|
| Status |
Public on Jun 07, 2023 |
| Title |
P1_ONC_2 |
| Sample type |
SRA |
| |
|
| Source name |
retina
|
| Organism |
Mus musculus |
| Characteristics |
tissue: retina
age: postnatal day (P) 1
strain: C57BL/6
genotype: wild type
treatment: optic nerve crush injury
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were removed and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) was used with 3 ug of total RNA for the construction of sequencing libraries.
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 |
Illumina Casava1.8 software used for basecalling.
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.
Assembly: mm10
Supplementary files format and content: Files include gene counts and FPKM values for each Sample
|
| |
|
| Submission date |
May 12, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Ling-Ping Cen |
| E-mail(s) |
cenlp@hotmail.com
|
| Organization name |
JSIEC
|
| Street address |
North Dongxia Road
|
| City |
Shantou |
| ZIP/Postal code |
515041 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE232373 |
Retinal transcriptome of neonatal mice after optic nerve injury |
|
| Relations |
| BioSample |
SAMN35056378 |
| SRA |
SRX20304340 |
