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Sample GSM2200206

Query DataSets for GSM2200206

Status

Public on Sep 08, 2017

Title

PTENhom_B457

Sample type

SRA

Source name

prostate

Organism

Mus musculus

Characteristics

tissue: prostate tumor
genotype: PTEN-flox/flox Pb-Cre4
age: 12 months

Extracted molecule

total RNA

Extraction protocol

Murine prostates were removed, half was frozen at -80C, and RNA was harvested from the frozen tissue using bead-based lysis in Trizol, followed by choroform extraction, isopropanol precipitation, and RNeasy cleanup.
Illumina TruSeq RNA Sample Prep Kit v2 with 6 cycles of PCR was used for library construction. Samples were barcoded and run on a Hiseq 2500 in a single read 50 bp run, using the TruSeq SBS Kit v3 (Illumina).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

prostate tumor from 12 month old PTEN-flox/flox Pb-Cre4 mouse, HHb457

Data processing

FASTQ output was mapped to the genome (UCSC MM10, Mus_musculus.GRCm38.80) using the rnaStar aligner23 that maps reads genomically and resolves reads across splice junctions. The 2 pass mapping method outlined in Engström, et al. in which the reads are mapped twice was then used.
The output SAM files were post processed using PICARD and converted it to compressed BAM format.
Expression counts were derived from the mapped reads using HTSeq.
DESeq2 was then used to normalize the dataset and analyze differential expression.
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited DESeq2 normalized counts
Supplementary_files_format_and_content: tab-delimited HTSeq raw counts

Submission date

Jun 14, 2016

Last update date

May 15, 2019

Contact name

Haley Hieronymus

Organization name

Memorial Sloan Kettering Cancer Center

Street address

1275 York Ave.

City

New York