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| Status |
Public on Feb 25, 2024 |
| Title |
C1_Condition_Control_Rep1 |
| Sample type |
SRA |
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| Source name |
Cartilage
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Cartilage
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
C1
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| Data processing |
Unique molecular identifier (UMI) counts were obtained by aligning FASTQ files to the human reference genome (GRCh38 3.0.0) through Cell Ranger (version 4.0) software from the 10X Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references). Gene expression raw count matrices were used for downstream analyses. Specifically, for each scRNA-seq dataset, the quality control steps included low-quality cell removal and mitochondrial count filtering. We performed the doublets removal step using the DoubletFinder (version 2.0.3) when the captured cell was larger than 10,000, with pK (the principal component neighbourhood size used to calculate pANN) set to 0.09, nEXP (the total number of doublet predictions produced) set to 0.075, and other parameters as the default settings.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes annotation information for each Sample
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| Submission date |
Feb 09, 2024 |
| Last update date |
Feb 25, 2024 |
| Contact name |
Yue Fan |
| E-mail(s) |
xafanyue@xjtu.edu.cn
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| Organization name |
Xi'an Jiaotong University
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| Street address |
Yanta West Road No.76
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| City |
Xi'an |
| ZIP/Postal code |
710061 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE255460 |
Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls |
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| Relations |
| BioSample |
SAMN39900239 |
| SRA |
SRX23585127 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8072834_C1_barcodes.tsv.gz |
8.7 Kb |
(ftp)(http) |
TSV |
| GSM8072834_C1_features.tsv.gz |
325.6 Kb |
(ftp)(http) |
TSV |
| GSM8072834_C1_matrix.mtx.gz |
15.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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