (9w).

first: Carlotta

last: Duval

first: Daniela

last: Donna

first: Denis

last: Baev

first: Ken

last: Natsuga

first: Tzachi

last: Hagai

first: Salvatore

last: Oliviero

first: Donati

last: Giacomo


title: SKIP regulates ABA-mediated alternative splicing and its signaling in Arabidopsis

city: Shenyang

first: Xiaoxue

last: Wang

state: Liaoning

address: 120 Dongling Road, Shenhe District

department: Rice Research Institute

institute: Shenyang Agricultural University

summary: Abscisic acid (ABA) plays a key role in plant development and responses to abiotic stress. A wide number of regulatory mechanisms on ABA perception and signaling are known, including transcriptional regulation and post-translational regulations; however, less to know about the post-transcriptional regulations. In this work, we have found that SKIP, a splicing factor in spliceosome, positively regulates ABA signal transduction. Mutation of SKIP, skip-1, confers ABA insensitive phenotype in seed germination, root growth, and ABA-responsive gene expression. Transformation of SKIP genomic DNA to skip-1 is able to recover its defects. SKIP binds to the pre-mRNA of genes in ABA signaling, such as PYL8, to regulate their splicing. The alternative splicing of PYL7, PYL8, ABF2, and ABI5 in ABA pathway is disrupted by skip-1, reducing the mRNA levels of them. The abnormal splicing of PP2Cs activates their transcription by skip-1, suggesting there is a feedback regulation for PP2Cs caused by skip-1. The down-regulation of PYL ABA receptors, ABF2 and ABI5 ABA response transcription factors, and the up-regulation of PP2Cs through alternative splicing reduce the plant responses to ABA in skip-1. SKIP is required for ABA-mediated genome-wide alternative splicing. ABA treatment enhances the novel splicing events in WT genome-widely. The novel alternative splicing events are increased by skip-1 in the absence and present of ABA. Our results first reveal a principle on how a splicing factor affects the ABA signaling.

overall_design: 13-day-old WT and skip-1 seedlings treated with 0 and 100 uM ABA  for 3 h were used for mRNA high thoughput sequencing.

first: Qi

last: Zhang

first: Wei

first: Zhaoxu

last: Gao


title: RNA Seq Analysis of BMSC cell line Transcriptomes under the different conditions.

city: wenzhou

first: huang

middle: dong

last: dong

address: juyi street 105

institute: wenzhou medical university

summary: The goal of this study are to compare the transcriptome profiling (RNA-seq) of rat bone marrow mesenchymal stem cells (BMSC) transcriptome profiling (RNA-seq) under the condition of infection of different lentiviruses(shRac1 or shLuci) and/or oxygen-glucose deprivation (OGD).

overall_design: Examination of mRNA profiling of normal BMSC cells or lentiviruses (shRac1 or shLuci) infected BMSC cells under the normal condition or treatment with OGD.

first: Dongdong

last: Huang

first: Jianjing

last: Yang


title: In vivo Chemical Reprogramming of Astrocytes into Functional Neurons

first: qian

middle: qian

last: zhang

address: Datun road, chaoyang district

department: State Key Laboratory of Brain and Cognitive Science

institute: Institute of Biophysics

summary: In mammals, many organs lack robust regenerative abilities. Lost cells in impaired tissue could potentially be compensated by converting nearby cells in situ through in vivo reprogramming. Small molecule-induced reprogramming offers a spatiotemporally flexible and non-integrative strategy for altering cell fate, which is, in principle, favorable for in vivo reprogramming in organs with notoriously poor regenerative abilities, such as the brain. Here, we demonstrate that in adult mouse brain, small molecules can reprogram astrocytes into functional neurons. The in situ chemically induced neurons resemble endogenous neurons in gene expression profiles, electrophysiological properties and synaptic connectivity. Our study demonstrates, for the first time, in vivo chemical reprogramming in the adult brain and provides a novel approach for developing neuronal replacement therapies.

overall_design: The mouse chemical induced neurons at BW12 were selected for single-cell RNA-seq.

first: Zhang

last: Qianqian


title: Rapid emergence of transcriptional heterogeneity upon molecular stress predisposes cells to two distinct states of senescence

first: Alexander

last: Mendenhall

state: Washington

address: 1959 NE Pacific St, HSB E072

summary: We used single-cell RNA-sequencing to characterize different types of senescent cells that arise upon oxidative stress

overall_design: IMR-90 fibroblasts were induced into senescence via oxidative stress. Transcriptional states of individual senescent cells were analyzed via SPLIT-seq method.

first: Nikolay

last: Burnaevskiy

first: Junko

last: Oshima


title: Single cell RNA sequencing for normal and Angiotensin Ⅱ-induced thoracic and abdominal aneurysmal aorta

city: Hangzhou

first: Hong

last: Wu

address: 79 Qingchun Road

department: Department of Cardiology

institute: the First Affiliated Hospital, Zhejiang University School of Medicine

summary: Aortic aneurysm is a life-threatening disease resulted from progressive dilatation of the aorta and weakness of the blood vessel walls .  While the two diseases share several etiological similarities, there are also significant differences in population prevalence rate, genetic patterns and susceptibility genes.  However, both TAAs and AAAs are complex, multifactorial and highly heterogeneous diseases, which greatly restricts our better knowledge of the two diseases. An improved knowledge of the cellular mechanism networks that trigger the development and succeeding expansion of aneurysms is critical to discovering innovative therapeutic targets.

overall_design: This entry contains 10x Single-cell RNA-seq data of FACS sorted nucleated living cells from normal or 4-week Angiotensin Ⅱ-induced mouse thoracic and abdominal aorta.

