|
| Status |
Public on Jan 09, 2017 |
| Title |
Non-Cachectic controls [7409] |
| Sample type |
SRA |
| |
|
| Source name |
Rectus abdominus
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Fresh frozen (FF) Muscle biopsy
tumor type: Colorectal
|
| Growth protocol |
Muscle biposies were preserved as Fresh frozen tissues
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol and Qiagen Rneasy kit according to manufacturer's instructions
Small RNAs were sequenced using Truseq Small RNA sequencing kit(Illumina), TruSeq SR cluster kit v5-CS-GA (Illumina) and TruSeq SBS kit v5-GA(Illumina) according to manufacturer's instructions. All samples were sequenced using MiSeq platform with 36 cycles single end protocol
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Genomic small RNA (size selected from total RNA)
|
| Data processing |
Base calling and demultiplexing was performed using MiSeq Reporter FastQ workflow
Cutadapt 1.4.1 was used to trim the adapters
Trimming of low quality reads were performed with a threshold of 30 on Sanger scale
Quality control for sequenced reads before and after adapter trimming was performed using FastQC v0.11.3 software
BWA aligner version 0.6.1 was used to align trimmed reads to the reference genome human genome 19 build, downloaded from Illumina iGenome website
Samtools version 0.1.18 was used to convert aligned .sam files to .bam format which was used for downstream analyses
Genome_build: hg 19, miRBAse v 20 for annotating miRNAs
Supplementary_files_format_and_content: tab-delimited txt files containing RPKM normalized values for all miRs
|
| |
|
| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sambasivarao Damaraju |
| E-mail(s) |
sdamaraj@ualberta.ca
|
| Phone |
7804328869
|
| Organization name |
University of Alberta
|
| Department |
Laboratory medicine and pathology
|
| Street address |
11560 University Ave
|
| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G1Z2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE75473 |
Small RNAome profiling from human skeletal muscle: Novel miRNAs and their targets associated with cancer cachexia |
|
| Relations |
| BioSample |
SAMN04299792 |
| SRA |
SRX1453728 |
