|
| Status |
Public on Apr 30, 2024 |
| Title |
MGT408#2 |
| Sample type |
SRA |
| |
|
| Source name |
MGT408#2
|
| Organism |
Canis lupus familiaris |
| Characteristics |
cell line: MGT408#2
|
| Growth protocol |
MGT cells were maintained in DMEM/F-12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using hybrid-R (GeneAll). 1 ug of total RNA was used processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
MGT 408#2
|
| Data processing |
Potentially existing sequencing adapters and raw quality bases in the raw reads were trimmed by Skewer ver 0.2.2.
The cleaned high quality reads after trimming the low quality bases and sequencing adapters were mapped to the reference genome by STAR ver 2.5 software.
Since the sequencing libraries were prepared strand-specifically by using Illumina’s strand-specific library preparation kit, the strand-specific library option, --library-type=fr-firststrand was applied in the mapping process.
To quantify the mapped reads on the reference genome in to the gene expression values, Cuffquant in Cufflinks ver 2.2.1 with the strand-specific library option,--library-type=fr-firststrandand other default options was used.
The gene annotation of the reference genome canfam3 from UCSC genome (https://genome.ucsc.edu) in GTF format was used as gene models and the expression values were calculated in Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) unit.
Assembly: canfam3
Supplementary files format and content: text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 21, 2023 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Sung-Hak Kim |
| E-mail(s) |
sunghakkim3@gmail.com
|
| Organization name |
chonnam national university
|
| Department |
Animal Science
|
| Lab |
animal molecular biochemistry lab
|
| Street address |
Yongbongro 77
|
| City |
Buk-gu |
| ZIP/Postal code |
61186 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL33357 |
| Series (1) |
| GSE230271 |
Establishment and characterization of canine mammary gland tumor(MGT) cell lines |
|
| Relations |
| BioSample |
SAMN34380490 |
| SRA |
SRX20381164 |
