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Sample GSM2653787 Query DataSets for GSM2653787
Status Public on Jul 12, 2017
Title BPH117BE
Sample type SRA
Source name Human prostate basal epithelia
Organism Homo sapiens
Characteristics phenotype: BCH
facs ab profile: CD326+/CD49fHI/CD26-
Treatment protocol Fresh surgical tissue samples were transported in ice-cold saline and immediately processed for an overnight enzymatic digestion into single cells at 37ÂșC. Single cells were flow sorted to isolate basal epithelia (CD326+/CD49fHI/CD26-).
Extracted molecule total RNA
Extraction protocol Total RNA from 500K FACS-purified basal cells was extracted using RNEasy micro columns (Qiagen). RNA quality and quantity were measured by a Bioanalyzer and NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description Basal Epithelia from Tissue with Basal Cell Hyperplasia
Data processing Illumina's RTA version was used for basecalling followed by bcl2fastq2 version to generate fastq files.
Reads were trimmed using Trimmomatic version 0.32.
Reads were mapped to GRCh37 using TopHat version 2.1.12, with Bowtie2 version 2.2.3).
Mapped reads were filtered using SAMtools version 0.1.19 to remove those with a quality score MAPQ less than 10.
Quality-filtered mapped reads were quantified using Cufflinks' (version 2.2.1) CuffQuant and CuffNorm to generate FPKM.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.
Submission date Jun 08, 2017
Last update date May 15, 2019
Contact name Gervaise H. Henry
Phone 2146480497
Organization name UT Southwestern Medical Center
Department Urology
Lab Strand Lab
Street address 5323 Harry Hines Blvd, Mail Code:9110
City Dallas
State/province Texas
ZIP/Postal code 75390
Country USA
Platform ID GPL18460
Series (1)
GSE99824 Molecular pathogenesis of human prostate basal cell hyperplasia reveals a keratinocyte metaplasia
BioSample SAMN07206299
SRA SRX2896432

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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