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Sample GSM3187930 Query DataSets for GSM3187930
Status Public on Apr 08, 2019
Title H.FBMet Rep 3
Sample type SRA
 
Source name forebrain 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_EW32
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)
GSE115701 Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis [MultiDisease]
GSE115702 Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis
Relations
BioSample SAMN09402967
SRA SRX4200411

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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