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Status |
Public on Jan 25, 2019 |
Title |
SATB1+P4 |
Sample type |
SRA |
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Source name |
skin lesion
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Organism |
Homo sapiens |
Characteristics |
tissue: skin tumor: CD30+LPD molecular classification: SATB1+
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Jan 25, 2018 |
Last update date |
Jan 25, 2019 |
Contact name |
Yang Wang |
E-mail(s) |
yangwang_dr@bjmu.edu.cn
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Organization name |
Peking University First Hospital
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Street address |
Xishiku Street
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City |
Beijing |
ZIP/Postal code |
100034 |
Country |
China |
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Platform ID |
GPL11154 |
Series (1) |
GSE109620 |
Gene Expression Profiling of Cutaneous CD30+ Lymphoproliferative Disorders by RNA-seq |
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Relations |
BioSample |
SAMN08395078 |
SRA |
SRX3599209 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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