 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 28, 2023 |
| Title |
EOMA _Empty- pLC5-ciR_rep1 [ncRNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
EOMA
|
| Organism |
Mus musculus |
| Characteristics |
cell line: EOMA
treatment: Empty- pLC5-ciR
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from EOMA cells using TRIzol reagent (Thermo Fisher Scientific, USA).
Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
C1
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw dataswere calculated.
For known miRNA alignment, the acquired clean data were mapped to miRBase20.0 using modified software mirdeep2 and srna-tools-cli to obtain the potential miRNA and draw the secondary structures.
For novel miRNA prediction, miREvo and mirdeep2 were used to predict novel miRNA through exploring the secondary structure.
MiRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Differential expression analysis of two groups was performed using the DESeq R package (3.0.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach.
Assembly: miRBase20.0
Supplementary files format and content: Matrix table with miRNA TPM (transcript per million) for each sample
|
| |
|
| Submission date |
Nov 22, 2022 |
| Last update date |
Jun 28, 2023 |
| Contact name |
shuaijie qian |
| E-mail(s) |
qsjbxh1997@outlook.com
|
| Phone |
13540675514
|
| Organization name |
West China Hospital, Sichuan University
|
| Lab |
Lab of Gastroenterology and Hepatology
|
| Street address |
NO. 1, 4th Keyuan Road, Chengdu,
|
| City |
chengdu |
| State/province |
sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE218579 |
The angiogenic role of circRNA-007371 in liver fibrosis [ncRNA-Seq] |
| GSE218581 |
The angiogenic role of circRNA-007371 in liver fibrosis |
|
| Relations |
| BioSample |
SAMN31840779 |
| SRA |
SRX18352840 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
