|
| Status |
Public on Oct 05, 2021 |
| Title |
MI_B1 |
| Sample type |
SRA |
| |
|
| Source name |
Oocyte
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: MI
sample id: 1
batch: B
cell type: Oocyte
strain: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After washed three times with 0.1% BSA/PBS, each oocyte was then transferred into 0.2 mL PCR tubes containing 2 μl lysis buffer.
Transcriptome libraries were prepared following the Smart-seq2 protocol. Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
htseq_gene_count_mat.txt.gz
rsem_gene_count_mat.txt.gz
rsem_trans_count_mat.txt.gz
|
| Data processing |
Illumina HSC 1.6.0/RTA 3.4.4 software used for sequencing and basecalling.
Trim Galore (v0.6.4) to trim adapters from reads and remove low quality bases in the data, with arguments length >= 25, stringency = 3 and quality = 25
STAR (v2.7.6a) to map the trimmed reads against the mouse reference genome (mm10) and its corresponding GENCODE gene annotation (VM20).
HTSeq (v0.12.4) to count the reads aligned to each gene for gene-level expression quantification.
In parallel, RSEM (v1.3.1) to align and calculate the expression at both the gene level and the transcript level.
Genome_build: mm10
Supplementary_files_format_and_content: txt: gene-level read counts by HTSeq
Supplementary_files_format_and_content: txt: gene-level expected read counts by RSEM
Supplementary_files_format_and_content: txt: isoform-level expected read counts by RSEM
|
| |
|
| Submission date |
Jun 24, 2021 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Xi Wang |
| Organization name |
Nanjing Medical University
|
| Street address |
Longmian Avenue 101, Jiangning District
|
| City |
Nanjing |
| ZIP/Postal code |
21116 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE178836 |
Pervasive 3'-UTR isoform switches during mouse oocyte maturation |
|
| Relations |
| SRA |
SRX11219351 |
| BioSample |
SAMN20035033 |
