|
| Status |
Public on Jul 14, 2021 |
| Title |
Chmm-2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
canine mammary gland tumor metastatic cell line
|
| Organism |
Canis lupus familiaris |
| Characteristics |
cell line: Chmm-2
cell type: canine mammary gland tumor metastatic cell line
|
| Treatment protocol |
Drug resistant cell lines were constructed by concentration gradient method at 10 months until the cells could normally proliferate in 10 μM TAM medium, then culture at 10 uM for 1 month . To avoid the influence of the experiment, the medium was changed without drugs for 1 week.
|
| Growth protocol |
The cells were cultured to contain phenol-red-free DMEM medium containing 10% charcoalstripped, steroid-depleted FBS (Sigma-Aldrich), antibiotics, and amphotericin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification or cDNA library construction. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
Hiseq Sequencing Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
R20004784-NBC20200225-A-Chmm-2_combined
processed data file: All_Counts.txt
|
| Data processing |
RNA-seq:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
miRNA-seq:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Dog miRNA database and Dog genome.
count counting
Genome_build: CanFam3.1
Supplementary_files_format_and_content: TXT file contain counts for each sample
|
| |
|
| Submission date |
Jan 12, 2021 |
| Last update date |
Jul 14, 2021 |
| Contact name |
Xu Enshuang |
| E-mail(s) |
abliuyun@yeah.net
|
| Organization name |
Northeast Agricultural University
|
| Street address |
NO.600 Changjiang Road, Xiangfang District
|
| City |
Harbin |
| ZIP/Postal code |
150038 |
| Country |
China |
| |
|
| Platform ID |
GPL27147 |
| Series (1) |
| GSE164721 |
LncRNA-42060 Regulates Tamoxifen Sensitivity and Tumor Development via Regulating the miR-204-5p/SOX4 Axis in Canine Mammary Gland Tumor Cells |
|
| Relations |
| BioSample |
SAMN17301364 |
| SRA |
SRX9838632 |
