 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 31, 2019 |
| Title |
MDA231-BrM MYC WT rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: brain metastatic derivative of MDA-MB-231
passage: 5-10
genotype: cMYC rescue
|
| Treatment protocol |
NA
|
| 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.
|
| 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 nextseq500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
shMYC_Rescue_2
|
| Data processing |
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the National Center for Biotechnology Information (NCBI) Genome database (assembly ID: GRCh38).
STAR was applied to tissue samples for mapping and to quantify reads to the reference genome (ver. 2.5). To estimate gene expression levels, counts per million (CPM) mapped reads values were calculated for each sample. The CPM data were normalised using quantile normalisation in the R language environment (version 3.2.5).
Genome_build: GRCh38
Supplementary_files_format_and_content: 'quantile normalised Log2 CPM'
|
| |
|
| Submission date |
Oct 30, 2017 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Mi Young Kim |
| E-mail(s) |
miyoungkim@kaist.ac.kr
|
| Organization name |
KAIST
|
| Street address |
Biological science
|
| City |
DaeJeon |
| ZIP/Postal code |
305-701 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE106312 |
Genome-wide RNA-seq from c-MYC-depleted and rescued MDA-MB-231BrM cells |
|
| Relations |
| BioSample |
SAMN07946484 |
| SRA |
SRX3342348 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
