|
| Status |
Public on Sep 22, 2022 |
| Title |
CRPC-HOXB13-C4K13A - 1 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: C4-2B media
origin: Metastatic CRPC cell line
disease state: prostate cancer
sample type: C4K13A
|
| Growth protocol |
Parental and HOXB13-K13A mutant C4-2B were grown in C4-2B media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using QIAshredder and RNeasy Plus Mini kits. After RNA purification, it was treated with DNAse I to remove DNA contaminants, purified again on Qiagen RNA easy. Sample was anayzed on bioanlyzer, concentration and purity determined before proceeding with RNA -sequencing.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.
RiboErase method was used for sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. R
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
May 21, 2021 |
| Last update date |
Sep 22, 2022 |
| Contact name |
Kiran Mahajan |
| E-mail(s) |
kiranm@wustl.edu
|
| Phone |
3142737728
|
| Organization name |
Washington University
|
| Department |
Surgery
|
| Lab |
Kiran Mahajan Lab
|
| Street address |
CB 8242 600 South Euclid Ave
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE169134 |
Targeted Escalation of Acetylated HOXB13 Regulated Super-Enhancers Promotes Prostate Tumor Autonomy |
| GSE174923 |
HOXB13 lysine 13 acetylation regulated transcriptional targets in castration-resistant prostate cancer |
|
| Relations |
| BioSample |
SAMN19302351 |
| SRA |
SRX10957939 |
