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Sample GSM4523500 Query DataSets for GSM4523500
Status Public on Feb 08, 2021
Title MDA-231EV1 (RNA-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 60ug/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 HiSeq 4000
 
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: GRCh38_ens92_ercc_sirv
Supplementary_files_format_and_content: counts
 
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 GPL20301
Series (2)
GSE150099 RNA 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 SAMN14854092
SRA SRX8291597

Supplementary file Size Download File type/resource
GSM4523500_MDA-231EV1_rawreadcounts.txt.gz 242.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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