|
| Status |
Public on Feb 21, 2024 |
| Title |
onc+msc.ev treated replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Retina cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Retina cells
genotype: WT
treatment: ONC+i.o.MSC.sEV
time: Day 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells and retinas were resuspended in 1 ml of Trizol buffer (Cat. No. 9109, TAKARA) for RNA extraction. Total RNA was purified, and the RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Libraries were constructed using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) 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 |
Illumina NovaSeq 6000 |
| |
|
| Description |
onc+msc.ev-1
|
| Data processing |
The quality of all datasets was checked by FastQC (v 0.11.8), and low-quality reads were removed.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. 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. The output matrix was utilized as input into BIOMEX software.
Identification of differentially expressed genes between experimental group and control group was performed by the default module of differential analysis based on LIMMA methods in BIOMEX. Pathway enrichment was performed by the GSEA module.
Supplementary files format and content: 10mm
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jan 23, 2023 |
| Last update date |
Feb 21, 2024 |
| Contact name |
xialin liu |
| E-mail(s) |
yangziqi@gzzoc.com
|
| Organization name |
Zhongshan Opythalmic Center, Sun yat-sen University
|
| Street address |
Jinsui Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE223529 |
Retinal Ly6Clow Mo/MΦ protect optic nerve against injury |
| GSE224068 |
MSC-sEV regulates Ly6Clow Mo/MΦ in neural restoration |
|
| Relations |
| BioSample |
SAMN32878213 |
| SRA |
SRX19144108 |
