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| Status |
Public on Mar 07, 2014 |
| Title |
follicular adenoma_FA4 |
| Sample type |
SRA |
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| Source name |
follicular thyroid adenoma cells
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| Organism |
Homo sapiens |
| Characteristics |
thyroid tissue type: follicular thyroid adenoma
place of origin: Poland
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| Extracted molecule |
total RNA |
| Extraction protocol |
500 ng of total RNA prepared from the tumor samples was used in the small RNA protocol with the TruSeq™ Small RNA sample prepkit v2 (Illumina) according to the instructions of the manufacturer. The barcoded libraries were size restricted between 140 and 165bp, purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPABiosystems) according to the instructions of the manufacturer.
A pool of ten libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 50 bp was performed with an Illumina HighScan-SQ sequencer using version 3 chemistry and flowcell according to the instructions of the manufacturer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
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| Description |
snap-frozen tissue
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| Data processing |
Pipeline A: direct mapping - adapter cutting (cutadapt), human mature miRBase v18 alignment (bowtie2), sam to bam format compression (samtools), reads counting (R/Bioconductor ShortRead library), RPM normalization
Pipeline B: individual counting - adapter cutting (cutadapt), reads counting, median counts per sequence > 0 filtering, isoform grouping (sequence sorting), RPM normalization
Pipeline C: summarized counting - adapter cutting (cutadapt), reads counting, median counts per sequence > 0 filtering, isoform grouping (sequence sorting), summary of sequences with the same seeds (first 8 bases), RPM normalization
Supplementary_files_format_and_content: Pipeline A: direct mapping - tab separated text file with normalized abundance measurements (RPM) of sequences aligned to hsa mature miRBase v18
Supplementary_files_format_and_content: Pipeline B: individual counting - tab separated text file with RPM normalized miRNA isoform counts in 20 samples
Supplementary_files_format_and_content: Pipeline C: summarized counting - tab separated text file with RPM normalized miRNA counts per seed in 20 samples
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| Submission date |
Jul 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Michal Swierniak |
| Organization name |
University of Warsaw
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| Department |
Centre of New Technologies
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| Street address |
Banacha 2C
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| City |
Warsaw |
| ZIP/Postal code |
02-097 |
| Country |
Poland |
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| Platform ID |
GPL15456 |
| Series (1) |
| GSE39112 |
miRNA high-throughput sequencing of follicular thyroid tumors |
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| Relations |
| BioSample |
SAMN01085813 |
| SRA |
SRX345043 |
| 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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