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| Status |
Public on Sep 06, 2018 |
| Title |
MII 111815_02 SOLO |
| Sample type |
SRA |
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| Source name |
MII Oocyte
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: oocyte
developmental stage: MII
library processing kit: SoLo
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| Growth protocol |
Control ovarian stimulation protocol (COS) was used for the collection of oocytes. Rhesus macaques were observed daily for signs of menses. Within day 1-4 of menses, animals were administered an intramuscular injection of recombinant macaque FSH (r-mFSH; National Hormone and Peptide Program, A. F. Parlow, UCLA) twice daily for a total of 7 days. On day 8 a subset of animals was used for collection of GV oocytes and another subset of animals were administrated an intramuscular injection of 1000 IU of human chorionic gonadotropin (hCG; LaJ olla Discount Pharmacy, La Jolla, CA). On day 9, ultrasound-guided needle aspiration of follicles was used for the collection of oocytes. Oocytes were observed for maturation status for both normal GV and MII, and FTM oocytes.
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| Extracted molecule |
total RNA |
| Extraction protocol |
All cumulus cells were removed by repeatedly pipetting oocytes with a narrow-gauge pipette that was just slightly larger than the oocytes while observing oocytes with a stereomicroscope. Using the PicoPureTM RNA Extraction kit, total RNA was isolated from each sample following the manufacturer protocol, including a DNAse digestion (RNase-Free DNase Set; Qiagen, Hilden, Germany) to remove any contaminating DNA.
SPIA libraries: 100 ng of each RNA sample was processed with the Ovation RNA-Seq System v2 using Ribo-SPIATM Technology (NuGen, San Carlos, CA). After this initial processing, a Covaris-2 sonicator was used to mechanically fragment the cDNA to an average of 300 bp. This was then followed by a brief S1 nuclease digestion as previously described (Head et al., 2011). After bead purification, the cDNA was processed through the Ovation Ultralow DR Multiplex Systems 1-16 (NuGen) for end repair, adaptor ligation and final library amplification.
SoLo libraries: cDNA libraries were produced with Nugen Ovation SoLo RNA-Seq(NuGEN, San Carlos, CA). After bead purification, the cDNA was processed: end repair, adaptor ligation and first round library amplification and purification. Then 20 ng of each library was used for the remainder of library preparation, which included use of InDA-C primers for rRNA depletion, as well as 2nd round library amplification and purification steps. SoLo Custom R1 primer was used instead of a standard Illumina R1 sequencing primer for the sequencing of the libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina Real Time Analysis (RTA) v1.18.64 (SPIA libraries) & v2.7.6 (SoLo libraries)
Hisat2 to the Ensembl rhesus monkey genome (Mmul build v8.1.0, genome annotation relase-91)
Removing "ExAmp" duplicates with distance threshold 2500 using in-house developed Python code
DESeq2 comparisons between groups of libraries
Genome_build: Mmul 8.1.0 (Macaca Mulatta)
Supplementary_files_format_and_content: raw counts
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| Submission date |
Mar 30, 2018 |
| Last update date |
Sep 06, 2018 |
| Contact name |
Uros Midic |
| E-mail(s) |
uros@msu.edu
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| Organization name |
Michigan State University
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| Department |
Animal Sciences
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| Lab |
Latham lab
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| Street address |
474 S. Shaw Lane
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| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824-1225 |
| Country |
USA |
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| Platform ID |
GPL23949 |
| Series (3) |
| GSE112534 |
Transcriptome analysis of rhesus monkey MII oocytes |
| GSE112536 |
Transcriptome analysis of rhesus monkey germinal vesicle, failed-to-mature oocytes and MII oocytes |
| GSE112537 |
Transcriptome analysis of rhesus monkey MII oocytes and embryos |
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| Relations |
| BioSample |
SAMN08822751 |
| SRA |
SRX3867039 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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