Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB35961 | ENA |
REPOSITORIES: ENA
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Project description:Single cells from human colorectal cancer and normal adjacent colon of 16 patients were used for single-cell RNA-seq, TCR-seq, CITE-seq and Cell hashing. In brief, single cells were incubated for 3h with or without PMA/Ionomycin, and were treated with Cell hashing and CITE-seq antibodies to distinguish samples, stimulation/non-stimulation, and cell surface proteins. Sorted viable CD3+TCRαβ+ single cells were loaded into 10x genomics ChromiumTM controller to make nanoliter-scale droplets with uniquely barcoded 5’ gel beads called GEMs. After GEM-RT and the following some cDNA amplification steps, cDNAs derived from cellular mRNA were pooled for downstream processing and library preparation according to the manufacturer’s instructions. The 5’ transcript library was sequenced with Illumina Novaseq. The single cell TCR enriched library was sequenced with Illumina Miseq using 150 paired-end reads. HTO/ADTs from Cell hashing or CITE-seq were amplified using specific primers that append P5 and P7 sequences for illumina sequencing (Miseq or Nextseq). All fastq files were demultiplexed. Cell hashing and CITE-seq barcodes are available in attached text files. Fastq files from RNA-seq and TCR-seq can be processed through cellranger and vdjranger by 10xgenomics. The datasets include the data of independent experiments at May 29, June 16, June 23, and Aug 13, 2019. Details are available in Masuda et al., bioRxiv, 2020, The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome.
2022-03-02 | E-MTAB-9455 | biostudies-arrayexpress
Project description:To trace immune responses in COVID-19 patients with severity, we performed in-depth, longitudinal single-cell multiomics involving T-cell receptor (TCR)/B-cell receptor (BCR) sequencing, feature barcoded antibody (Ab) panel detection (i.e., cellular indexing of transcriptomes and epitopes by sequencing, CITE-seq) followed by RNA sequencing in a single-cell resolution.
2025-01-27 | GSE196198 | GEO
Project description:The aim was to examine changes in gene expression of the endometrium exposed to long-term tamoxifen treatment in comparison to age matched controls. To achieve this, endometrial tissues were obtained from women receiving tamoxifen treatment who were undergoing a hysterectomy. Using cDNA microarrays, gene expression changes in the postmenopausal endometrium of these women was compared with that in endometrium of age matched women not receiving tamoxifen. Keywords: Gene expression changes in the postmenopausal endometrium of women following tamoxifen treatment
2005-12-02 | GSE3626 | GEO
Project description:Global gene expression patterns associated with early stage endometrial cancer have been reported, but changes in molecular expression associated with tumor grade, depth of myometrial invasion, and non-endometrioid histology have not been previously elucidated. Our group hypothesized there are unique genetic events underlying early endometrial carcinogenesis. Ninety-two samples of pathologically reviewed stage I endometrial cancers (80 endometrioid and 12 serous) with a heterogeneous distribution of grade and depth of myometrial invasion (i.e. 9 IAG1, 14 IAG2, 7 IAG3, 14 IBG1, 12 IBG2, 13 IBG3, 7 ICG1, 10 ICG2, and 6 ICG3) were examined in relation to 12 samples of atrophic endometrium from postmenopausal women. Specimens were analyzed using oligonucleotide microarray analysis and a subset of the differentially expressed transcripts was validated using quantitative PCR. Comparison of early stage cancers with normal endometrium samples by the univariate t-test with 10,000 permutations identified 900 genes that were differentially regulated by at least 4-fold at a p value of <0.001. Unsupervised analysis revealed that when compared to normal endometrium, serous and endometrioid stage I cancers appeared to have similar expression patterns. However, when compared in the absence of normal controls, they were distinct. Differential expression analysis revealed a number of transcripts that were common as well as unique to both histologic types. This data uncovers previously unrecognized, novel pathways involved in early stage endometrial cancers and identifys targets for prevention strategies that are inclusive of both endometrioid and serous histologic subtypes. Ninety-one samples of pathologically reviewed stage I endometrial cancers (79 endometrioid and 12 serous) with a heterogeneous distribution of grade and depth of myometrial invasion (i.e. 9 IAG1, 14 IAG2, 7 IAG3, 14 IBG1, 12 IBG2, 13 IBG3, 7 ICG1, 10 ICG2, and 6 ICG3) were examined in relation to 12 samples of atrophic endometrium from postmenopausal women. Specimens were analyzed using oligonucleotide array analysis.
2011-12-13 | E-GEOD-17025 | biostudies-arrayexpress
Project description:The inner lining of the human uterus, termed the endometrium, is replete with glands that are hypothesized to be important for establishment of pregnancy through interactions with other endometrial cells and the embryo. A three-dimensional culture system was utilized to establish and generate endometrial epithelial organoids from normal human endometrium that display long-term expandability, can be cryopreserved, and are hormone responsive. Here, single cell RNA-seq was used to create a high-resolution gene expression atlas of the endometrial epithelial organoids and to define responsiveness to reproductive hormones.
