|
| Status |
Public on May 23, 2023 |
| Title |
EAOC4 |
| Sample type |
SRA |
| |
|
| Source name |
Endometriosis-associated ovarian cancer over time (EAOC)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Endometriosis-associated ovarian cancer over time (EAOC)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction adopts traditional trizol method
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp 0.20.1
Trimmed sequence reads were mapped to GRCm38 using hisat2 2.2.1
read count extraction and normalization were performed using stringtie 2.1.5（-e -b）and R Package "ballgown"
|
| |
|
| Submission date |
Mar 03, 2023 |
| Last update date |
May 23, 2023 |
| Contact name |
Lijing Zhao |
| E-mail(s) |
zhao_lj@jlu.edu.cn
|
| Phone |
13756281155
|
| Organization name |
The second hospital of jilin university
|
| Department |
gynaecology and obstetrics
|
| Street address |
Office Building, School of Nursing, Jilin University, No. 965 Xinjiang Street
|
| City |
Changchun |
| State/province |
jilin |
| ZIP/Postal code |
130012 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE226575 |
A comprehensive analysis of the mechanism of FOS in the progression of endometrialcyst of ovary to endometriosis-associated ovarian cancer |
|
| Relations |
| BioSample |
SAMN33577972 |
| SRA |
SRX19558063 |
