|
| Status |
Public on Dec 02, 2019 |
| Title |
3-day-4T1 |
| Sample type |
SRA |
| |
|
| Source name |
murine mammary carcinoma triple negative 4T1 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: balb/c
injected cell type: murine mammary carcinoma triple negative 4T1 cells
tissue: blood plasma
dpi: 3
|
| Treatment protocol |
4T1 cells (1 x 106 cells in a total volume of 200 µL of Ringer-HEPES) were xenografted, under isoflurane anesthesia, in the right common carotid artery of female 7-8 weeks old Balb/c mice, purchased from Charles River Laboratories (Wilmington, MA, USA). Control mice were inoculated with Ringer-HEPES.
|
| Growth protocol |
4T1 breast cancer cells, purchased from ATCC (Middlesex, UK), were maintained in RPMI 1640 medium (PAN Biotech, Aidenbach, Germany) supplemented with ultraglutamine I (Lonza, Basel, Switzerland) and 5% heat-inactivated fetal bovine serum (PAN Biotech) in a 5% CO2 atmosphere at 37 ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
500ul of blood was collected from live mice under isofluorene anesthetic, collected with 40ul of the anticoagulant and spun down for 10mins @ 2000 RPM at 4°C to collect the plasma
Libraries were prepared as per manufacturer using Illumina's TruSeq smallRNA kit with 15 cycles of PCR amplification performed. Desired product size of libraries (~146bp) were isolated using Sage Science's Blue Pippin machine on a 3% agarose gel and confirmed on Agilent's Bioanalyzer using a High Sensitivity DNA chip, followed by sequencing on Illumina's MiSeq using the MiSeq v3 reagent kit
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
miRNA reads per million list.xlsx
3-day-4T1_S1_L001_R1_001.fastq
|
| Data processing |
Resulting FASTQ files were uploaded into Genboree Workbench (genboree.org) where miRNA read counts were determined using the ExceRpt small RNA-seq pipeline v4.6.2
Genome_build: mm10
Supplementary_files_format_and_content: excel matrix table of miRNA reads per million of all samples generated from Genboree Workbench ExceRpt small RNA-seq pipeline v4.6.2
|
| |
|
| Submission date |
Aug 21, 2019 |
| Last update date |
Dec 02, 2019 |
| Contact name |
Sarah Medina |
| E-mail(s) |
sarah.medina@phac-aspc.ca
|
| Phone |
204-789-7048
|
| Organization name |
Public Health Agency of Canada
|
| Department |
One Health
|
| Street address |
1015 Arlington Street
|
| City |
WInnipeg |
| State/province |
Manitoba |
| ZIP/Postal code |
R3E 3R2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE136149 |
Circulating miR 802-5p and miR 194-5p and brain expression of MEF2C as novel biomarkers of breast cancer brain metastasis |
|
| Relations |
| BioSample |
SAMN12617071 |
| SRA |
SRX6749037 |
