|
| Status |
Public on Nov 17, 2020 |
| Title |
small RNA sequencing [222T] |
| Sample type |
SRA |
| |
|
| Source name |
paraffin-embedded NSCLC tissue sample
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: NSCLC
tissue: Tumor
patient: 222
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Qiagen miRNeasy kit and 500 ng was subject to library preparation using the Illumina TruSeq small RNA kit. Molecules with the size of 40-200 nt were purified from a gel before sequencing.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Small RNA sequencing
small_RNA_seq_counts.txt
small_RNA_seq_RPM.txt
|
| Data processing |
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ.
CASAVA BclToFastq was used to export fastq files.
Illumina adapter sequences were removed using Cutadapt.
Reads were mapped using Bowtie2 and further processed to BAM format using samtools.
Regions with coverage were called from mapped reads using the bedtools genomeCoverageBed algorithm.
Sequences from the extracted regions were compiled to a consensus sequence which was subject to BLAST against a custom small RNA database. Furthermore, UCSC genome browser tracks for sno/miRNA, tRNA and repetitive elements were used to annotate the regions with coverage. Read counts were extracted for regions with an annotation and aggregated by name. Reads per million (RPM) was calculated by further normalizing to the total number of mapped reads.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Each processed file contains a column for the identified small nucleolar RNA (snoRNA) elements and the normalized average coverage for the respective sample.
Supplementary_files_format_and_content: small_RNA_seq_counts.txt: Tab-delimited text file includes read counts.
Supplementary_files_format_and_content: small_RNA_seq_RPM.txt: Tab-delimited text file includes RPM values.
|
| |
|
| Submission date |
Nov 05, 2020 |
| Last update date |
Nov 17, 2020 |
| Contact name |
Christian Rohde |
| E-mail(s) |
[email protected]
|
| Organization name |
Heidelberg University
|
| Lab |
Molecular Hematology and Oncology
|
| Street address |
Im Neuenheimer Feld 410
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE160928 |
NOP10 predicts NSCLC prognosis and its associated small nucleolar RNAs drive proliferation and migration [ncRNA-seq] |
| GSE161232 |
NOP10 predicts NSCLC prognosis and its associated small nucleolar RNAs drive proliferation and migration |
|
| Relations |
| BioSample |
SAMN16676849 |
| SRA |
SRX9444950 |
