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Sample GSM6212073 Query DataSets for GSM6212073
Status Public on Jun 07, 2023
Title PTEN-WT-1
Sample type SRA
 
Source name PTEN-wt mouse prostate organoids
Organism Mus musculus
Characteristics cell line: PTEN-wt mouse prostate organoids
cell type: prostate
source: mouse prostate
genotype: WT
treatment: NONE
Treatment protocol ARD-69 or DT-061 treatments were done at a concentration of 100 nM and 10 uM for12 hours respectivily.
Growth protocol MDVR cell lines were grown in the medium supplemented with Enzalutamide.
Extracted molecule total RNA
Extraction protocol RNA was harvested using miRNeasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA library preparation kit Illumina following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina bcl2fastq for demultiplexing to generate fastq files
fastq files were aligned to hg19 reference genome using STAR aligner (2.7.3a) with default parameters
samtools (v1.9) was used to convert SAM to BAM and filter out duplicates and reads q<30
bamCoverage was used to convert Bam to bigwig using “--normalizeUsing CPM”
Assembly: mm10, hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
 
Submission date Jun 02, 2022
Last update date Jun 07, 2023
Contact name Irfan Asangani
E-mail(s) asangani@upenn.edu
Phone 215-746-8780
Organization name University of Pennsylvania
Department Cancer Biology
Lab Asangani Lab
Street address 421 Curie Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL19057
Series (1)
GSE205419 Loss of LCMT1 and biased protein phosphatase 2A heterotrimerization drive prostate cancer progression and therapy resistance
Relations
BioSample SAMN28853333
SRA SRX15581521

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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