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Sample GSM4272724 Query DataSets for GSM4272724
Status Public on Jan 01, 2023
Title Normal2_Small
Sample type SRA
 
Source name normal lung biopsy tissue
Organism Homo sapiens
Characteristics tissue: normal lung biopsies
Growth protocol Tumor specimens were obtained by surgical procedures
Extracted molecule total RNA
Extraction protocol Frozen tissues were immediately lysed, and small and large RNA fractions were extracted and isolated using PureLink RNA mini Kit and mirVana miRNA Isolation Kit (Ambion)
Ion Total RNA-Seq Kit v2 protocol for small RNA sequencing
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Ion Torrent PGM
 
Description RNA from normal lung biopsies followed by size selection
miRNAs.xlsx
tRFs.xlsx
Data processing miRNAs, tRFs and tRNAs were analyzed using an in-house build script.
human tRFs from the tRFdatabase (http://genome.bioch.virginia.edu/trfdb/) were counted directly in the fastq files.
tRNAs were mapped to an artificial tRNA genome consisting of unique sequences of hg38 tRNAs (http://gtrnadb.ucsc.edu/) using bowtie and further counted using bedtools coverage
miRNAs were mapped to an artificial miRNA genome consisting of human miRNAs from the miRdatabase (http://www.mirbase.org/) using bowtie and further counted using bedtools coverage
Genome_build: hg38
Supplementary_files_format_and_content: abundance measurements
 
Submission date Jan 15, 2020
Last update date Jan 01, 2023
Contact name Constantinos Stathopoulos
E-mail(s) cstath@med.upatras.gr
Organization name University of Patras
Department Department of Biochemistry
Street address Asklipiou 1
City Patras
ZIP/Postal code 26504
Country Greece
 
Platform ID GPL17301
Series (1)
GSE143694 Monitoring the differential expression of miRNAs, tRNAs and tRFs in lung cancer biopsies.
Relations
BioSample SAMN13865379
SRA SRX7566015

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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