|
| Status |
Public on Jan 01, 2019 |
| Title |
MDA_msLung_12h Input_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA_msLung_12h Input
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: MDA231 Lung Xenograft
cell type: breast cancer cell line
metastatic derivative: Parental
sample group: Dox 2d, 250 mg/Kg 5-FC, 12h
|
| Treatment protocol |
For TGFB experiments, cells were treated with TGFB or SB-505124 for 150 minutes. 5-FC treatment was done for 3 hours for TGFB experiments, and 4 hours or 12 hours for other experiments as indicated.
|
| Growth protocol |
MDA231-BrM2 cells were cultured in DMEM with 10% fetal bovine serum (FBS) and 2 mM L-Glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNAs were isolated by Oligo dT magnetic beads. Either the mRNAs were sequenced directly or immunoprecipitated with anti-BrdU antibody, and bound mRNAs were eluted using BrdU solution, and the eluted mRNAs were sequenced.
TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. For the immunopurified RNAs, the RNAs were amplified by SMARTer amplification and library was prepared by Nextera Kit followinf manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file:
Flura-seq in vivo RawCounts.csv
|
| Data processing |
Samples were barcoded
run on a Hiseq 2000 platform in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).
An average of 25 million paired reads were generated per sample.
The data were analyzed using the STAR-HTSeq-DESeq2 pipeline as previously described.
Flura-seq in vivo experiments were aligned to hybrid genome containing combined human and mouse genome. Mouse gene is indicated by "m" in front of the gene name whereas human gene is indicated by "h" in front of the gene name. For the other reamining experiments, the reads were aligned to human genome.
Genome_build: hg19, mm10, Hybrid genome containing hg19 and mm10
Supplementary_files_format_and_content: Three separate count files in csv format are provided for three different experiments (5-FC Time course, Flura-seq in vivo, and TGFB treatment)
|
| |
|
| Submission date |
Jan 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Danilo G Macalinao |
| E-mail(s) |
macalind@sloankettering.edu
|
| Organization name |
MSKCC
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16512 |
| Series (1) |
| GSE93605 |
Flura-Seq Identifies In Situ Transcriptomes of Micrometastases |
|
| Relations |
| BioSample |
SAMN06229851 |
| SRA |
SRX2492257 |
