|
| Status |
Public on Aug 02, 2021 |
| Title |
CR3_CR011_oocyte |
| Sample type |
SRA |
| |
|
| Source name |
a single oocyte of a fully grown follicle
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6D2F1 (C57BL/6 x DBA/2)
age/diet: CR (9 months with calorie restriction)
mouse: CR3
cell type: oocyte
oocyte-cumulus complex: CR011
|
| Extracted molecule |
total RNA |
| Extraction protocol |
single oocyte or their surrounding cumulus cells pool were lysed using cell lysis buffer [10 U RNasein plus (Promega), 10% RealTime ready Cell Lysis Buffer (Roche), 0.3% NP40 (Thermo Fisher Scientific), and RNase-free water (TAKARA)] in 0.2 mL single tube.
RamDA-seq sequencing libraries were constructed by using the advanced method of RamDA-seq (refer to the Methods section in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs" DOI: https://doi.org/10.1038/s41467-018-02866-0). However, to adapt to the manually picked single oocyte and their cumulus cells, the reaction volume from the cell lysis to the genomic DNA digestion step was modified. For details, refer to the protocol in "Aging-associated effects on transcriptome landscape and chromosome cohesion in single oocytes are influenced by life stage and calorie restriction".
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
count_GENCODEvM15_oocyte_cumulus.txt.gz
rpkm_GENCODEvM15_oocyte_cumulus.txt.gz
|
| Data processing |
fastq files were aligned to mouse reference genome GRCm38 using the Hisat2 v2.0.5
BAM files resulting from the alignments were summarized to genes using the featureCounts v1.5.1 with the parameters '-M -O --fraction'
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values or rpkms for each sample
|
| |
|
| Submission date |
Oct 09, 2020 |
| Last update date |
Aug 03, 2021 |
| Contact name |
Tomoya S KITAJIMA |
| E-mail(s) |
[email protected]
|
| Organization name |
RIKEN
|
| Department |
Center for Biosystems Dynamics Research
|
| Lab |
Laboratory for Chromosome Segregation
|
| Street address |
2-2-3 Minatojima-minamimachi
|
| City |
Kobe |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE159281 |
Single-oocyte transcriptome analysis reveals aging-associated effects influenced by life stage and calorie restriction |
|
| Relations |
| BioSample |
SAMN16402511 |
| SRA |
SRX9269311 |
