|
| Status |
Public on Apr 18, 2020 |
| Title |
KO3 |
| Sample type |
SRA |
| |
|
| Source name |
Aortae from homozygous floxed Srf with Itga8-CreERT2 driver
|
| Organism |
Mus musculus |
| Characteristics |
genotype: homozygous floxed Srf with Itga8-CreERT2 driver
tissue: aortae
|
| Growth protocol |
Mice were maintained on a normal chow diet and allowed water ad libitum over the 10 days period following 5 sequential days of i.p. injection of Tamoxifen. Please note that we have used the best possible control with heterozygous floxed Srf mice carrying the Itga8-CreERT2 allele and receiving the same schedule of tamoxifen injections as the experimental homozygous floxed Srf/Itga8CreERT2 mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized and the aorta (from descending arch to the renal bifurcations) was rapidly excised and placed in ice cold PBS. The adventitia and endothelium were gently removed to create as pure a population of medial smooth muscle cells as possible. Aortae were individually snap frozen in liquid nitrogen and then homogenized with a Bertin Minilys Personal Homogenizer (Bertin Instruments) in a 1.5ml microfuge tube containing 1ml of Trizol. Total RNA was isolated according to instructions by the manufacturer and then samples were treated with DNAse I for 15 minutes at 37C. DNAse I was removed by phenol/chloroform extraction following by standard sodium acetate/ethanol preciptation. Samples were resuspended in RNAse-free water and submitted to the University of Rochester Genomics Research Core for quality assessment and library construction.
Illumina TruSeq Stranded mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
KO3_1241
|
| Data processing |
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - fastp 0.20.0, "--in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json"
MAPPING - STAR_2.7.0f, "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.6.4, featurecounts, "-s 2 -t exon -g gene_name"
Genome_build: GRCm38 + Gencode-M22
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample
|
| |
|
| Submission date |
Oct 14, 2019 |
| Last update date |
Apr 18, 2020 |
| Contact name |
Joseph M Miano |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Rochester
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE138824 |
Vascular smooth muscle selective deletion of Srf |
|
| Relations |
| BioSample |
SAMN13026748 |
| SRA |
SRX6988539 |
