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| Status |
Public on Feb 08, 2021 |
| Title |
RJ423c141C (RNA-seq) |
| Sample type |
SRA |
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| Source name |
murine mammary tumor cell line
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| 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
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| 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
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RJ423c141F
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| 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
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| Submission date |
May 08, 2020 |
| Last update date |
Feb 08, 2021 |
| Contact name |
Roger Moorehead |
| E-mail(s) |
rmoorehe@uoguelph.ca
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| Organization name |
University of Guelph
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| Department |
Biomedical Sciences
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| Street address |
50 Stone Rd E
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| City |
Guelph |
| ZIP/Postal code |
N1G2W1 |
| Country |
Canada |
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| 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 |
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| Relations |
| BioSample |
SAMN14854094 |
| SRA |
SRX8291610 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4523613_RJ423c141F_rawreadcounts.txt.gz |
219.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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