|
| Status |
Public on Mar 27, 2024 |
| Title |
ovary, VCD affected for 30 days, rep 5 |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Mus musculus |
| Characteristics |
tissue: ovary
developmental stage: 8-week-old
Sex: female
treatment: Intraperitoneal Injection VCD
time: 15 days
|
| Treatment protocol |
All the mice were treated intraperitoneally once a day for 15 days and starting the same day. The control group was injected with sesame oil and the experimental group had VCD dissolved in sesame oil at a concentration of 160 mg/kg.
|
| Growth protocol |
Mice are kept in separate cages (Total six cages with five mice per cage) and have free to access food and water. The environment has a normal circadian rhythm and a constant temperature and humidity (24 ± 2°C/40%).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ovarian tissues’ RNA extraction using TRLzol kit. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalentcationsunder elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
V30_5
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through fastp software
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.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include readcount values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Dec 01, 2023 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Yi Li |
| E-mail(s) |
liy21@lzu.edu.cn
|
| Phone |
18996460417
|
| Organization name |
Lanzhou University
|
| Street address |
甘肃省兰州市城关区东岗西路1号兰州大学第一医院
|
| City |
兰州市 |
| State/province |
甘肃 |
| ZIP/Postal code |
700030 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE249151 |
Transcriptome analysis during VCD exposure-induced POI in mice |
|
| Relations |
| BioSample |
SAMN38566019 |
| SRA |
SRX22708045 |
