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| Status |
Public on May 05, 2017 |
| Title |
N31-Control |
| Sample type |
SRA |
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| Source name |
Thyroid
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Thyrocyte
passages: 6-10
genotype/variation: Normal
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| Growth protocol |
Thyrocyte was isolated from normal thyroid tissue. Briefly, normal thyroid tissue was washed five times by PBS (phosphate-buffered saline) and cut into small pieces, followed by treatment with 0.2% collagenase I (Worthington Biochemical, Lakewood, NJ) in HEPES buffer for 6 hours at 32°C. Cell were resuspended in complete F12K media (F12K, Gibco BRL, Bethesda, MD; TSH, 10mU/ml; insulin, 0.01mU/ml; hydrocortisone, 10nM; transferrin, 0.005mg/ml; somatostatin, 10ng/ml; glycyl-L-histidyl-Llysine acetate, 10ng/ml) and placed in 10cm culture dishes.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from control and BRAFV600E thyrocyte samples using Macherey-Nagel RNA kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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: FPKM
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| Submission date |
May 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tea jun Park |
| E-mail(s) |
skyblue32@nate.com
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| Organization name |
Ajou University School of Medicine
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| Department |
Biochemistry and Molecular Biology
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| Street address |
206, World cup-ro, Yeongtong-gu
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| City |
swon |
| ZIP/Postal code |
443-721 |
| Country |
South Korea |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE81144 |
Gene expression in BRAFV600E thyrocyte |
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| Relations |
| BioSample |
SAMN04956418 |
| SRA |
SRX1743594 |
| 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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