|
| Status |
Public on Feb 08, 2021 |
| Title |
MDA-231EV3 (miRNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
human mammary tumor cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: human mammary tumor cell line
genotype: stably transfected with empty vector
|
| Growth protocol |
cells were grown in DMEM media supplemented with 10% FBS, 1 mM sodium pyruvate, 4 mM glutamine, 1% antibiotic/antimycotic and 300ug/ml puromycin (InvivoGen, San Diego, CA). RNA was extracted from sub-confluent cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) RiboZero Magnetic Gold Kit (Human/Mouse/Rat), NEB multiplex small RNA library Prep set for Illumina
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MDA234CLSC3
|
| Data processing |
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads
adapter sequences were trimmed with cutadapt and the adaptor-trimmed-reads (>= 15nt) were left
miRDeep2 software was used to quantify known miRNA and predict the novel miRNAs
The CPM value for miRNA were calculated with R package edgeR and differentially expressed miRNAs were filtered using edgeR
Genome_build: GRCh38/miRBase22
|
| |
|
| Submission date |
May 08, 2020 |
| Last update date |
Feb 08, 2021 |
| Contact name |
Roger Moorehead |
| E-mail(s) |
rmoorehe@uoguelph.ca
|
| Organization name |
University of Guelph
|
| Department |
Biomedical Sciences
|
| Street address |
50 Stone Rd E
|
| City |
Guelph |
| ZIP/Postal code |
N1G2W1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE150104 |
miRNA sequencing of MDA-231EV, MDA-231c141 and MDA-231ba429 cells |
| GSE150107 |
miR-200b/200a/429 cluster prevents metastasis and induces dormancy in murine claudin-low mammary tumor cells |
|
| Relations |
| BioSample |
SAMN14854268 |
| SRA |
SRX8293115 |
