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> Anatomy > Body Part > Thymus Gland

Thymus Gland

The thymus gland is a vital organ located in the upper chest that plays a crucial role in the development and regulation of the immune system.
It is responsible for the maturation of T cells, a type of white blood cell essential for fighting infections and diseases.
The thymus gland is particularly active during childhood and adolescence, but it continues to have important functions throughout adulthood.
Optimizing research on the thymus gland can lead to advancements in understanding and treating a wide range of immunological disorders.
PubCompare.ai, an AI-driven platform, enhances the reproducibility and accuracy of thymus gland research by helping researchers easily locate the best protocols from literature, preprints, and patents using advanced search and AI-powered comparisons.
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Most cited protocols related to «Thymus Gland»

1
Thymocyte Immunophenotyping in Foxn1 Mice
Thymocyte suspensions were prepared from thymi from newborn C57BL/6, Foxn1ex9cre homozygous, Foxn1ex9lacZ homozygous and Foxn1ex9lacZ heterozygous mice. The red blood cells were lysed and total cell numbers were counted. 1 × 106 thymocytes were stained with the following monoclonal antibodies conjugated to PE, FITC, APC directly, or Biotin-labeled monoclonal antibodies, followed by streptavidin-PerCP: anti-CD4 (RM4-5), anti-CD8a (53-6.7), anti-CD44 (IM7) or anti-CD25 (7D4) (BD Pharmingen, San Diego, CA). Anti-CD16/32 (2.4G2) (BD Pharmingen) and normal rat serum were used to block FC-receptors before staining. Four-color immunofluorescence analysis was performed using a FACSCalibur system. The data were analyzed using CellQuest software (Becton Dickson, Franklin Lake, NJ).
Gordon J., Xiao S., Hughes B I.I.I., Su D.M., Navarre S.P., Condie B.G, & Manley N.R. (2007). Specific expression of lacZ and cre recombinase in fetal thymic epithelial cells by multiplex gene targeting at the Foxn1 locus. BMC Developmental Biology, 7, 69.
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Publication 2007
Biotin Cardiac Arrest CD44 protein, human Erythrocytes Fc Receptor Fluorescein-5-isothiocyanate Fluorescent Antibody Technique Heterozygote Homozygote IL2RA protein, human Infant, Newborn Monoclonal Antibodies Mus Serum Streptavidin Thymocyte Thymus Gland
2
In Vitro Generation and Characterization of Murine Double Negative T Cell Populations

