|
| Status |
Public on Feb 01, 2020 |
| Title |
Par_RNA_REP2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: mammary gland/breast epithelial cell
|
| Growth protocol |
Cells were grown in monolayer in DMEM + 10% FBS + Penicillin-streptomycin at 37ºC, 5% CO2 for 3 days for each replicate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested in QIAzol reagent, homogenized using QIAshredder, and RNA isolated using miRNeasy kit with on-column DNAse digestion
Libraries were prepared using TruSeq stranded mRNA library prep kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
STAR.counts.geo.txt
DESeq2.results.geo.txt
par.rna.merge.hg19.bw
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were aligned using STAR aligner v2.7.0 to hg38 using standard parameters and quant mode for gene counts
Reads were aligned using STAR aligner v2.7.0 to hg19 using standard parameters for bigwig signal tracks
DEseq2 was used to determine differential gene expression using counts.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig (Merged), txt (DESeq2 results comparing metastatic sub-population and Par), txt (raw counts)
|
| |
|
| Submission date |
Sep 27, 2019 |
| Last update date |
May 05, 2020 |
| Contact name |
Qin Yan |
| E-mail(s) |
qin.yan@yale.edu, craig.wilen@yale.edu
|
| Organization name |
Yale University
|
| Department |
Pathology
|
| Lab |
BML338
|
| Street address |
310 Cedar St.
|
| City |
New Haven |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE129647 |
Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain |
| GSE138122 |
Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain [RNAseq] |
|
| Relations |
| BioSample |
SAMN12863765 |
| SRA |
SRX6917539 |
