|
| Status |
Public on Mar 01, 2019 |
| Title |
C4-2B HOXB13 KO1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Bone-metastatic CRPC cell line C4-2B
type: Androgen-independent
|
| Treatment protocol |
C4-2B treated with DMSO and or various inhibitors.
HOXB13 pKO genetic deletion were generated by CRISPR/Cas9 strategy
|
| Growth protocol |
grown in C4-2B specialized media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from C4-2B using the Qiagen RNeasy kit protocol followed by Dnase I treatment. 1-2ug of total RNA was used for the construction of the libraries.
The Illumina Hi-seq platform with 50 bp single end sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
1. Reference genome and transcript annotations: hg38 from UCSC
2. Mapping: TopHat splice-aware aligner (Kim et al Genome Biol. 2013)
3. Feature summarization: Expectation-Maximization(EM) approach used to estimate transcript abundance (Jiang and Wong, Bioinformatics, 2009)
4. Normalization:
Within sample: RPKM (reads per kilobase of transcript per million, Mortazavi et al, Nat. Meth. 2008)
Between sample: TMM (Trimmed mean of M values ,Robinson and Oshlack Genome Biol. 2010)
5. Differential test: non-replicates analysis with DESeq software (Anders and Huber Genome Biol 2010)
Genome_build: hg 38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Mar 24, 2018 |
| Last update date |
Mar 01, 2019 |
| Contact name |
Kiran Mahajan |
| E-mail(s) |
[email protected]
|
| 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 |
GPL18460 |
| Series (1) |
| GSE112300 |
Identification of HOXB13 target genes responsive to BET inhibitors |
|
| Relations |
| BioSample |
SAMN08793611 |
| SRA |
SRX3843264 |