2020-11-22 | GSE161937 | GEO
Project description:The inner lining of the human uterus, termed the endometrium, is replete with glands that are hypothesized to be important for establishment of pregnancy through interactions with other endometrial cells and the embryo. A three-dimensional culture system was utilized to establish and generate endometrial epithelial organoids from normal human endometrium that display long-term expandability, can be cryopreserved, and are hormone responsive. Here, single cell RNA-seq was used to create a high-resolution gene expression atlas of the endometrial epithelial organoids and to define responsiveness to reproductive hormones.
2019-09-04 | GSE136795 | GEO
Project description:Limited CITE-seq antibody panel and 5' gene expression profiling of human nasopharyngeal cells collected with flocked swabs, paired with TCR and BCR sequencing of NP lymphocytes. FACS-sorted SARS-CoV-2 antigen-specific memory B and T cells with 5' gene expression profiling and scBCR and scTCRseq.
2024-06-24 | GSE270518 | GEO
Project description:Global gene expression patterns associated with early stage endometrial cancer have been reported, but changes in molecular expression associated with tumor grade, depth of myometrial invasion, and non-endometrioid histology have not been previously elucidated. Our group hypothesized there are unique genetic events underlying early endometrial carcinogenesis. Ninety-two samples of pathologically reviewed stage I endometrial cancers (80 endometrioid and 12 serous) with a heterogeneous distribution of grade and depth of myometrial invasion (i.e. 9 IAG1, 14 IAG2, 7 IAG3, 14 IBG1, 12 IBG2, 13 IBG3, 7 ICG1, 10 ICG2, and 6 ICG3) were examined in relation to 12 samples of atrophic endometrium from postmenopausal women. Specimens were analyzed using oligonucleotide microarray analysis and a subset of the differentially expressed transcripts was validated using quantitative PCR. Comparison of early stage cancers with normal endometrium samples by the univariate t-test with 10,000 permutations identified 900 genes that were differentially regulated by at least 4-fold at a p value of <0.001. Unsupervised analysis revealed that when compared to normal endometrium, serous and endometrioid stage I cancers appeared to have similar expression patterns. However, when compared in the absence of normal controls, they were distinct. Differential expression analysis revealed a number of transcripts that were common as well as unique to both histologic types. This data uncovers previously unrecognized, novel pathways involved in early stage endometrial cancers and identifys targets for prevention strategies that are inclusive of both endometrioid and serous histologic subtypes.
2011-12-13 | GSE17025 | GEO
Project description:Uterine dendritic cells (uDCs) are critical for endometrial function, yet their origin, molecular characteristics, and specific roles during the pre- and post-implantation periods in the human endometrium remain largely unknown. The complexity of the endometrial environment makes defining the contributions of uDCs subtypes challenging. We hypothesize that distinct uDC subsets carry out specialized functions, and that resident progenitor DCs generate these subtypes. Employing single-cell RNA sequencing on uterine tissues collected across different menstrual phases and during early pregnancy, we identify several uDCs subtypes, including resident progenitor DCs. CITE-seq was performed on endometrial single-cell suspensions to link surface protein expression with key genes identified by the RNAseq analysis. Our analysis revealed the developmental trajectory of the uDCs along with the distinct functional roles of each uDC subtype, including immune regulation, antigen presentation, and creating a conducive environment for embryo implantation. This study provides a comprehensive characterization of uDCs, serving as a foundational reference for future studies for better understanding female reproductive disorders such as infertility and pregnancy complications.
2025-08-08 | GSE288249 | GEO
Project description:The human endometrium is a highly regenerative tissue that undergoes cyclical proliferation, differentiation and shedding each month. The upper functionalis layer of the endometrium is shed in response to circulating levels of estrogen and progesterone, while the lower basalis layer remains. Clonogenic epithelial stem/progenitor cells likely responsible for regenerating endometrial epithelium have been identified in pre-menopausal (Pre-M) and post-menopausal (Post-M) endometrium and may reside in the basalis layer. We undertook a transcriptional profiling of purified epithelial cells from full-thickness Pre-M and Post-M endometrium to identify differentially expressed genes. The hypothesis tested in the present study was that Post-M endometrial epithelial gene profile would be similar to the quiescent basalis epithelium of Pre-M endometrium. We found striking differential gene expression of many Wnt family members between Pre-M and Post-M and other stem cell network genes. Comparative analysis of our endometrial epithelial gene expression profiles to that of endometrial epithelial cells in remodelling endometrium also provides new evidence showing that Post-M endometrial epithelium has a similar gene signature to that of basalis epithelium of menstrual endometrium. Human endometrial tissue was obtained from 8 pre-menopausal and 3 post-menopausal women undergoing hysterectomy for various benign gynaecologic conditions. Endometrial tissue was digested and isolated using combination of DNase and collagenase. Anti-human EpCAM antibody-coated magnetic Dynabeads was used to positively select total epithelial cells from the digested single cell suspensions. Total RNA was extracted from the purified endometrial epithelial cells and hybridised to Illumina Sentrix HT12 beadchip. Resulting data was compared between pre-menopausal and post-menopausal samples.
2012-04-10 | E-GEOD-35221 | biostudies-arrayexpress