|
| Status |
Public on Oct 21, 2021 |
| Title |
involved.6.2 |
| Sample type |
SRA |
| |
|
| Source name |
Du145 prostate cancer cell line grown in mouse
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: mouse bones grossly involved by tumor
|
| Treatment protocol |
none
|
| Growth protocol |
cardiac left ventricular injection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy micro kit
Clontech SMART-seq V4 Ultra Low kit
poly-A / mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
mouse bones grossly involved by tumor
|
| Data processing |
The Tuxedo Suite of software was used for alignment, differential expression analysis, and post-analysis diagnostics.
Reads were aligned to the reference genome using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.), with default parameter settings for alignment, except: “--b2-very-sensitive” was set.
Cufflinks/CuffDiff (version 2.1.1) for expression quantitation, normalization, and differential expression analysis.
For normalization of expression values, “--multi-read-correct” was used to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile–norm”.
Genome_build: UCSC hg19
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text - raw reads quantified by Cufflinks
|
| |
|
| Submission date |
Oct 18, 2021 |
| Last update date |
Oct 21, 2021 |
| Contact name |
Bioinformatics Core |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Street address |
BRCF Bioinformatics Core, 2800 Plymouth Rd
|
| City |
Ann Arbor |
| State/province |
Mi |
| ZIP/Postal code |
48109-2800 |
| Country |
USA |
| |
|
| Platform ID |
GPL25431 |
| Series (1) |
| GSE186061 |
Comparison of rare vs macroscopic human prostate cancer cells in mouse bone |
|
| Relations |
| BioSample |
SAMN22370965 |
| SRA |
SRX12669729 |
