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Sample GSM4041655 Query DataSets for GSM4041655
Status Public on Dec 02, 2019
Title 3-day-control
Sample type SRA
 
Source name Ringer-HEPES
Organism Mus musculus
Characteristics strain: balb/c
injected cell type: n/a
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-contol_S2_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 SAMN12617069
SRA SRX6749038

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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