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| Status |
Public on Jan 01, 2021 |
| Title |
WT golden hamster small intestine |
| Sample type |
SRA |
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| Source name |
golden hamster small intestine
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| Organism |
Mesocricetus auratus |
| Characteristics |
strain: RjHan:AURA
developmental stage: Adult
tissue: small intestine
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| Extracted molecule |
total RNA |
| Extraction protocol |
After tissue preparation and cell digestion, single-cell suspensions were processed on the 10X chromium system following the manufacturer's protocols.
cDNA libraries were constructed using Chromium Single cell 3' v3 Reagent Kit (10X genomics)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
WT golden hamster
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| Data processing |
Cell Ranger (v3.0.2) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to MesAur1.0 reference genome
Aligned reads were then read by Seurat (v3.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control, expression matrices were log normalized and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: MesAur1.0
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for WT hamster organs' single cell data
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| Submission date |
Jul 16, 2020 |
| Last update date |
Jan 03, 2021 |
| Contact name |
Myung Jin Yang |
| E-mail(s) |
mjyang@kaist.ac.kr
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| Organization name |
Institute for Basic Science
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| Street address |
34141
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| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platform ID |
GPL28882 |
| Series (1) |
| GSE154564 |
Single-cell RNA sequencing of golden hamster upper respiratory tract (nasal mucosa and trachea), lung, kidney and small intestine |
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| Relations |
| BioSample |
SAMN15555071 |
| SRA |
SRX8743902 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4673475_hamster_small_intestine_expression_matrix.csv.gz |
56.7 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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