|
| Status |
Public on Sep 09, 2021 |
| Title |
Control_DHT_sgAr_rep.3 |
| Sample type |
SRA |
| |
|
| Source name |
Control_DHT_sgAr_prostate organoids
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: : control with sgAr
tissue/cell type: prostate
treatment: 1 nM DHT
|
| Treatment protocol |
sgAr = sgRNA targeting AR exon 2 of NM_013476.4
|
| Growth protocol |
Murine organoids were grown in mouse organoid media as per standard protocol.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were processed as previously described in Grbesa I, et al. J Vis Exp 2017. PMID 29155775
Libraries were made as described previously in Grbesa I, et al. J Vis Exp 2017. PMID 29155775
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Reads were aligned to mouse genome with Bowtie2 v.2.3.4.1.
Duplicates and mitochondrial reads were removed with Samtools v1.8. or as part of the ENCODE ATAC-seq pipeline
Peaks were called with Genrich (https://github.com/jsh58/Genrich) in ATAC-seq mode.
Genome_build: mm10 genome
Supplementary_files_format_and_content: peaks
|
| |
|
| Submission date |
Jan 02, 2021 |
| Last update date |
Sep 09, 2021 |
| Contact name |
Ivana Grbesa |
| E-mail(s) |
ivana.grbesa3@gmail.com
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Urology
|
| Lab |
Barbieri
|
| Street address |
413 E 69th St
|
| City |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE145332 |
SPOP mutation reshapes chromatin landscape and transcriptional response to androgens [ATAC-seq] |
| GSE145333 |
SPOP mutation reshapes chromatin landscape and transcriptional response to androgens. |
|
| Relations |
| BioSample |
SAMN17200270 |
| SRA |
SRX9768216 |
