 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 22, 2024 |
| Title |
cumulus cells with pre-incubation time equals 2 hours, T2 |
| Sample type |
SRA |
| |
|
| Source name |
cumulus cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: cumulus cells
treatment: pre-incubation
time: 2 hours
|
| Treatment protocol |
The extracted Cumulus-oocyte Complex (COC) samples were washed with GMOPS medium (Vitrolife, Gothenburg, Sweden) to remove the blood contamination.
In the T0 group, COCs were immediately dissected to separate the cumulus cells from around the oocytes and prepare the oocytes for ICSI. Then, CCs related to mature metaphase II (MII) oocyte were centrifuged at 200 g, for 10 min and after washing with phosphate-buffered saline (PBS) stored in liquid nitrogen
In the T2 group, dissection and preparation of CCs were done after 2 hours of incubation. pre-incubation was performed at 37°C, 95% humidity, 6% CO2 and 5% O2 condition. All the media were from Vitrolife (Vitrolife, Gothenburg, Sweden).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using the RNeasy Mini kit (Qiagen, Germany).
RNA libraries for RNA-Seq were prepared using rRNA Depletion stranded Library prep kit by BGI company following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
sample 2
|
| Data processing |
Raw data in fastq.gz format downloaded from MGI company FTP address
Quality of the raw data and potential contaminations analyzed by fastqc (Version 0.12.0) software in Linux environment.
The alignment process done using hisat2 (Version 2.2.1).
Stringtie (version 2.2.0) and cuffdiff (version 2.2.1) tools used to extract the gene and transcript counts based on reference GTF file (knowngene) and normalized them using FPKM measure.
EnrichR web application was used for enrichment of upregulated and downlegulated genes
Assembly: hg38
Supplementary files format and content: tab deliminated text file including FPKM normalized expression of samples and differential expression test results such as fold change and adjusted p-value.
|
| |
|
| Submission date |
Dec 26, 2023 |
| Last update date |
Jun 22, 2024 |
| Contact name |
Naser Elmi Ghiasi |
| E-mail(s) |
naser.elmi@gmail.com
|
| Organization name |
University of Tehran
|
| Department |
Bioinformatics
|
| Lab |
CBB
|
| Street address |
Bioinformatics Deparment, Qods Street, Enghelab Street
|
| City |
Tehran |
| ZIP/Postal code |
14174 |
| Country |
Iran |
| |
|
| Platform ID |
GPL28038 |
| Series (1) |
| GSE252038 |
Changes in the transcriptomic profile of cumulus cells under the influence of pre-incubation of human oocytes in patients treated in ART cycles |
|
| Relations |
| BioSample |
SAMN39126354 |
| SRA |
SRX23028652 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
