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Sample GSM2209647 Query DataSets for GSM2209647
Status Public on Jun 09, 2017
Title T_72_P
Sample type SRA
 
Source name Papillary thyroid cancer invasive region
Organism Homo sapiens
Characteristics group: PTC invasive region
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from papillary thyroid cancer central and invasive regions using Macherey-Nagel RNA kit (Macherey-Nagel GmbH & Co. KG, D├╝ren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing [raw read cleaning] Illumina TruSeq adapter sequence that may included in raw reads were trimmed by CutAdapt (https://pypi.python.org/pypi/cutadapt).
[mapping on the reference genome] Adapter trimmed reads were mapped by TopHat2 (http://tophat.cbcb.umd.edu) with bowtie2 (http://bowtie-bio.sourceforge.net).
[expression quantification] Normalized gene expression values were calculated by CuffLinks (http://cufflinks.cbcb.umd.edu) with default options.
Genome_build: hg19
Supplementary_files_format_and_content: [.xlsx] DEG test result file by CuffDiff
 
Submission date Jun 21, 2016
Last update date May 15, 2019
Contact name Tea jun Park
E-mail(s) skyblue32@nate.com
Organization name Ajou University School of Medicine
Department Biochemistry and Molecular Biology
Street address 206, World cup-ro, Yeongtong-gu
City swon
ZIP/Postal code 443-721
Country South Korea
 
Platform ID GPL18573
Series (1)
GSE83560 Gene expression profiling of papillary thyroid cancer from central and invasive regions
Relations
BioSample SAMN05277426
SRA SRX1868480

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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