first: Ruilin

first: Qingbo

last: Xu

first: Haige

last: Zhao


title: Copper ions inhibit Streptococcus mutans-Veillonella parvula dual biofilm by activating Streptococcus-mutans reactive nitrogen species

city: Chengdu

first: Yun

address: Qingyang District first Ring Road west second section

institute: Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China

summary: To investigate the inhibition mechanism of copper ions on S. mutans-V. parvula dual biofilm.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Streptococcus mutans nomo biofilm and Streptococcus mutans-Veillonella parvula dual biofilm with and without copper ions' addition

first: Xianghong

last: Liu

first: Qin

last: Du


title: Pedigree Study and Functional Analysis of Novel Germline p. R21Afs MEN1 Mutation in a Multiple Endocrine Neoplasia Type 1 Family

city: Shanghai

first: Le

last: Bu

state: Please Select

address: Tenth People's Hospital of Shanghai,301 Yanchang Road, Jing'an District, Shanghai

institute: Shanghai Tenth People's Hospital

summary: We found a novel MEN1 p. R21Afs mutaion in a multiple endocrine neoplasia type 1 family. To investigate the pathogenic function of p.R21Afs MEN1 mutation, the leukocyte transcriptoma profilings derived from MEN1 patients with heterozygote p.R21Afs MEN1 mutation was compared with the unaffected relatives without p.R21Afs MEN1 mutation.

overall_design: 3 blood samples from unaffected relatives without p.R21Afs MEN1 mutation, 3 blood samples from MEN1 patients with heterozygote p. R21Afs MEN1 mutation. Comparative transcriptoma profiling analysis of RNA-seq data for leukocyte was performed between MEN1 patients and unaffected relatives..

first: Nannan

last: Li


title: Lysine-specific histone demethylase 1A (KDM1A/LSD1) inhibition attenuates DNA double strand break repair and augments efficacy of temozolomide in glioblastoma

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary:
To understand the mechanistic insights on how KDM1A inhibition sensitizes glioblastoma (GBM) to temozolomide, we performed genome wide localization studies of KDM1A in patient derived glioma stem cells (GSCs) using CUT&Tag-seq. GSC082209 (GSC08) cells were treated with vehicle or NCD38 (5 μM) for 24 h and 250,000 cells per condition were used. Data analysis on CUT&Tag sequencing reads was performed by the nf-core/cutandrun bioinformatic analysis pipeline. We detected 75,491 KDM1A peaks in the genome of GSCs (p<0.0001). Pathway analysis of KDM1A binding genes using Gene Ontology showed KDM1A binding genes were enriched in DNA repair, cell cycle, and UPR signaling pathways .
CUT&Tag sequencing for KDM1A in patient derived glioma stem cells.

overall_design: Gangadhara Sareddy

first: Yidong

last: Chen

first: Zhao

last: Lai

first: Yi

last: He


title: Synergy between IDH2 and TET2 mutations modulates Tfh cell functional interaction with the angioimmunoblastic T-cell lymphoma microenvironment [Tfh RNA-seq]

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

summary: Angioimmunoblastic T-cell lymphoma (AITL) is a peripheral T-cell lymphoma that originates from T follicular helper (Tfh) cells and is characterized by a prominent tumor microenvironment (TME). IDH2 and TET2 mutations co-occur frequently in AITL but their contribution to tumorigenesis is poorly understood. We have developed an AITL mouse model that is driven by Idh2 and Tet2 mutations and in which Tfh cells exhibit aberrant transcriptomic and epigenetic programming. Neoplastic Tfh cells bearing combined Idh2 and Tet2 mutations show altered crosstalk with normal germinal center B cells that promotes B clonal expansion while decreasing Fas-FasL interaction and reducing B cell apoptosis. This altered Tfh-B cell communication could explain the unique relationship between Idh2 mutation and the prototypical AITL TME. Our mouse model also recapitulates important features of human IDH2-mutated AITL, providing a rationale for exploring the therapeutic targeting of Tfh-TME crosstalk for AITL treatment.

overall_design: CD4+ CXCR5+ PD-1+ (Tfh) cells from 2 month old +/-; CD4-Cre (control), Idh2LSL-R172K/+;CD4-Cre, Tet2-/-;CD4-Cre, Idh2LSL-R172K/+; Tet2-/-;CD4-Cre mice were analyzed. For each genotype,  4 mice each (each forming a biological replicate), were analyzed.

first: Julie

last: Leca

first: Francois

last: Lemonnier

first: Jonathan

last: Foox

first: Ari

last: Melnick

first: Christopher

last: Mason

first: Philippe

last: Gaulard

first: Tak

middle: W

last: Mak


title: Synergy between IDH2 and TET2 mutations modulates Tfh cell functional interaction with the angioimmunoblastic T-cell lymphoma microenvironment [ATAC-Seq]

overall_design: CD4+ CXCR5+ PD-1+ (Tfh) cells from 2 month old CD4-Cre (control), Idh2LSL-R172K/+;CD4-Cre, Tet2-/-;CD4-Cre, Idh2LSL-R172K/+; Tet2-/-;CD4-Cre mice were analyzed. For each genotype,  4 mice each (each forming a biological replicate), were analyzed.


title: Synergy between IDH2 and TET2 mutations modulates Tfh cell functional interaction with the angioimmunoblastic T-cell lymphoma microenvironment [AITL Tumor RNA-seq]

overall_design: Lymph node tissue from 7/9 month old transplanted mice with CD3 cells from CD4-Cre (control), Idh2LSL-R172K/+;CD4-Cre, Tet2-/-; CD4-Cre, Idh2LSL-R172K/+;Tet2-/-; CD4-Cre were analyzed. For each genotype, 4 mice each (each forming a biological replicate), were analyzed.