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| Status |
Public on May 31, 2023 |
| Title |
CD33-1 |
| Sample type |
SRA |
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| Source name |
Ovary
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| Organism |
Cricetulus griseus |
| Characteristics |
tissue: Ovary
cell line: Chinese hamster ovary cells (CHO-S)
cell type: Monclonal cell line
genotype: human CD33 knock in
treatment: site-specific integration of human CD33 at C12orf35 site of CHO cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Cat# 74106, Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme) following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
gene_expression_CD33.xls
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| Data processing |
Seqtk
Remove the linker sequence contained in the reads
Remove bases with a quality Q lower than 20 at the 3' end, that is, the base error rate is less than 0.01, where Q=-10logerror_ratio
Remove reads whose length is less than 25
Remove the ribosome RNA reads of the species to which they belong
Assembly: CHOK1GS_HDv1
Supplementary files format and content: xls files include count and FPKM values for each sample
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| Submission date |
May 17, 2022 |
| Last update date |
May 31, 2023 |
| Contact name |
Hui Wang |
| E-mail(s) |
[email protected]
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| Phone |
18521306979
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| Organization name |
Shanghai Jiao Tong University
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| Department |
School of Pharmacy
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| Street address |
Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, China
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| City |
Shanghai |
| State/province |
China |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platform ID |
GPL27425 |
| Series (1) |
| GSE203219 |
Stability and transcriptomic study of C12orf35 site-specific integrated CHO cell line |
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| Relations |
| BioSample |
SAMN28495777 |
| SRA |
SRX15316775 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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