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| Status |
Public on Jul 07, 2020 |
| Title |
Sample 17 [WGS] |
| Sample type |
SRA |
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| Source name |
primary thyroid tumor
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| Organism |
Homo sapiens |
| Characteristics |
tumor subtype: PTC
tissue: thyroid
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Feb 19, 2019 |
| Last update date |
Jul 07, 2020 |
| Contact name |
Danny Misiak |
| E-mail(s) |
[email protected]
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| Phone |
+49345573962
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| Organization name |
Martin Luther University Halle-Wittenberg
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| Department |
Molecular Cell Biology
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| Lab |
Hüttelmaier Lab
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| Street address |
Kurt-Mothes-Str. 3a
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| City |
Halle (Saale) |
| ZIP/Postal code |
06120 |
| Country |
Germany |
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| 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 |
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| Relations |
| BioSample |
SAMN10964456 |
| SRA |
SRX5390025 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3611879_NT-23_CTRL.csv.gz |
3.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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