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Sample GSM3611880 Query DataSets for GSM3611880
Status Public on Jul 07, 2020
Title Sample 18 [WGS]
Sample type SRA
 
Source name primary thyroid tumor
Organism Homo sapiens
Characteristics tumor subtype: PTC
tissue: thyroid
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using the AllPrep Kit (Quiagen). 10mg of snap-frozen tissue was homogenized in RLT Plus buffer with a Precellys 24 tissue homogenizer (Bertin Instruments) and processed, according to the manufacturer's instructions. Integrity of genomic DNA was testet on an agarose gele.
A total amount of 1.0μg DNA per sample was used as input material for the DNA sample preparations. Sequencing libraries were generated using NEBNext® DNA Library Prep Kit following manufacturer's recommendations and indices were added to each sample. The genomic DNA is randomly fragmented to a size of 350bp by shearing, then DNA fragments were end polished, A-tailed, and ligated with the NEBNext adapter for Illumina sequencing, and further PCR enriched by P5 and indexed P7 oligos. The PCR products were purified (AMPure XP system) and resulted libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified using real-time PCR.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Library strategy: shallow whole genome sequencing
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -q --no-spliced-alignment --rna-strandness RF --dta -k 5
Secondary alignments were filtered out using samtools (v 1.5)
Copy number variatons were analyszed using R/cn.MOPS (v 1.28.0) using chromosome normalization (poisson) excluding sex chromosomes
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including genomic regions, log ratios of read counts and copy number values for each sample
 
Submission date Feb 19, 2019
Last update date Jul 07, 2020
Contact name Danny Misiak
E-mail(s) danny.misiak@medizin.uni-halle.de
Phone +49345573962
Organization name Martin Luther University Halle-Wittenberg
Department Molecular Cell Biology
Lab Hüttelmaier Lab
Street address Kurt-Mothes-Str. 3a
City Halle (Saale)
ZIP/Postal code 06120
Country Germany
 
Platform ID GPL24676
Series (2)
GSE126728 IGF2BP1 is the first positive marker for anaplastic thyroid carcinoma diagnosis [sWGS]
GSE126729 IGF2BP1 is the first positive marker for anaplastic thyroid carcinoma diagnosis
Relations
BioSample SAMN10964455
SRA SRX5390026

Supplementary file Size Download File type/resource
GSM3611880_NT-24_CTRL.csv.gz 3.1 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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