|
| Status |
Public on Jan 11, 2022 |
| Title |
MII2 YMA |
| Sample type |
SRA |
| |
|
| Source name |
MII oocyte young maternal age
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: Late oogenesis
cell type: Gamete
maternal age: young maternal age (<30 yo)
|
| Growth protocol |
Human oocytes donated for research.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Isolated oocytes were inserted separate into lysis buffer with RNase Inhibitor (Clontech, USA) and frozen at -80°C until required.
RNA libraries were prepared for sequencing using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) and Nextera XT DNA library preparation kit (Illumina), according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
hMII2_S44_L006
|
| Data processing |
Paired-end read trimming was performed to remove adapters and poor quality sequence using Trim galore
Read mates were mapped to the Human reference genome (hg38) using the HISAT2 aligner version 2.0.4, with the following parameters -p 8 -k 1 --dta --rna-strandness FR --no-mixed --no-discordant.
Unmapped reads and incorrectly paired reads were removed and the remaining reads converted to bam format with the view function of samtools version 1.3.
Potential PCR duplicates were tagged using Picard MarkDuplicates version 2.1.1
StringTie was used to identify potential novel transcripts, using the UCSC hg38 annotation of the human genome as a guide.
We used both the Python script prepDE.py (https://ccb.jhu.edu/software/stringtie/dl/prepDE.py) and Rsubread's featureCounts function to count assigned reads to genomic features. Only uniquely mapped, non-duplicated and correctly paired-end reads were considered in this study.
The edgeR function calcNormFactors was used to normalize library sizes, based on the trimmed mean M value (TMM). The copies-per-million (cpm) threshold was set at 1 in at least half of the libraries to be included in the analysis. Differential gene expression (DGE) between successfully and non-successfully implanted blastocysts was tested statistically using the edgeR Exact test with FDR 0.05.
Genome_build: hg38
|
| |
|
| Submission date |
Jan 07, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Panagiotis Ntostis |
| Organization name |
University of Leeds
|
| Department |
Medicine and Health
|
| Lab |
LICAMM
|
| Street address |
Clarendon Way
|
| City |
Leeds |
| ZIP/Postal code |
LS2 9JT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE164371 |
The impact of ageing on the transition of the euploid human GV oocytes to in vivo matured MII oocytes |
|
| Relations |
| BioSample |
SAMN17248508 |
| SRA |
SRX9799476 |
