|
| Status |
Public on May 19, 2016 |
| Title |
Older_4 |
| Sample type |
SRA |
| |
|
| Source name |
cumulus oophorus cells_older
|
| Organism |
Homo sapiens |
| Characteristics |
donor patient status: male factor infertility/oocyte donation and oocyte freezing couples only
age group: >40 y.o.
cell type: cumulus oophorus cells
|
| Treatment protocol |
CCs were bipsied from cumulus-oocyte-complexes approximatey 2 hours post follicular aspiration. Samples were washed in PBS and centrifuged at 1500g. Dry pellets were snap frozen in liquid nitrogen
|
| Growth protocol |
Patients undergoing controlled ovarian stimulation for in vitro fertilization (IVF) procedures
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen samples were treated with Actarus pico pure kit for total RNA extraction, and genomic DNA was removed with DNAseI
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg19 whole genome using bowtie v2-2.1.0 with parameters -p 8 -r 150 --library-type fr-firststrand --b2- 'very-sensitive'
Raw gene counts were estimated with HTSeq (Simon Anders, Bioinformatics, 2014)
Normalized gene expression levels, represented as counts per million (CPM), were obtained for transcripts from Ensembl database and were processed for statistical analysis with EdgeR (Robinson et al., Bioinformatics, 2010)
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated files (.csv) include normalized gene counts (counts per million) values for each Sample
|
| |
|
| Submission date |
May 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Pasquale Patrizio |
| E-mail(s) |
pasquale.patrizio@yale.edu
|
| Organization name |
Yale University
|
| Department |
Ob/Gyn
|
| Street address |
150 Sargent drive
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE81579 |
Transcriptome analysis of human cumulus cells reveals hypoxia as the main determinant of follicular senescence. |
|
| Relations |
| BioSample |
SAMN05010836 |
| SRA |
SRX1771712 |
