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Sample GSM4523613 Query DataSets for GSM4523613
Status Public on Feb 08, 2021
Title RJ423c141C (RNA-seq)
Sample type SRA
Source name murine mammary tumor cell line
Organism Mus musculus
Characteristics cell line: RJ423
cell type: murine mammary tumor cell line
genotype: stably transfected with vector containing miR-200c and miR-141
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
KAPA stranded Illumina kits for the RNA-seq library preparation, which include procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Library prep performed by Arraystar Inc (Rockville, MD)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description RJ423c141F
Data processing reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming
preprocessed reads are aligned by STAR aligner
aligned reads are summarized to gene-level counts by the featureCounts tool
Genome_build: GRCm38_ens92_ercc_sirv
Supplementary_files_format_and_content: counts
Submission date May 08, 2020
Last update date Feb 08, 2021
Contact name Roger Moorehead
Organization name University of Guelph
Department Biomedical Sciences
Street address 50 Stone Rd E
City Guelph
ZIP/Postal code N1G2W1
Country Canada
Platform ID GPL24247
Series (2)
GSE150101 RNA sequencing of RJ423EV and RJ423c141 cells
GSE150107 miR-200b/200a/429 cluster prevents metastasis and induces dormancy in murine claudin-low mammary tumor cells
BioSample SAMN14854094
SRA SRX8291610

Supplementary file Size Download File type/resource
GSM4523613_RJ423c141F_rawreadcounts.txt.gz 219.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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