|
| Status |
Public on Jan 01, 2023 |
| Title |
Tumor5_Small |
| Sample type |
SRA |
| |
|
| Source name |
lung cancer biopsy tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung cancer 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 lung cancer 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 |
SAMN13865370 |
| SRA |
SRX7566024 |
