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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 27, 2024 |
| Title |
S1D0.5,scRNA-seq |
| Sample type |
SRA |
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| Source name |
induced from hADSC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: induced from hADSC
cell line: 0618
cell type: induced from hADSC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and resuspended at 1 x 106 cells per milliliter in PBS supplemented with 0.04% BSA.
Using Single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension containing 300-600 living cells per microliter was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion (GEMs) according to the manufacturer’s protocol. On an S1000TM Touch Thermal Cycler (Bio Rad), captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEM. These steps were carried out at 53 °C for 45 minutes, followed by 85 °C for 5 minutes, and held at 4 °C. Single-cell RNA sequencing libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics) and sequenced by IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150).
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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 |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Oct 27, 2024 |
| Last update date |
Oct 27, 2024 |
| Contact name |
Jingxiao Cao |
| E-mail(s) |
Jingxiao.Cao@stu.pku.edu.cn
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| Organization name |
Peking University
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| Department |
School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.
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| Lab |
Hongkui Deng's Lab
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| Street address |
No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100091 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE264658 |
A Fast Chemical Reprogramming System to Generate Human Pluripotent Stem Cells [RNA-seq] |
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| Relations |
| BioSample |
SAMN44467292 |
| SRA |
SRX26512764 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8596541_S1D0.5_barcodes.tsv.gz |
17.4 Kb |
(ftp)(http) |
TSV |
| GSM8596541_S1D0.5_features.tsv.gz |
302.7 Kb |
(ftp)(http) |
TSV |
| GSM8596541_S1D0.5_matrix.mtx.gz |
72.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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