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| Status |
Public on Jun 15, 2024 |
| Title |
CKO |
| Sample type |
SRA |
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| Source name |
immune cells from lymph nodes
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: RPA1 conditional knockout
tissue: Lymph nodes
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
B20210624-4_S5_L003
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| Data processing |
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 4000 or less than 1000, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with NormalizeData function.
Merge function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 4.0.3). Top 30 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 4.0.3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell (gene-barcode counts, gene file, and cell barcode file)
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| Submission date |
Nov 24, 2021 |
| Last update date |
Jun 15, 2024 |
| Contact name |
Jia Song |
| E-mail(s) |
songjia@bjmu.edu.cn
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| Phone |
+18830053918
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| Organization name |
Peking University
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| Street address |
Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing
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| City |
Beijing |
| State/province |
China |
| ZIP/Postal code |
100080 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
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| Relations |
| BioSample |
SAMN23429412 |
| SRA |
SRX13225283 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5703498_2_barcodes.tsv.gz |
66.7 Kb |
(ftp)(http) |
TSV |
| GSM5703498_2_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM5703498_2_matrix.mtx.gz |
94.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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