|
| Status |
Public on Aug 23, 2023 |
| Title |
Ube2i cKO GV oocyte 16 [6322b_SB39] |
| Sample type |
SRA |
| |
|
| Source name |
GV stage Oocyte
|
| Organism |
Mus musculus |
| Characteristics |
cell type: GV stage Oocyte
genotype: Ube2i(loxp/loxp) Zp3-cre(+)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq library was generated according to SMART-seq v4 Ultra low input RNA kit (Takara). In brief, isolated cells were lysed in lysis buffer, 3-SMART-seq CDS primer II and V4 oligonucleotide were added for first stranded cDNA synthesis. cDNA was amplified using PCR Primer II A, and subsequently purified using Ampure XP beads (Beckman).
Illumina library was prepared using Nextera XT DNA library preparation kit (Illumina) and sequenced using Illumina Novaseq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequencing reads were preprocessed using BBDuk for quality-trimming and filtering, adapter-trimming.
Reads were aligned to reference genome using STAR Aligner.
The gene count table was generated from from subreads using featureCounts.
The raw counts were filtered, normalized, and analyzed using DESeq2.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized gene counts for each Sample
|
| |
|
| Submission date |
Nov 21, 2022 |
| Last update date |
Aug 23, 2023 |
| Contact name |
Peixin Jiang |
| Organization name |
Baylor College of Medicine
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE218484 |
The E2 SUMO-conjugating enzyme UBE2I is essential for chromatin dynamics and transcriptional silencing in mouse oocytes |
|
| Relations |
| BioSample |
SAMN31820827 |
| SRA |
SRX18333069 |
