Aa6721c8-2d18-4959-8cf0-d45916435a16 - samples
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ABSTRACT:
PROVIDER: EGAD00001006644 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Purpose: To dissect the transcriptomic profiles and unravel population-specific transcriptional heterogeneity of self renewing hair follicle stem cells in vivo Methods: We performed 10x genomics single-cell RNA sequencing (scRNA-seq) of FACS sorted CD34+/K14-H2BGFP+ hair follicle stem cells from mouse skin at mid-anagen. FACS purified CD34+/K14-H2BGFP+ single-cell suspension was processed for the barcoded single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3. The final libraries were quantified using Agilent Bioanalyzer high sensitivity DNA chip and sequenced using an Illumina NextSeq-500. The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-3.0.0) using the 10x Genomics Cell Ranger pipeline (v3.1.0). The raw scRNA-seq data was processed using Cell Ranger from the 10x platform to generate an expression matrix that was further analyzed in R using the Seurat package version 3.1. Only high-quality cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained. Results: We obtained a total of 6736 high quality cells from two datasets for further analysis by Seurat workflow Conclusions: Obtained high quality single cell transcriptomic data to dissect molecular heterogeneity of hair follicle stem cells
2021-04-14 | GSE162333 | GEO
Project description:Purpose: To unravel the molecular heterogeneity and characterise cell states of LRC/Non-LRC domains in interfollicular epidermis in vivo Methods: We performed 10x genomics single-cell RNA sequencing (scRNA-seq) of FACS purified basal (Sca1+/alpha6-integrin+) IFE cells as H2BGFP LRCs, mid-LRCs, and non-LRCs from K5-tTA x pTRE-H2BGFP mice. Single-cell suspension from back (2-week chase) and tail skin (3-week chase) was processed for the barcoded single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3. The final libraries were quantified using Agilent Bioanalyzer high sensitivity DNA chip and sequenced using an Illumina NextSeq-500. The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-3.0.0) using the 10x Genomics Cell Ranger pipeline (v3.1.0). The raw scRNA-seq data was processed using Cell Ranger from the 10x platform to generate an expression matrix that was further analyzed in R using the Seurat package version 3.1. Only high-quality cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained. Results: We obtained a total of 13484 and 14884 high quality cells from two different skin types after combining two datasets each from LRCs/mid-LRCs/Non-LRCs for further analysis by Seurat workflow Conclusions: Obtained high quality single cell transcriptomic data to dissect molecular and proliferative heterogeneity of interfollicular epidermis (IFE)
2022-07-05 | GSE205745 | GEO
Project description:Purpose: To comprehensively characterize VE-cadherin expressing lineages during adult skin homeostasis, to dissect their population-specific transcriptomic heterogeneity, and to investigate role of Alk1 in these linegease in vivo. Methods: We performed 10x genomics single-cell RNA sequencing (scRNA-seq) of FACS sorted tdTomato+ cells from tdTomato;Cdh5-CreERT2;Krt14-H2BGFP mice (for WT) or Alk1 flox flox;tdTomato;Cdh5-CreERT2 (For Alk1KO) back skin at indicated stage/genotype. FACS purified tdTomato+ single-cell suspension was processed for the barcoded single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3. The final libraries were quantified using Agilent Bioanalyzer high sensitivity DNA chip and sequenced using an Illumina NextSeq-500. The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-2020-A) using the 10x Genomics Cell Ranger pipeline (v6.0.1). The raw scRNA-seq data was processed using Cell Ranger from the 10x platform to generate expression matrix for each sample that was further analyzed in R using the Seurat package version 4.0. Only high-quality cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained for further analysis. Results: We obtained more than 2000 high quality cells at each stage/genotype for further analysis by Seurat pipeline Conclusions: Obtained high quality single cell transcriptomic data to dissect cellular and molecular heterogeneity of VE-cadherin expressing endothelial and non-endothelial lineages in adult mouse back skin.
2023-03-01 | GSE211381 | GEO
Project description:We performed single-cell RNA sequencing (using Cell Ranger Single Cell Pipeline v.4.0.0 to process data de-multiplexing, barcode processing, and single cell 3' gene counting generated by the 10X Chromium platform) in KD patients (within 24 hours before IVIG treatment) and age-matched fever controls.
2024-06-01 | GSE254657 | GEO
Project description:We performed single-cell RNA sequencing (using Cell Ranger Single Cell Pipeline v.4.0.0 to process data de-multiplexing, barcode processing, and single cell 3' gene counting generated by the 10X Chromium platform) in KD patients (within 24 hours before IVIG treatment) and age-matched fever controls.
2022-09-06 | GSE200743 | GEO
Project description:scRNA-seq was used to characterise hiPSC-derived kidney organoids differentiated within fully synthetic self-assembling peptide hydrogels of variable mechanical strengths and compare these to organoids differentiated within the animal-derived matrix, Matrigel. Organoids were matured in the respective matrices until day 24 of differentiation and 6 organoids per support matrix were then pooled and dissociated using the cold-active protease from Bacillus licheniformis. Cells were processed on the 10x Genomics Chromium platform using the Single-Cell 3’ v3.1 protocol. The NextSeq500 (Illumina) was used to sequence the libraries generated and initial processing of the data was carried out using the 10X Genomic Cell Ranger v3.1.0 pipeline.
2022-10-31 | E-MTAB-11149 | biostudies-arrayexpress
Project description:Head and neck squamous cell carcinoma (HNSCC) includes a large subset of cancers that are driven by the human papilloma virus (HPV) and occur primarily in the oropharynx. Here, we use 10x single cell RNA-seq to profile 70,970 cells from 11 HPV-positive and 5 HPV-negative oropharyngeal tumors in order to uncover diversity in chromosomal aberrations, cellular states and viral gene expression between and within tumors.
2022-11-30 | GSE182227 | GEO
Project description:12 cervicothoracic sections of mouse embryos were dissected at E9.5 (2 replicates), E10.5 (2 replicates), E11.5 (2 replicates), E12.5 (3 replicates), E13.5 (3 replicates). Single-cell RNA-seq libraries were encapsulated, sequenced, aligned, and counted with the 10X Genomics’ Chromium platform and Illumina’s HiSeq 4000 platform.
2018-11-29 | E-MTAB-7320 | biostudies-arrayexpress
Project description:Monocytes isolated from skin wounds on non-diabetic and diabetic mice on day 6 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per strain. Fresh cells with viability over 85% processed using the 10x Chromium platform . Libraries sequenced on HiSeq with paired-end reads. Fastq files were generated and iesdemultiplexed into single cells using Cell Ranger software
2020-11-24 | GSE154400 | GEO
Project description:Monocytes and macrophages isolated from skin wounds on male C57BL6/J mice on day 3, 6, and 10 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per time point. Fresh cells with viability over 70% processed using the 10x Chromium platform. Libraries sequenced on HiSeq with paired-end reads. Fastq files were generated and demultiplexed into single cells using Cell Ranger software
2022-09-08 | GSE203244 | GEO