|
| Status |
Public on Apr 08, 2019 |
| Title |
BrMet Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
brain tumors
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
mouse strain: athymic nu/nu mice
human cell line: H2030-BrM3
|
| Treatment protocol |
For orthotopic lung tumors, 1x10^5 cells were injected intratracheally.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
36673
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv
|
| Data processing |
Illumina software used for basecalling.
The R1 sequenced reads were trimmed for adaptor sequence, then mapped to mm10 and hg38 whole genome using the BMX-seq pipeline.
Reads mapped uniquely were counted to Gencode annotations for mm10 (vM10) and hg38 (v24).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from the gene count matrix and median length of the transcripts of a gene annotation.
Genome_build: mm10 (GRCm38) and hg38 (GRCh38)
Supplementary_files_format_and_content: *.rpkm.csv: Comma-delimited text files include RPKM values for each gene (row) each Sample (column).
|
| |
|
| Submission date |
Jun 12, 2018 |
| Last update date |
Apr 09, 2019 |
| Contact name |
Don Nguyen |
| E-mail(s) |
don.nguyen@yale.edu
|
| Phone |
2037374514
|
| Organization name |
Yale Shcool of Medicine
|
| Street address |
310 Cedar St
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
| |
|
| Platform ID |
GPL22245 |
| Series (2) |
| GSE115699 |
Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis [BrainMet_Othotopic] |
| GSE115702 |
Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis |
|
| Relations |
| BioSample |
SAMN09402821 |
| SRA |
SRX4200348 |
