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Sample GSM3187889 Query DataSets for GSM3187889
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
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
BioSample SAMN09402821
SRA SRX4200348

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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