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| Status |
Public on Feb 27, 2022 |
| Title |
BJ2020-12049-2 |
| Sample type |
SRA |
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| Source name |
Cecum cell
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| Organism |
Sus scrofa |
| Characteristics |
age: 1 day
tissue: cecum
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics Inc., Pleasanton, CA, USA) following the manufacture’s introduction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes
map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: susScr11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
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| Submission date |
Dec 15, 2020 |
| Last update date |
Feb 27, 2022 |
| Contact name |
Yong Zhao |
| E-mail(s) |
yzhao818@hotmail.com
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| Phone |
86-18661613617
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| Organization name |
Qingdao Agricultural University
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| Department |
College of Life Sciences
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| Lab |
B604
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| Street address |
700 Changcheng Road
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| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266109 |
| Country |
China |
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| Platform ID |
GPL26351 |
| Series (1) |
| GSE163272 |
Swine cecum development at single cell level |
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| Relations |
| BioSample |
SAMN17086296 |
| SRA |
SRX9688461 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4976427_1day_barcodes.tsv.gz |
68.5 Kb |
(ftp)(http) |
TSV |
| GSM4976427_1day_features.tsv.gz |
161.1 Kb |
(ftp)(http) |
TSV |
| GSM4976427_1day_matrix.mtx.gz |
81.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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