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| Status |
Public on Feb 15, 2021 |
| Title |
COS_2_3 |
| Sample type |
SRA |
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| Source name |
Blastocysts
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| Organism |
Macaca mulatta |
| Characteristics |
diet: Western Style Diet
morphology durign development: Fragmented, non-multipolar
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| Treatment protocol |
Blastocysts were collected and incubated in EmbryoMax Acidic Tyrode’s Solution EMD Millipore, Burlington MA) for ~30 seconds for removal of the zona pellucida. These zona free blastocysts were then transferred to the extraction buffer of the ARCTURUS PicoPure RNA Isolation Kit (ThermoFisher Scientific KIT0204, Waltham, MA) and frozen at -80oC until RNA isolation.
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| Growth protocol |
After IVF for 14-16 hr, oocytes were stripped of excess sperm by pipetting and visually assessed for fertilization; i.e., the presence of two pronuclei and/or two polar bodies. The zygotes were cultured for 6-8 days till they reached the blastocyst stage of development in 100 μL of one-step commercial medium supplemented with 10% serum protein (LifeGlobal, Guildford, CT) under mineral oil (Sage™, Trumbull, CT) at 37°C with 6% CO2, 5% O2
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the blastocysts and cDNA prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (TakaraBio, Shiga, Japan) and the amplified cDNA was purified using the Agencourt AMPure XP Kit (Beckman Coulter, Brea, CA), both according to manufacturer’s instructions. cDNA was then sheared to approximately 250 base pairs in length using a Covaris M220 sonicator.
Sheared cDNA was resuspended in Tru-seq Resuspension Buffer and libraries prepared using a Tru-Seq Nano kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, except that 16 cycles of amplification were performed to account for the low input samples. Fragment size was measured using a Fragment Analyzer 5200 and samples quantified with qPCR and pooled at equimolar concentration. Multiplexed samples were sequenced across seven lanes of a single-read, 75 cycle run on an Illumina HiSeq 4000 sequencer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
raw_counts_table.txt
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| Data processing |
base calling and demultiplexed with bcl2fastq
Sequencing quality was assessed with FastQC (v0.11.8)
Trimming of adapters and low quality bases with Trimmomatic (v0.39)
Trimmed reads were aligned to the Ensembl rhesus macaque reference genome (Mmul_10) with STAR (v2.7.0) using default parameters
Gene counts were obtained via STAR with the "--quantMode GeneCounts" parameter and Ensembl annotation (Mmul_10.99)
Genome_build: Mmul_10
Supplementary_files_format_and_content: tab delimited text file containing the raw counts for each gene (Ensembl Gene ID) in each sample
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| Submission date |
Dec 07, 2020 |
| Last update date |
Feb 15, 2021 |
| Contact name |
Brett Davis |
| E-mail(s) |
davibr@ohsu.edu
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| Organization name |
Oregon Health and Science University
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| Street address |
3181 SW Sam Jackson Park Rd
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| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platform ID |
GPL23949 |
| Series (1) |
| GSE162817 |
Short-Term Western-Style Diet Negatively Impacts Reproductive Outcomes in Primates |
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| Relations |
| BioSample |
SAMN17021499 |
| SRA |
SRX9644976 |
| 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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