|
| Status |
Public on May 26, 2022 |
| Title |
Adjacent Non-Tumor mammary tissue Pool 1 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary tissue
|
| Organism |
Canis lupus familiaris |
| Characteristics |
disease: Non-tumor Tissue
pool: Pool 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from tissue from mammary ductal carcinoma and adjacent non-tumor mammary tissue. A 50 mg sample of tissue was ground using Precellys®24-Dual homogenizer (Bertin Technologies, Rockville, Washington D.C., USA). Total RNA was extracted using TRIzol (Thermo Scientific, USA) according to the manufacturer's instructions.
The cDNA libraries were built with the TruSeqTM Stranded Total RNA Sample Preparation Kit v2 (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were performed quality assessment using FastQC. Reads with phred score >30 were accepted
Adapters were removed using trimomatic in the default options
Paired-end reads for mRNA were mapped to the CamFam3.1 genome using STAR with default options
Counts for RefSeq genes were obtained using Featurecounts with the default settings
DESeq2 was used to normalize expression counts.
Assembly: CamFam3.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 23, 2022 |
| Last update date |
May 27, 2022 |
| Contact name |
Geysson Javier Fernandez Garcia |
| E-mail(s) |
fernandez.garcia@unesp.br
|
| Organization name |
UNESP
|
| Street address |
Departamento morfologia IBB UNESPRubiao Junior
|
| City |
Botucatu |
| State/province |
Sao Paulo |
| ZIP/Postal code |
18603191 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL21400 |
| Series (1) |
| GSE203589 |
Transcriptomic profile of canine mammary ductal carcinoma |
|
| Relations |
| BioSample |
SAMN28597210 |
| SRA |
SRX15414424 |
