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Sample GSM956286 Query DataSets for GSM956286
Status Public on Mar 07, 2014
Title follicular adenoma_FA4
Sample type SRA
 
Source name follicular thyroid adenoma cells
Organism Homo sapiens
Characteristics thyroid tissue type: follicular thyroid adenoma
place of origin: Poland
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 TruSeqâ„¢ 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiScanSQ
 
Description snap-frozen tissue
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
 
Submission date Jul 05, 2012
Last update date May 15, 2019
Contact name Michal Swierniak
Organization name University of Warsaw
Department Centre of New Technologies
Street address Banacha 2C
City Warsaw
ZIP/Postal code 02-097
Country Poland
 
Platform ID GPL15456
Series (1)
GSE39112 miRNA high-throughput sequencing of follicular thyroid tumors
Relations
BioSample SAMN01085813
SRA SRX345043

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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