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Sample GSM2586890

Query DataSets for GSM2586890

Status

Public on Nov 21, 2017

Title

KO rep2

Sample type

SRA

Source name

Heart

Organism

Mus musculus

Characteristics

strain: C57BL/6
tissue: Whole Heart
age: Embryonic day 13.5
genotype: Tie2Cre INO80 flox/flox

Growth protocol

The mouse colony was housed in and cared for by the Stanford Veterinary Service Center in accordance to protocols approved by Stanford’s Institutional Animal Care and Use Committee (IACUC). The mouse colony consisted of approximately 10 cages containing a total of up to 50 mice for propagation. The population consisted of approximately 20% males and 80% females with ages ranging from newborn to six months old.

Extracted molecule

total RNA

Extraction protocol

Crosses between male and female mice commenced at 6 to 8 weeks of age in order to obtain progeny. To obtain embryos of a given embryonic stage, timed pregnancy was verified by checking for the presence of a vaginal plug, which was designated as embryonic day 0.5. Female mice 13.5 days after impregnation were euthanized by CO2 followed by cervical dislocation in accordance with guidelines for euthanasia from the American Veterinarian Medical Association (AVMA). The embryos were harvested and the heart dissected out. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). We recovered approximately 40 ng/uL of RNA from each embryonic heart. We used the NEB Next Ultra RNA Library Prep Kit for Illumina for mRNA library preparation.
RNA libraries were prepared for sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

E13_5_Tie2_Ino80_KO_DESeq2.csv

Data processing

Raw sequencing reads (FASTQ) were generated at the Stanford Center for Genomics and Personalized Medicine (SCGPM)
Read quality was assessed using FastQC
76bp paired-end reads were mapped to genome GRCm38 (mm10) using STAR (v2.4.2a), with gene annotations from GENCODE's evidence-based annotation of the mouse genome (GRCm38), version 6 (Ensembl 81)
Reads aligning to annotated transcripts were counted using the summarizeOverlaps() function from the GenomicAlignments R package
Significance results and log2-fold-change values were generated using the DESeq2 package on untransformed count data
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: comma-delimited text file includes default DESeq2 output: baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, symbol

Submission date

Apr 23, 2017

Last update date

May 15, 2019

Contact name

Devin Aalpoel King

E-mail(s)

devking@stanford.edu

Organization name

Stanford University

Department

Biology