|
| Status |
Public on Mar 11, 2021 |
| Title |
RNA-seq Sample 38 Perigastric lymph node |
| Sample type |
SRA |
| |
|
| Source name |
Sample 38 Perigastric lymph node
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Metastatic castration resistant prostate cancer
tissue: Perigastric lymph node
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purified RNA was used to prepare a sequencing library and sequenced on Applied Biosystems SOLiD (V3).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
RNAseq_38_Perigastric_LN
RNA-seq for AR in Sample 38_Perigastric_LN
processed data file: rna_seq_processed_data_counts_matrix.txt
|
| Data processing |
Sequencing library was sequenced on Applied Biosystems SOLiD (V3) with paired-end 34 x 74 bp reads.
Sequencing reads were aligned to hg18 (NCBI36) and raw counts were generated using Bioscope.
Raw counts were normalized with DESeq2 (v1.22.2). All genes not expressed across all samples were removed (normalized count data < 10). Subsequently data were log transformed.
Genome_build: hg18 (NCBI36)
Supplementary_files_format_and_content: rna_normalized_log_transformed_ge_matrix.txt: Gene expression matrix of normalized and log transformed counts.
|
| |
|
| Submission date |
Jun 10, 2020 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Tesa Severson |
| E-mail(s) |
t.severson@nki.nl
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
Molecular Carcinogensis
|
| Street address |
121 Plesmanlaan
|
| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9442 |
| Series (2) |
| GSE152230 |
Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases [RNA-seq] |
| GSE152231 |
Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases |
|
| Relations |
| BioSample |
SAMN15203129 |
| SRA |
SRX8525056 |
