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Sample GSM2252899 Query DataSets for GSM2252899
Status Public on Feb 01, 2017
Title control RNASeq rep1
Sample type SRA
Source name control RNASeq rep1
Organism Homo sapiens
Characteristics cell line: PC-3
tissue: prostate; derived from metastatic site: bone
sirna transfection: PC-3 control
Treatment protocol no treatment
Growth protocol RPMI1640 supplied with 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd. Transcriptome reads from RNA-Seq experiments were mapped to the reference genome (hg19) by using BWA/Bowtie tool. Genes expression level is quantified by a software package called RSEM.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description control-1
Data processing Raw reads were subjected to quality control (QC) to determine if a resequencing step is needed.
After QC, raw reads were filtered into clean reads which will be aligned to the reference sequences.Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Use Bowtie2 to map clean reads to reference gene and use BWA to reference genome.
RSEM was used to computed maximum likelihood abundance estimates. FPKM method is used in calculated expression level.
Use NOISeq to screen differentially expressed genes between two groups.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.
Submission date Jul 26, 2016
Last update date May 15, 2019
Contact name Ni Li
Organization name Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences
Lab Laboratory of Tumor Progression and Metastasis
Street address 320 Yueyang Road, Shanghai, 200025 P.R. China
City Shanghai
State/province Shanghai
ZIP/Postal code 200031
Country China
Platform ID GPL20301
Series (1)
GSE84868 Expression data from control and WHSC1 siRNA treated PC3 cells
BioSample SAMN05441414
SRA SRX1978380

Supplementary file Size Download File type/resource
GSM2252899_control_1.gene.FPKM.txt.gz 312.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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