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Sample GSM4272741 Query DataSets for GSM4272741
Status Public on Jan 01, 2023
Title A549 cells, tRF-5003b
Sample type SRA
 
Source name Lung cancer cell line (A549)
Organism Homo sapiens
Characteristics cell line: A549 lung cancer cell line
treatment: tRF-5003b
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description RNA extracted after using tRF-5003b in A549 lung cancer cell line
tRF_5003.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 GPL21290
Series (1)
GSE143694 Monitoring the differential expression of miRNAs, tRNAs and tRFs in lung cancer biopsies.
Relations
BioSample SAMN13865362
SRA SRX7566032

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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