|
| Status |
Public on Oct 31, 2023 |
| Title |
DL4 |
| Sample type |
SRA |
| |
|
| Source name |
granulosa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: granulosa cells
gender: Female
condition: bPOI
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from human granulosa cells was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany ) following the manufacturer’s instruction.
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instruction. The Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) was used to evaluate the RNA integrity.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
mRNA expression of granulosa cells from the bPOI patients
|
| Data processing |
Raw data (raw reads) were processed using Trimmomatic to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks and the read counts of each gene were obtained by htseq count. DEGs were identified using the DESeq (2012) R package functions estimateSizeFactors and nbinomTest.
Pvalue < 0.05 and foldChange > 2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern.
GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Assembly: GRCh38.p12
Supplementary files format and content: *_counts.txt: Tab-delimited text files include raw count values for each gene.
|
| |
|
| Submission date |
Apr 22, 2022 |
| Last update date |
Oct 31, 2023 |
| Contact name |
Liu Dan |
| E-mail(s) |
wutongyun_1990@hotmail.com
|
| Organization name |
Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University
|
| Street address |
2699 Gaoke West Road, Pudong District
|
| City |
Shanghai |
| ZIP/Postal code |
201204 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE201276 |
Differentially expressed mRNA in biological premature ovarian insufficiency (bPOI) |
|
| Relations |
| BioSample |
SAMN27737621 |
| SRA |
SRX14963984 |
