|
| Status |
Public on Apr 11, 2018 |
| Title |
Ad libitum AL |
| Sample type |
SRA |
| |
|
| Source name |
thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: MMTV-TGF-alpha
tissue: thymus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Thymus tissues were removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 mouse genome using TopHat2
Gene expression levels were quantified by Cufflinks 2.2.1 and normalized by the fragments per kilobase of transcript per milion fragments mapped method (FPKM) (Trapnell et al. 2010)
The differential expressed genes (DEGs) were identified with Cuffdiff
MMTV-TGF- α female mice
|
| |
|
| Submission date |
Feb 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nehir Ozdemir Ozgenturk |
| Organization name |
Yildiz Technical University
|
| Department |
Mol. Bio. and Genetics
|
| Street address |
Davutpasa/Esenler
|
| City |
Istanbul |
| ZIP/Postal code |
34000 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE95371 |
RNA-seq analysis in MMTV-TGF- α Mice thymus |
|
| Relations |
| SRA |
SRX2588925 |
| BioSample |
SAMN06464785 |
