|
| Status |
Public on Mar 25, 2019 |
| Title |
MDA_Lung_Input_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA231 Lung Xenograft
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: MDA-MB-231
metastatic derivative: Lung
reporter gene: Firefly Luciferase
protocol: Dox 2d, 250 mg/Kg 5-FC, 12h, Lung, Input
|
| Growth protocol |
MDA231 cells were cultured in DMEM with 10% fetal bovine serum (FBS), 2 mM L-Glutamine, 200 ug/mL Hygromycin and 8 ug/mL Blasticidin.
|
| 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 |
MDA_Lung_Input = MDA231 cells injected intracardiacally in mouse, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 12 hours later mouse lung was harvested, homogenized, mRNAs were isolated and sequenced.
Counts_expressed_normalized_Fluraseq.csv
|
| Data processing |
Library strategy: Flura-seq
Samples were barcoded
run on a Hiseq 2000 platform in a 125bp/125bp 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 remaining experiments, the reads were aligned to human genome.
Genome_build: hg19, mm10, Hybrid genome containing hg19 and mm10
Supplementary_files_format_and_content: Two separate count files in csv format are provided for two different profiling methods (Counts_expressed_normalized_Fluraseq.csv, Counts_expressed_normalized_inVitro.csv)
|
| |
|
| Submission date |
Aug 22, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Lin Tian |
| E-mail(s) |
tianl1@mskcc.org
|
| Phone |
6468882063
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Cancer Biology & Genetics Program
|
| Lab |
Joan Massagué
|
| Street address |
Mortimer B. Zuckerman Research Center, 417 East 68th Street
|
| City |
New York City |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16512 |
| Series (1) |
| GSE118937 |
Flura-seq identifies organ-specific adaptations in metastasis-initiating cells |
|
| Relations |
| BioSample |
SAMN09882500 |
| SRA |
SRX4597504 |
