 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 06, 2024 |
| Title |
RNA-con 1 |
| Sample type |
SRA |
| |
|
| Source name |
oocyte
|
| Organism |
Mus musculus |
| Characteristics |
cell line: oocyte
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Oocytes were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the Single Cell Full Length mRNA-Amplification Kit(N712, Vazyme) according to the manufacturer’s instructions.
Library preparation was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD502, Vazyme) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
count.txt
|
| Data processing |
CUT&Tag paired-end reads were aligned to the mouse genome (mm10) using Bowtie 2 (version 2.2.5) with a default setting after removing adaptor sequences and low-quality reads by fastp (version 0.12.4). Reads from PCR duplicates were removed using Picard ‘MarkDuplicates’. After confirming reproducibility between replicates, they were merged using Samtools‘merge’. Final bam files were converted to bigWig files of read coverages normalized to RPKM using deepTools (version 3.5.1) bamCoverage.
For RNA-seq analysis of all data, we downloaded the mouse reference genome (genome assembly: mm10) from the Ensembl database and used the HISAT2 software for read alignment with a default setting after removing adaptor sequences and low-quality reads by fastp (version 0.12.4). The gene-level quantification approach was used to aggregate raw counts of mapped reads using the featureCounts tool. The expression level of each gene was quantified in terms of the normalized fragments per kilobase of transcript per million mapped reads (FPKM). Next, we used the R package DESeq2 for differential gene expression analysis.
Assembly: mm10
|
| |
|
| Submission date |
Feb 26, 2024 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Ming Zong |
| E-mail(s) |
ZongMing1112@126.com
|
| Organization name |
Wenzhou Medical University
|
| Street address |
University Town, Chashan, Wenzhou
|
| City |
33-浙江省 |
| ZIP/Postal code |
325035 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE259264 |
Low-dose exposure to microplastics retards meiotic maturation via HDACs insufficiency |
|
| Relations |
| BioSample |
SAMN40140689 |
| SRA |
SRX23743375 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