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Publication 2012
Care, Prenatal CD4 Positive T Lymphocytes CD8-Positive T-Lymphocytes CD44 protein, human Chromatin Immunoprecipitation Sequencing Dietary Supplements Hematopoietic System IL2RA protein, human Liver Population Group RNA-Seq Thymus Gland
3
Transcriptional profiling of immune cell subsets
RNA from sorted cells was purified (QIAGEN) and hybridized to Affymetrix mouse 430 2.0 arrays (Memorial Sloan-Kettering Cancer Center, Genomics Core Facility). Raw data (CEL files) were normalized by RMA using Affy R package. Principal component analysis was performed using arrayQualityMetrics R package. Differential expression analysis was performed between any two subsets using limma R package (Adjusted P-value < 0.05 and fold-change > 1.5). Gene Set Enrichment Analysis (GSEA) was run for each cell subset in pre-ranked list mode with 1,000 permutations (nominal P-value cutoff < 0.01). As gene sets for the GSEA analyses, we used Reactome pathways (http://www.reactome.org/); the MSigDB gene sets related to haematopoietic stem cells34 ; and gene signatures associated with TFH or TH1 CD4+ T cells33 , memory precursor/terminal effector CD8+ T cells35 and thymic innate TFH-like CD4+ T cells36 . To define these signatures, we downloaded the microarray data from GEO database (GSE16697, GSE8678 and GSE64779); collapsed probe sets that matched to the same gene symbol by taking the one with highest expression across all samples; removed genes with lowest 30% mean expression; and performed differential expression analysis between the two classes using limma (adjusted P-value < 0.01 and fold-change > 2). Enrichment scores were visualized using the corrplot package in R. Enrichment scores of Reactome pathways and the genes shared by two pathways were represented as nodes and links, respectively using Cytoscape software. The microarray data are available in the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo) under the accession number GSE84105.
Im S.J., Hashimoto M., Gerner M.Y., Lee J., Kissick H.T., Burger M.C., Shan Q., Hale J.S., Lee J., Nasti T.H., Sharpe A.H., Freeman G.J., Germain R.N., Nakaya H.I., Xue H.H, & Ahmed R. (2016). Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy. Nature, 537(7620), 417-421.
Publication 2016
Cells Gene Expression Genes Hematopoietic System Malignant Neoplasms Memory Microarray Analysis Mus Stem, Plant Thymus Gland
4
Single-cell sequencing of thymus nuclei
Single cells for the purpose of single-cell sequencing were isolated from thymuses by dissecting the organ and mincing the tissue through a 100 μm cell strainer. Cells were washed in PBS twice before stored in FBS with 10 % DMSO at −80 °C until sorted. Prior to sorting, cells were thawed, and incubated for 10 min on ice in the dark in a DNA-staining buffer containing 10 μg/mL propidium iodide and 10 μg/mL Hoechst, as well as 0.1 % Nonidet P-40 to dissociate the cytoplasm. The G1 population was sorted as individual nuclei into a 96-well plate format. Per sample, 10 nuclei were sorted into a single well to serve as a positive control, as well as an empty well acting as a negative control. Library preparation was performed using a modified scWGS protocol [24 , 31 (link)] using a Bravo Automated Liquid Handling Platform (Agilent Technologies, Santa Clara, CA, USA). Clusters for sequencing were generated on the cBot (Illumina). Single-end 50 bp sequencing was performed on an Illumina HiSeq 2500 at ERIBA (Illumina, San Diego, CA, USA). Raw sequencing data were demultiplexed based on library-specific barcodes and converted to fastq format using standard Illumina software (bcl2fastq version 1.8.4). The resulting reads were mapped to mouse (mm10) or human (hg19) reference genome using Bowtie2 (version 2.2.4). Duplicate reads were marked using BamUtil (version 1.0.3). All single-cell sequencing data have been deposited at ArrayExpress under accession no. E-MTAB-4183.
Bakker B., Taudt A., Belderbos M.E., Porubsky D., Spierings D.C., de Jong T.V., Halsema N., Kazemier H.G., Hoekstra-Wakker K., Bradley A., de Bont E.S., van den Berg A., Guryev V., Lansdorp P.M., Colomé-Tatché M, & Foijer F. (2016). Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies. Genome Biology, 17, 115.
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Publication 2016
Buffers Cell Nucleus Cells Cytoplasm DNA, A-Form DNA Library Genome Homo sapiens Mus Nonidet P-40 Propidium Iodide Sulfoxide, Dimethyl Thymus Gland Tissues
5
FACS and scRNA-seq Protocols for Thymus Cell Analysis
For FACS sorting of isolated thymus cells, dissociated cells were stained with a panel of antibodies prior to sorting based on CD45 or CD3 expression gate. Enrichment of EpCAM-positive cells was performed using CD326 (EpCAM) microbeads (Miltenyi Biotec, 130-061-101) according to manufacturer’s protocol. CD45 depleted cells were obtained using CD45 microbeads (Miltenyi Biotec, 130045-801) according to manufacturer’s protocol. Cell number and viability were checked after the enrichment to ensure that no significant cell death has been caused by the process.
For the droplet-encapsulation scRNA-seq experiments, 8000 live, single, CD45+ or CD45− FACS-isolated cells or MACS-enriched cells were loaded on to each of the Chromium Controller (10x Genomics). Single-cell cDNA synthesis, amplification, and sequencing libraries were generated using the Single Cell 3’ and 5’ Reagent Kit following the manufacturer’s instructions. The libraries from up to eight loaded channels were multiplexed together and sequenced on an Illumina HiSeq 4000. The libraries were distributed over eight lanes per flow cell and sequenced using the following parameters: Read1: 26 cycles, i7: 8 cycles, i5: 0 cycles; Read2: 98 cycles to generate 75-bp paired-end reads. For the plate-based scRNA-seq experiments, a slightly modified Smart-Seq2 protocol was used. After cDNA generation, libraries were prepared (384 cells per library) using the Illumina Nextera XT kit. Index v2 sets A, B, C, and D were used per library to barcode each cell for multiplexing. Each library was sequenced (384 cells) per lane at a sequencing depth of 1 to 2 million reads per cell on HiSeq 4000 using v4 SBS chemistry to create 75-bp paired-end reads.
Park J.E., Botting R.A., Conde C.D., Popescu D.M., Lavaert M., Kunz D.J., Goh I., Stephenson E., Ragazzini R., Tuck E., Wilbrey-Clark A., Roberts K., Kedlian V.R., Ferdinand J.R., He X., Webb S., Maunder D., Vandamme N., Mahbubani K.T., Polanski K., Mamanova L., Bolt L., Crossland D., de Rita F., Fuller A., Filby A., Reynolds G., Dixon D., Saeb-Parsy K., Lisgo S., Henderson D., Vento-Tormo R., Bayraktar O.A., Barker R.A., Meyer K.B., Saeys Y., Bonfanti P., Behjati S., Clatworthy M.R., Taghon T., Haniffa M, & Teichmann S.A. (2020). A cell atlas of human thymic development defines T cell repertoire formation. Science (New York, N.Y.), 367(6480), eaay3224.
Publication 2020
Anabolism Antibodies cDNA Library Cell Death Cells Chromium DNA, Complementary Microspheres Single-Cell RNA-Seq TACSTD1 protein, human Thymus Gland

