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Sample GSM2134295 Query DataSets for GSM2134295
Status Public on Jun 06, 2016
Title PDX_TX_DFBM354_rep1
Sample type SRA
Source name HER2+ breast cancer brain metastases
Organism Homo sapiens
Characteristics sample type: breast cancer brain metastases
tissue: patient-derived xenograft
tumor type: HER2+
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen) and the RNeasy Mini Kit (Qiagen).
cDNA libraries were constructed using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher). Samples were barcoded using the Ion Xpress™ Barcode Adapter kits (Thermo Fisher)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description AmpliSeq™ Transcriptome sequencing of patient-derived HER2+ breast cancer brain metastatic xenograft
Data processing Data were analyzed by Torrent Suite and ampliSeqRNA analysis plugin (Thermo Fisher) to generate read counts
Bed file for target region is hg19_AmpliSeq_Transcriptome_21K_v1.bed, which was downloaded from
human genome hg19 fasta, index_version tmap-f3, was downloaded from
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited matrix table excel files, each includes raw counts of sequencing reads of 5 Samples for each repeat
Submission date Apr 27, 2016
Last update date May 15, 2019
Contact name Jean Zhao
Organization name Dana Farber Cancer Institute
Department Cancer Biology
Lab Jean Zhao
Street address 450 Brookline Ave, SM936
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platform ID GPL17303
Series (1)
GSE80722 Transcriptome analysis of patient-derived xenograft models of HER2+ breast cancer brain metastases
BioSample SAMN04909396
SRA SRX1733562

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

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