|
| Status |
Public on Mar 16, 2022 |
| Title |
2-sh-LINC00958 |
| Sample type |
SRA |
| |
|
| Source name |
endometrial carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Ishikawa cells
treatment: LINC00958 silenced
|
| Treatment protocol |
Hairpin-derived small RNAs (shRNAs) targeting LINC00958 was purchased from Shanghai GeneChem of China. Seventy-two hours after lentivirus infection, 2.5 µg/ml puromycin was applied to screen for stably infected cells.
|
| Growth protocol |
Ishikawa cells were cultured in RPMI 1640 medium with 10% fetal bovine serum. All cells were cultured at 37°C in 5% CO2 with saturated humidity and routinely tested negative for mycoplasma.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Total RNA Extractor（Trizol）kit (B511311, Sangon, China) according to the manufacturer’s protocol, and treated with RNase-free DNase I to remove genomic DNA contamination.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Description |
2-sh-LINC00958
|
| Data processing |
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data.
Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters.
RSeQC (version 2.6.1) was used to statistics the alignment results
Gene expression values of the transcripts were computed by StringTie (version 1.3.3b).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includeTPM values for each Sample ...
|
| |
|
| Submission date |
Mar 14, 2022 |
| Last update date |
Mar 18, 2022 |
| Contact name |
Cuicui Wang |
| E-mail(s) |
wangcc@sj-hospital.org
|
| Organization name |
China Medical University
|
| Street address |
Sanhao Street
|
| City |
Shenyang |
| State/province |
Liaoning |
| ZIP/Postal code |
110000 |
| Country |
China |
| |
|
| Platform ID |
GPL29480 |
| Series (1) |
| GSE198619 |
RNA sequencing of LINC00958 silenced and LINC00958 non-silenced Ishikawa cells |
|
| Relations |
| BioSample |
SAMN26660337 |
| SRA |
SRX14464149 |
