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Sample GSM2947320 Query DataSets for GSM2947320
Status Public on Jan 25, 2019
Title SATB1-P5
Sample type SRA
 
Source name skin lesion
Organism Homo sapiens
Characteristics tissue: skin
tumor: CD30+LPD
molecular classification: SATB1-
Extracted molecule total RNA
Extraction protocol Lesional skin biopsies were obtained from 7 patients with CD30+LPDs (4 SATB1+, 3 SATB1-), from which total RNA samples were extracted and purified.
According to the TruSeq RNA Sample Prep Kit v2 (Illumina, San Francisco, CA), RNA libraries were prepared as follows. Firstly, 200ng total RNA samples extracted from 7 CD30+LPDs skin lesions were purified by oligo-dT beads, then poly (A)-containing mRNA were fragmented into small pieces with Elute, Prime, Fragment Mix. Then double-strand cDNA was synthesized by First Strand Master Mix, Super Script II (Thermo Fisher Scientific, Waltham, MA) reverse transcription and Second Strand Master Mix. In the next, the purified fragmented cDNA was combined with End Repair Mix and added with A-Tailing Mix. Adaptor ligation was made as well. After several rounds of PCR, the final library was constructed. Then the library was qualified through Agilent 2100 bioanalyzer instrument (Agilent Technologies, Santa Clara, CA) and Quantitative real-time polymerase chain reaction. The qualified library was sequenced on an Illumina HiSeqTM 2000 platform using paired-end reads. 10G raw data for each sample were obtained. The reads were aligned to the hg19 genome with SOAPaligner/SOAP2 (Li et al., 2009).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences with SOAPaligner/SOAP2.
Gene expression levels were calculated by reads per kilobase transcriptome per million mapped reads(RPKM)method.
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample
 
Submission date Jan 25, 2018
Last update date Jan 25, 2019
Contact name Yang Wang
E-mail(s) yangwang_dr@bjmu.edu.cn
Organization name Peking University First Hospital
Street address Xishiku Street
City Beijing
ZIP/Postal code 100034
Country China
 
Platform ID GPL11154
Series (1)
GSE109620 Gene Expression Profiling of Cutaneous CD30+ Lymphoproliferative Disorders by RNA-seq
Relations
BioSample SAMN08395081
SRA SRX3599210

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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