Most recents protocols related to «Thymus Gland»

1
Genetic Factors in HSCT Outcomes
The study has been approved by the Institutional Review Board (IRB) of Chang Gung Memorial Hospital (CGMH) and was performed according to the ethical regulations and requirements. The approved ID was 201304949B0 and 202100302B0. Because HLA-G was mainly expressed in the saliva, peritoneal fluid, plasma, thymus, semen, cerebrospinal fluid but not in the immune cells (7 (link)), and only the HLA haplotypes of the recipients but not donors were associated with the outcomes after HSCT (18 (link), 22 (link)), the analysis focused on the genetic components of the recipients. The inclusion criteria of participants were male and female adults (over 20 years old) who suffered from AML or ALL and underwent HSCT. Exclude the patients who had other hematological malignancies. A total of 164 patients receiving HSCT was enrolled in this study, in which 106 patients were diagnosed as AML and 58 patients were ALL. The clinical characteristics of the 164 patients are shown in Table 1. All recipients of unrelated HSCT signed informed consents and had fully matched HLA with the donors as revealed by using the SeCore kit (Thermo Fisher, Waltham, MA) for high-resolution HLA typing. The ambiguous alleles of the SeCore typing were resolved by using the MicroSSP Allele Specific Tying Tray with sequence-specific primers (Thermo Fisher, Waltham, MA).
Chen D.P., Wang P.N., Hour A.L., Lin W.T., Hsu F.P., Wang W.T, & Tseng C.P. (2023). The association between genetic variants at 3’-UTR and 5’-URR of HLA-G gene and the clinical outcomes of patients with leukemia receiving hematopoietic stem cell transplantation. Frontiers in Immunology, 14, 1093514.
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Publication 2023
Adult Alleles Cells Cerebrospinal Fluid Donors Ethics Committees, Research Gene Components Haplotypes Hematologic Neoplasms HLA-G Antigen Males Oligonucleotide Primers Patients Peritoneal Fluid Plant Embryos Plasma Saliva Thymus Gland Woman
2
Igk Repertoire Analysis in Thymic and Splenic B Cells
FASTQ files from 3H9 thymic and splenic B cells sequenced for Igk were downloaded from the Gene Expression Omnibus (GEO, GSE85366) and processed using IMGT/HighV-QUEST (62 –65 (no link found, link, link)). Calculated Junction data were parsed using R (v. 4.0.5), and the frequency of productive Igk with no N-nucleotide additions was calculated.
Martinez R.J., Breed E.R., Worota Y., Ashby K.M., Vobořil M., Mathes T., Salgado O.C., O’Connor C.H., Kotenko S.V, & Hogquist K.A. (2023). Type III interferon drives thymic B cell activation and regulatory T cell generation. Proceedings of the National Academy of Sciences of the United States of America, 120(9), e2220120120.
Publication 2023
B-Lymphocytes Gene Expression Nucleotides Spleen Thymus Gland
3
Isolation and Labeling of B Cells
Spleens were isolated and pressed through a 70-μm nylon screen to generate a single-cell suspension. B cells were isolated using the EasySep Mouse B cell kit (StemCell Technologies) per the manufacturer’s protocols. CTV or CFSE labeling was performed following the manufacturer’s protocols. 5 × 106 purified B cells were injected into each lobe of the thymus using ultrasound guidance as previously described (59 ).
Martinez R.J., Breed E.R., Worota Y., Ashby K.M., Vobořil M., Mathes T., Salgado O.C., O’Connor C.H., Kotenko S.V, & Hogquist K.A. (2023). Type III interferon drives thymic B cell activation and regulatory T cell generation. Proceedings of the National Academy of Sciences of the United States of America, 120(9), e2220120120.
Publication 2023
5-(6)-carboxyfluorescein diacetate succinimidyl ester B-Lymphocytes Cells Mus Nylons Stem Cells Thymus Gland Ultrasonic Shockwave
4
Thymic B Cell Transcriptomics: scRNA-seq Analysis
