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Status |
Public on Sep 08, 2017 |
Title |
PTENhom_locusHom_9560 |
Sample type |
SRA |
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Source name |
prostate
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Organism |
Mus musculus |
Characteristics |
tissue: prostate tumor genotype: FOXP1-SHQ1-flox/flox PTEN-flox/flox Pb-Cre4 age: 12 months
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
prostate tumor from 12 month old FOXP1-SHQ1-flox/flox PTEN-flox/flox Pb-Cre4 mouse, HH9560
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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 EngstroĢm, 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
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Submission date |
Jun 14, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Haley Hieronymus |
Organization name |
Memorial Sloan Kettering Cancer Center
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Street address |
1275 York Ave.
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City |
New York |
State/province |
New York |
ZIP/Postal code |
10065 |
Country |
USA |
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Platform ID |
GPL17021 |
Series (1) |
GSE83358 |
FOXP1-SHQ1 deletion cooperates with PTEN deletion in oncogenesis |
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Relations |
BioSample |
SAMN05249966 |
SRA |
SRX1845272 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
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