|
| Status |
Public on May 10, 2018 |
| Title |
LuCaP_23.1_Organoid_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
LuCaP 23.1 Organoid
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: LuCaP 23.1
gender: male
replicate: 1
tissue: PDX-derived organoid
|
| Treatment protocol |
Organoids were passaged.
|
| Growth protocol |
LuCaP tumors were grown in mice and then as organoids.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fresh organoids using the Qiagen AllPrep DNA/RNA mini kit
rRNA-depleted RNA was converted into cDNA and assembled into libraries using Illumina TruSeq v2 kit with standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove reads from mouse RNA using tophat/bowtie2 and aligning to either hg19 or mm10.
Bowtie-mapped reads were compared with Disambiguate and human-reads were converted back to FASTQ files.
Paired-end human-only FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, 75th percentile-normalized TPM estimate of expression
|
| |
|
| Submission date |
Apr 27, 2018 |
| Last update date |
Jun 14, 2019 |
| Contact name |
Adam Sowalsky |
| Organization name |
National Cancer Institute
|
| Department |
LGCP
|
| Lab |
Sowalsky Lab
|
| Street address |
37 Convent Drive Building 37 Room 1062B
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE113741 |
Establishment and characterization of prostate cancer organoids [RNA-seq] |
| GSE113743 |
Establishment and characterization of prostate cancer organoids |
|
| Relations |
| BioSample |
SAMN08993188 |
