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| Status |
Public on Apr 13, 2024 |
| Title |
WT_3 |
| Sample type |
SRA |
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| Source name |
wild type
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
treatment: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs of the wild type and IRAIN over-expression K562 cells were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).
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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 |
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 33, GRCh38).
The Gene abundances are given as read counts with “--quantMode GeneCounts” parameter using the STAR.
Assembly: hg38
Supplementary files format and content: Excel file include gene counts for each Sample …
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| Submission date |
Apr 10, 2024 |
| Last update date |
Apr 13, 2024 |
| Contact name |
Jinsong Yan |
| E-mail(s) |
[email protected]
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| Organization name |
Dalian Medical University
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| Department |
Institute of Cancer Stem Cell
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| Street address |
9 west section, Lvshun south road, Dalian, Liaoning Province, China
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| City |
Dalian |
| ZIP/Postal code |
116044 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE263645 |
Whole transcriptome sequencing for wild type and IRAIN over-expression K562 cells |
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| Relations |
| BioSample |
SAMN40918282 |
| SRA |
SRX24209782 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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