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Sample GSM4681870

Query DataSets for GSM4681870

Status

Public on Jul 23, 2020

Title

Stout6_3mo_S3

Sample type

SRA

Source name

Ovary

Organism

Mus musculus

Characteristics

strain: C57BL/6
age: 3mo
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