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Sample GSM2227415 Query DataSets for GSM2227415
Status Public on Jan 20, 2017
Title BICA, rep2
Sample type SRA
Source name cancer-containing bone-in-culture array
Organisms Homo sapiens; Mus musculus
Characteristics cell type: MCF-7 and local mouse cells
passage: P140-P142
reporter gene: Firefly Luciferase (MCF-7)
Growth protocol For MCF-7, cells are cultured in DMEM with 2% FBS. For BICA, bone pieces were prepared from metaphysis of femurs and tibias harvested from mice receiving intra-iliac injection. The bones were crushed with a bone plier (F.S.T. 16025-14) and transferred to low attachment 96-well plate. Bone pieces bearing tumor cells were cultured in media comprised of DMEM/F12.
Extracted molecule total RNA
Extraction protocol After homogenization, total RNA were extracted by Direct-zol RNA miniprep kit. The first and second strand cDNA were prepared by SuperScript III First-Strand Synthesis System and NEBNext mRNA Second Strand Synthesis Module from at least 200ng total RNA for each sample.
Illumina Nextera XT DNA Sample Prep Kit was used with 1 ng of dsDNA for the construction of sequencing libraries.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Sample 9
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData
Data processing Illumina NextSeq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace.
RNA-seq NGS reads derived from xenograft materials contain a mixture of human and mouse reads were separated using Xenome (version 1.0.1).
RNA-seq NGS reads were mapped using STAR RNA-seq aligner (version 2.4.1d).
RSEM (version 1.2.28) was used to quantify gene and isoform expression.
DESeq2 R package is used to normalize the gene/isoform expression matrix.
Genome_build: Human: GRCh38.83
Genome_build: Mouse: GRCm38.83
Supplementary_files_format_and_content: BICA_RNAseq.RData: Rdata object; RSEM read counts.
Supplementary_files_format_and_content: BICA_RNAseq.Normalized.RData: Rdata object; DESeq2 normalized gene/isoform expression matrix.
Submission date Jul 06, 2016
Last update date May 15, 2019
Contact name Hai Wang
Organization name Roswell Park Cancer Institute
Department Molecular and Cellular Biology
Lab Hai Wang
Street address Elm and Carlton Streets, MRC 328
City Buffalo
State/province NY
ZIP/Postal code 14263
Country USA
Platform ID GPL19415
Series (1)
GSE84114 Profiling in vivo Bone Lesion and ex vivo Bone-In-Culture Array Samples by Next-Generation Sequencing
BioSample SAMN05363395
SRA SRX1901140

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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