 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 31, 2023 |
| Title |
CLL1-3 |
| Sample type |
SRA |
| |
|
| Source name |
Ovary
|
| Organism |
Cricetulus griseus |
| Characteristics |
tissue: Ovary
cell line: Chinese hamster ovary cells (CHO-S)
cell type: Monclonal cell line
genotype: human CLL1 knock in
treatment: site-specific integration of human CLL1 at C12orf35 site of CHO cells
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
gene_expression_CLL1.xls
|
| 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
|
| |
|
| Submission date |
May 17, 2022 |
| Last update date |
May 31, 2023 |
| Contact name |
Hui Wang |
| E-mail(s) |
[email protected]
|
| Phone |
18521306979
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
School of Pharmacy
|
| Street address |
Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, China
|
| City |
Shanghai |
| State/province |
China |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL27425 |
| Series (1) |
| GSE203219 |
Stability and transcriptomic study of C12orf35 site-specific integrated CHO cell line |
|
| Relations |
| BioSample |
SAMN28495778 |
| SRA |
SRX15316774 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
