|
| Status |
Public on May 31, 2020 |
| Title |
NEXTflex RA 3 |
| Sample type |
SRA |
| |
|
| Source name |
Lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
library prep kit: NEXTflex
mix type/state: Disease state: rheumatoid arthritis
replicate: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Synthetic miRNA samples: no RNA extraction needed, human samples: RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
NEBNext, NEXTflex
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
total RNA
BioO-18
|
| Data processing |
Primary base calling and quality scoring was performed using RTA v1.18.66.4 (Illumina)
demultiplexing and processing with Bcl2fastq v2.18.0.12 (Illumina)
3' adapter were trimmed using cutadapt v1.15 with parameter -m 10
Remaining reads were mapped to the synthetic miRNA reference or customized miRNA reference based on miRBase v21 using Bowtie v1.1.2 with parameter -a and --norc, no mismatches allowed
Reads were counted a custom python script
Genome_build: synthetic miRNA reference and customized miRNA reference based on miRBase v21
|
| |
|
| Submission date |
Dec 09, 2019 |
| Last update date |
May 31, 2020 |
| Contact name |
Fatima Heinicke |
| E-mail(s) |
fatima.heinicke@gmail.com
|
| Organization name |
Oslo University Hospital
|
| Department |
Department of Medical Genetics
|
| Street address |
Kirkeveien 166
|
| City |
Oslo |
| ZIP/Postal code |
0450 |
| Country |
Norway |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE141658 |
An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits |
|
| Relations |
| BioSample |
SAMN13512568 |
| SRA |
SRX7290807 |
