|
Status |
Public on Jun 28, 2023 |
Title |
EOMA _Empty- pLC5-ciR_rep2 |
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). RNA libraries were prepared for sequencing using standard Illumina protocols.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
C2
|
Data processing |
Raw data were firstly processed through in-house perl scripts to remove reads containing adapter, reads containing ploy-N and low quality reads, and were then filtered by Q20, Q30 and GC contents. The acquired clean data were mapped to the mouse reference genome (mm10) using HISAT2 (v2.0.4). For each sample, read counts for each gene were obtained with HTSeq(v0.6.1) and were standardized as fragments per kilobase million (FPKM). Differential expression analysis of two groups was performed using the DESeq R package (1.10.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Assembly: mm10 Supplementary files format and content: Matrix table with mRNA FPKM 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 |
GPL24247 |
Series (2) |
GSE218578 |
The angiogenic role of circRNA-007371 in liver fibrosis [RNA-Seq] |
GSE218581 |
The angiogenic role of circRNA-007371 in liver fibrosis |
|
Relations |
BioSample |
SAMN31840443 |
SRA |
SRX18352756 |