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Status |
Public on Jul 23, 2020 |
Title |
Stout4_3mo_S1 |
Sample type |
SRA |
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Source name |
Ovary
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 age: 3mo Sex: female
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Extracted molecule |
total RNA |
Extraction protocol |
Ovaries were isolated and frozen with dry ice. RNA were isolated using the AllPrep DNA/RNA mini kit (Qiagen, Germantown, MD). 25ug of RNA with integrity >7 were subsequently used for the library construction. Libraries were constructed using the NEBNext Ultra II Directional Library Prep Kit for Illumina (New England Biolabs Inc., Ipswich, MA) and standard Illumina sequencing protocols.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina MiSeq |
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Data processing |
Sequenced reads were trimmed, aligned to the Mm10 mouse genome build, differential expression statistics and correlation analyses were performed using Strand NGS software package (Agilent). Adapter trimming, fixed 5bp trim from 5’ and 2bp from 3’ ends and a maximum number of one novel splice was allowed per read. Read 1 and Read 2 were aligned directionally with Read 1 in the reverse and Read 2 in the forward orientation. Transcripts considered for quantitation and analysis had an average read count value >20 in at least 100% of the samples in at least one time-point. A one-way ANOVA across the time points with a Benjamini-Hochberg Multiple Testing Correction was used to analyse differential expression across the timepoints. For anscripts that met this statistical criterion, we employed a fold change >|1.25| pairwise cutoff 6M, 9M, or 12M vs 3M) to eliminate genes which were statistically significant but unlikely to be biologically significant. Genome_build: mm10 Supplementary_files_format_and_content: matrix table of raw gene counts of all genes for each sample Supplementary_files_format_and_content: matrix table of normalized gene counts for each sample Supplementary_files_format_and_content: matrix table with all differentiallly expressed genes across the timepoints for each sample
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Submission date |
Jul 22, 2020 |
Last update date |
Jul 23, 2020 |
Contact name |
VICTOR AFRIYIE ANSERE` |
E-mail(s) |
victor-ansere@ouhsc.edu
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Phone |
4053086786
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Organization name |
UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER
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Department |
PHYSIOLOGY
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Lab |
WILLARD FREEMAN LAB
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Street address |
Genes and Human Disease Research Program MS57, Oklahoma Medical Research Foundation 825 NE 13th Street
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City |
Oklahoma City |
State/province |
Oklahoma |
ZIP/Postal code |
73104 |
Country |
USA |
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Platform ID |
GPL16417 |
Series (1) |
GSE154890 |
Ovarian senescence, transcriptomic, and epigenomic changes with aging |
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Relations |
BioSample |
SAMN15596017 |
SRA |
SRX8789043 |
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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