|
| Status |
Public on Dec 01, 2014 |
| Title |
ctl1 |
| Sample type |
SRA |
| |
|
| Source name |
control_ventral dermis
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed; CD1 and C57BL/6
genotype/variation: HoxB6CreERT/+; R26-YFP/+
age: 3 weeks
tissue: ventral dermis
|
| Treatment protocol |
HoxB6CreERT/+; R26-YFP/+; CatnbΔex3/+ "activated beta-catenin" mice and double-transgenic HoxB6CreERT/+; R26-YFP/+ littermate control mice received tamoxifen (3mg/40 mg maternal weight) at embryonic day 16.5 (E16.5) by maternal gavage. Mice were born and aged to 3 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were anesthesized and sacrificed by cervical dislocation. Hair was clipped and ventral skin dissected from the abdominal wall. Skin was held in 0.25% trypsin-EDTA at 4C overnight, then incubated at 37C for 45 minutes. The epidermis was removed to isolating the dermis. The dermis was flash-frozen, mechanically homogenized, and lysed in Trizol. RNA was extracted by standard Trizol protocol.
Libraries were prepared in the CWRU Genomics Sequencing Core using TruSeq Stranded Total RNA kit (Illumina, San Diego, CA, USA; RS-122-2301).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
raw data average insert size: 375
|
| Data processing |
Alignment of paired-end reads to mm10 was performed using GSNAP, with 2 mismatches allowed for the full length of the reads.
Mapped unique raw reads that mapped to genes in the RefSeq database were counted using HTSeq and normalized to the total of mapped reads in each condition.
Differential gene expression analysis was performed. Genes were considered statistically significant if they had p-values less than 0.05 after adjusting for false discovery rate with the Benjamini and Hochberg method {Benjamini:1995ws} in a negative binomial test and showed 1.5 fold-changes between compared conditions.
Genome_build: mm10
|
| |
|
| Submission date |
Aug 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Radhika Paresh Atit |
| E-mail(s) |
[email protected]
|
| Phone |
2163688819
|
| Organization name |
Case Western Reserve University
|
| Department |
Biology
|
| Street address |
2074 Adelbert Road, Millis 316
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE60569 |
Sustained expression of activated beta-catenin in dermal fibroblasts causes skin fibrosis |
|
| Relations |
| BioSample |
SAMN02999659 |
| SRA |
SRX683781 |
