|
| Status |
Public on Jul 19, 2023 |
| Title |
T88 |
| Sample type |
SRA |
| |
|
| Source name |
Osteosarcoma sample
|
| Organism |
Homo sapiens |
| Characteristics |
individual: 88
disease state: osteosarcoma
tissue: Osteosarcoma sample
age: 18
Sex: Male
site: Lower-extremity
|
| Treatment protocol |
Appropriate surgical operations were performed based on the characteristics of osteosarcoma. Tumor and normal adjacent tissues were excised and properly stored.
|
| Growth protocol |
Patients with osteosarcoma were included in this study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted and the purity, concentration and integrity of RNA samples were detected by advanced equipment to ensure that qualified samples can be used for transcriptome sequencing.
1) primer annealing, reverse transcription to get cDNA, add switch oligo; 2) synthesis of complementary chains; 3) DNA damage repair and end repair, magnetic beads purification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Base calling performed by Guppy software in MinKNOW2.2 package
Full-length sequences were obtained from the original sequences which have been filtered the low-quality (length less than 500bp, Qscore less than 6) reads and ribosomal RNA sequences.
Full-length sequences were aligned with the reference genome by minmap2 software. After clustering the alignment information, the consistent sequences were obtained by pinfish software.
Gffcompare is used to align transcripts obtained by full-length sequencing to known transcripts of the genome, so novel genes and transcripts can be obtained to supplement genome annotation.
Astalavista is used to obtain the alternative splicing types of each sample. TAPIS pipeline was used to further analyze full-length non-chimeric sequence (FLNC) to identify APA. The transcripts above 500bp were screened from the novel transcripts, and MISA software was used for SSR analysis.
Assembly: Full-length sequences were aligned with the reference genome by minmap2 software.
Supplementary files format and content: tab-delimited text files include CPM values for each Sample
|
| |
|
| Submission date |
Nov 15, 2022 |
| Last update date |
Jul 19, 2023 |
| Contact name |
Lin Qi |
| Organization name |
The Second Xiangya Hospital, Central South University
|
| Street address |
139 Renmin Road
|
| City |
Changsha |
| ZIP/Postal code |
410011 |
| Country |
China |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE218035 |
Long-read transcriptome sequencing reveals expression characteristics of osteosarcoma |
|
| Relations |
| BioSample |
SAMN31743294 |
| SRA |
SRX18275996 |
