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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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