|
| Status |
Public on May 15, 2023 |
| Title |
Perthes' disease Rabbit, replicate 1 [TB-1] |
| Sample type |
SRA |
| |
|
| Source name |
femoral head
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
tissue: femoral head
genotype: Perthes' disease
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5 μg RNA of each sample were utilized with ribosomal RNA removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, United States)
NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (NEB, United States)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adapters, low-quality reads (percentages of base quality lower than 15 higher than 20%), reads with unknown base higher than 5% were removed with SOAPnuke V1.5.2
Clean reads were mapped to reference genome with HISAT2 V2.0.4 with default parameters. Then, gene expressions were quantified by RSEM V1.1.17 and HTSeq V1.99.2
Supplementary files format and content: GCA_000003625.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Nov 14, 2022 |
| Last update date |
May 15, 2023 |
| Contact name |
hu xiaolin |
| E-mail(s) |
184514@shsmu.edu.cn
|
| Organization name |
Shanghai Jiaotong University School of Medicine
|
| Street address |
south congqing road 227#
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
20025 |
| Country |
China |
| |
|
| Platform ID |
GPL25392 |
| Series (1) |
| GSE217908 |
Construction of ceRNA network based on an RNA‑seq shows prognostic lncRNA biomarkers in Perthes’ disease |
|
| Relations |
| BioSample |
SAMN31711955 |
| SRA |
SRX18249273 |
