|
| Status |
Public on Apr 30, 2024 |
| Title |
siF1 |
| Sample type |
SRA |
| |
|
| Source name |
Umbilical cord
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mesenchymal stem cells
treatment: Follistatin like 1(FSTL1) silencing
|
| Treatment protocol |
MSCs were transfected with NC-siRNA or FSTL1 siRNA for 24 h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit
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 |
| |
|
| Data processing |
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
RNA sequencing libraries were generated with an insert size ranging from 370 to 420 bp, and sequenced using the Illumina NovaSeq 6000 platform (Novogene-Tianjin, China). Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.5) software. Quantification of gene expression level featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for all Samples
|
| |
|
| Submission date |
May 05, 2022 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Xiaohong Zheng |
| E-mail(s) |
jinghuan1989@126.com
|
| Organization name |
Fourth Military Medical University
|
| Department |
Xijing Hospital of Digestive Diseases
|
| Lab |
State Key Laboratory of Cancer Biology
|
| Street address |
127 Changle West Road
|
| City |
Xi’an |
| State/province |
Shaanxi |
| ZIP/Postal code |
710032 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE202320 |
Follistatin-like 1 guarantees the immunomodulatory properties of mesenchymal stem cells during liver fibrotic therapy |
|
| Relations |
| BioSample |
SAMN28102582 |
| SRA |
SRX15168191 |
