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Status |
Public on Nov 30, 2024 |
Title |
Colon WT |
Sample type |
SRA |
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Source name |
murine colon infiltration immune cells
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: colon
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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. 10x scRNA-Seq
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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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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 3.2.3) was used for generation of Seurat object. Low-quality cells with UMI numbers greater than 3000 or less than 300, or having over 10% mitochondrial-derived UMI counts were removed. The count matrix was normalized with SCTransform function. IntegrateData function was used to integrate data and create a new matrix with 3000 features. PCA was performed by R package Seurat (version 3.2.3). Top 40 PCs were used for tSNE and UMAP. tSNE and UMAP were performed by R package Seurat (version 3.2.3). Assembly: mm10 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.
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Submission date |
Nov 01, 2022 |
Last update date |
Nov 30, 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) |
GSE217030 |
Loss of RPA1 impairs peripheral T cell homeostasis and exacerbates inflammatory damage through triggering T cell necroptosis |
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Relations |
BioSample |
SAMN31559607 |
SRA |
SRX18112172 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6703834_WT_barcodes.tsv.gz |
13.8 Kb |
(ftp)(http) |
TSV |
GSM6703834_WT_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
GSM6703834_WT_matrix.mtx.gz |
13.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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