scRNA-seq experiments were performed as previously described (61 ). Briefly, MHC-II-expressing thymic cells were FACS sorted and captured using the 10× Genomics 3′ Single Cell V3 chemistry platform and were sequenced on a NovaSeq instrument. CellRanger (v 4.0.0) was used to process raw sequencing data, followed by the “count” function used to obtain gene (mRNA) and protein (HTO) count data for all cells. The Seurat R package (v3.2.2, R version 4.0.0) was used for analysis. Highly variable features (n = 2,000) from log normalized mRNA count data were identified by “FindVariableFeatures” function from the Seurat package, and HTO count data were added into the dataset, followed by centered-log ratio normalization. Doublet cells and cells derived from OT-I mice (by HTO) were identified using “HTODemux” and were removed from analysis. Principal components analysis and generation of a two-dimensional representation of data were generated using “RunPCA” and “RunUMAP,” respectively. Cells were clustered using the “FindNeighbors” and “FindClusters” Seurat functions. For the “FindClusters” function, different resolution values were tested and the resolution value of 0.1, which identified 14 clusters, was empirically chosen. The cluster representing B cells was selected, followed by selection of C57BL/6 and Ifnar1−/−/Ifnlr1−/−-derived cells (by HTO) and subset as a new object. This new object was reclustered as described above (resolution of 0.1). Differentially expressed genes from the WT B cells were identified by a Wilcoxon Rank Sum test implemented in the “FindMarkers” function in Seurat. For scoring of the expression of multiple genes of single cells, the Hallmark Interferon Alpha Response gene set was used as features to generate a new module score (“AddModuleScore” in Seurat) and plotted. Other MHCII-expressing thymic cells will be analyzed and reported elsewhere. scRNA-seq data generated are available from the National Center for Biotechnology Information Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) under accession GSE192716.
Martinez R.J., Breed E.R., Worota Y., Ashby K.M., Vobořil M., Mathes T., Salgado O.C., O’Connor C.H., Kotenko S.V, & Hogquist K.A. (2023). Type III interferon drives thymic B cell activation and regulatory T cell generation. Proceedings of the National Academy of Sciences of the United States of America, 120(9), e2220120120.
Publication 2023
B-Lymphocytes Cells Gene Expression Genes Interferon-alpha Mus Proteins RNA, Messenger Single-Cell RNA-Seq Thymus Gland
5
Multi-tissue Immune Cell Isolation
Thymi, spleen and Peyer’s patches (PPs) were isolated from mice. Spleen and thymi single-cell suspensions were generated as described above. PPs were pressed through a 70-μm nylon screen to generate a single-cell suspension. Single-cell suspensions were stained for 30 min at 4 °C with the indicated antibodies. Staining for CD40L was performed as previously described (58 (link)). For intracellular Ig H + L staining, the BD Cytofix/Cytoperm kit was used as per the manufacturer’s instructions. For intranuclear transcription factor staining, the Tonbo Foxp3 / Transcription Factor Staining Buffer Kit was used as per the manufacturer’s instructions. Samples were acquired with a BD LSRII or Fortessa X-20 (BD Biosciences) and analyzed with FlowJo version 10.8.1 (FlowJo LLC).
Martinez R.J., Breed E.R., Worota Y., Ashby K.M., Vobořil M., Mathes T., Salgado O.C., O’Connor C.H., Kotenko S.V, & Hogquist K.A. (2023). Type III interferon drives thymic B cell activation and regulatory T cell generation. Proceedings of the National Academy of Sciences of the United States of America, 120(9), e2220120120.
Publication 2023
Antibodies Buffers Cells Mus Nylons Peyer Patches Protoplasm Spleen Thymus Gland Transcription Factor

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More about "Thymus Gland"

thymus, immune system, T cells, autoimmune, immunodeficiency, cancer, flow cytometry, DNase I, FACSAria II, LSRFortessa, FACSCanto II, LSRII, FACSCalibur, FACSAria, FBS, Collagenase D