|
| Status |
Public on Dec 14, 2025 |
| Title |
shNS |
| Sample type |
SRA |
| |
|
| Source name |
Leukemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Leukemia
shRNA: shNS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Immunoprecipitated samples were subjected to Proteinase K digestion at 55°C for 1 hour. Total RNAs were extracted from both the input and immunoprecipitated samples by adding 5 volumes of TRIzol reagent, followed by Direct-zol RNA Miniprep (Zymo).
Libraries for high-throughput sequencing were constructed using the TruSeq Stranded v2 mRNA Sample Prep Kit (Illumina) and were quantified by a BioAnalyzer High Sensitivity DNA chip.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads with low-quality base (base quality less than or equal to 15) ratio more than 20%; (3) Removing reads with unknown base ratio more than 5%.
Bowtie2 was applied to align the clean reads to the gene set.
Expression level of gene was calculated by RSEM.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCh38
Supplementary files format and content: FPKM value of genes calculated by RSEM.
|
| |
|
| Submission date |
Feb 12, 2024 |
| Last update date |
Dec 14, 2025 |
| Contact name |
Siyao Guo |
| E-mail(s) |
guosy6@mail2.sysu.edu.cn
|
| Organization name |
The First Affiliated Hospital, Sun Yat-sen University
|
| Street address |
No.58 Zhongshan Er Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE255603 |
Function and mechanism of PAPOLA-mediated poly(A) lengthening in leukemia [RIP-Seq] |
| GSE255668 |
Function and mechanism of PAPOLA-mediated poly(A) lengthening in leukemia |
|
| Relations |
| BioSample |
SAMN39942192 |
| SRA |
SRX23619514 |
