|
| Status |
Public on Apr 08, 2019 |
| Title |
HBMet Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
hindbrain with tumors
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
mouse strain: athymic nu/nu mice
human cell line: H2030-BrM3
|
| Treatment protocol |
Monolayer cell cultures were passaged every 3-4 days and cultured unperturbed for at least three days before harvesting. Tumor tissue was macrodissected including surrounding stromal regions and then flash frozen.
|
| Growth protocol |
Brain metastatic cells were cultured under the same conditions as their parental lines and as recommended by the American Type Culture Collection. For human cell xenografts, 5-6 week old athymic nu/nu mice were injected intracardially (1-5x10e5 cells in 100ul PBS), subcutaneously (5x10e5 cells in 100ul PBS mixed with 50% growth factor reduce Matrigel).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Lipid Tissue mini kit (QIAGEN).
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 |
Sample_EW19
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) |
| GSE115700 |
Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis [BrainMet_SQ_2D] |
| GSE115702 |
Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis |
|
| Relations |
| BioSample |
SAMN09402942 |
| SRA |
SRX4200392 |
