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Status |
Public on Aug 22, 2019 |
Title |
MDA231-LM2 shCntr rep1 |
Sample type |
SRA |
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Source name |
Breast cancer cells
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Organism |
Homo sapiens |
Characteristics |
cell type: Lung metastatic derivative of MDA-MB-231 passage: 5-10 genotype: nontargeting shRNA
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Treatment protocol |
NA
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Growth protocol |
MDA-MB-231 cells were cultured in DMEM (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (FBS; JR Scientific, Woodland, CA) for 2 days.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNAs were isolated using Qiazol (Qiagen, Valencia, CA) followed by chloroform extraction. Total RNAs were subjected to enrichment of polyA+ RNA using Dynabeads Oligo (dT)25 (Invitrogen, Carlsbad, CA). Strand-specific RNA-seq libraries were prepared from the polyA+ RNA. The RNA-seq libraries were sequenced using single-end methodology with a length of 50 nt (SE50) (two replicates each) using an Illumina HiSeq 2500.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
RNA-Seq reads were aligned to the human reference genome (NCBI 37, hg19) using the spliced read aligner TopHat version 1.4.0 (1). The bam files from TopHat were assembled using Cufflinks The individual transcript assemblies from multiple RNA-Seq libraries are assembled into one master transcriptome using Cuffmerge using Cuffdiff comparisons of expression levels of genes from the different conditions was performed Genome_build: hg19
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Submission date |
Aug 17, 2015 |
Last update date |
Aug 22, 2019 |
Contact name |
Mi Young Kim |
E-mail(s) |
miyoungkim@kaist.ac.kr
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Organization name |
KAIST
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Street address |
Biological science
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City |
DaeJeon |
ZIP/Postal code |
305-701 |
Country |
South Korea |
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Platform ID |
GPL16791 |
Series (1) |
GSE72111 |
Genome-wide RNA-seq from GALNT14-depleted and GALNT14 overexpressing MDA-MB-231 LM2 and Par cells |
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Relations |
BioSample |
SAMN03996581 |
SRA |
SRX1153664 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1855559_MK4.bw |
61.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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