|
| Status |
Public on Nov 13, 2023 |
| Title |
COR: Oocytes, cor, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
oocytes
|
| Organism |
Spalacopus cyanus |
| Characteristics |
cell type: oocytes
|
| Growth protocol |
Oocytes were isolated from freshly sacrificed females by manual disruption of the ovary in M2 media and washed in PBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Picopure RNA extraction kit (Arcturus)
Ribosomal RNA was depleted with NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) with sample purification beads (NEB, E7405) according to the manufacturer’s instructions, including DNase treatment by TURBO DNase (Thermo Fisher Scientific, AM2238) followed by library preparation using NEBNext Ultra II Directional RNA Library Prep with sample purification beads (NEB, E7765S) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
read trimming (Trim Galore! v0.6.1)
read mapping (Hisat2 v2.1.0)
data quantification (Seqmonk)
Assembly: HetGla2/HetGla_female_1.0; Cavpor3.0; degu sequences XM_023711114.1, XM_004630806.2 and XM_023716073.1
Supplementary files format and content: txt file with raw read counts of individual genes
|
| |
|
| Submission date |
Aug 17, 2023 |
| Last update date |
Nov 13, 2023 |
| Contact name |
Lenka Gahurova |
| E-mail(s) |
lenka.veselovska@gmail.com
|
| Organization name |
University of South Bohemia
|
| Department |
Department of molecular biology and genetics
|
| Lab |
Laboratory of early mammalian development
|
| Street address |
Branisovska 1760
|
| City |
Ceske Budejovice |
| ZIP/Postal code |
37005 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL33695 |
| Series (1) |
| GSE236457 |
Expression analysis suggests that DNMT3L is required for oocyte de novo DNA methylation only in Muridae and Cricetidae rodents |
|
| Relations |
| BioSample |
SAMN37041630 |
| SRA |
SRX21404677 |
