|
| Status |
Public on Jan 20, 2017 |
| Title |
BICA, rep5 |
| 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 12
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 |
| E-mail(s) |
hai.wang@roswellpark.org
|
| 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 |
|
| Relations |
| BioSample |
SAMN05363398 |
| SRA |
SRX1901143 |
