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Sample GSM4681881 Query DataSets for GSM4681881
Status Public on Jul 23, 2020
Title Stout28_9mo_S14
Sample type SRA
 
Source name Ovary
Organism Mus musculus
Characteristics strain: C57BL/6
age: 9mo
Sex: female
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
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
 
Submission date Jul 22, 2020
Last update date Jul 23, 2020
Contact name VICTOR AFRIYIE ANSERE`
E-mail(s) victor-ansere@ouhsc.edu
Phone 4053086786
Organization name UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER
Department PHYSIOLOGY
Lab WILLARD FREEMAN LAB
Street address Genes and Human Disease Research Program MS57, Oklahoma Medical Research Foundation 825 NE 13th Street
City Oklahoma City
State/province Oklahoma
ZIP/Postal code 73104
Country USA
 
Platform ID GPL16417
Series (1)
GSE154890 Ovarian senescence, transcriptomic, and epigenomic changes with aging
Relations
BioSample SAMN15596037
SRA SRX8789056

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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