|
| Status |
Public on Apr 21, 2015 |
| Title |
CMCW13 |
| Sample type |
SRA |
| |
|
| Source name |
Wilms tumor
|
| Organism |
Homo sapiens |
| Characteristics |
mutation status of dicer1 or drosha: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs were prepared from 50 ng of each tumor sample using the mirVana PARIS kit according to the standard manufacturer protocol.
Small RNA libraries were prepared using the protocol for small RNA library preparation in the SOLiD Total RNA-Seq kit from Life Technologies.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Reads demultiplexed on machine
Analyzed using LifeScope v2.5.1 using default small RNA parameters
filter out SOLiD adapter sequences, rRNA, tRNA
map to hg19 and miRbase, using seed-and-extend algorithm
mapping utilized seed-and-extend algorithm
Genome_build: hg19 and miRbase 16
Supplementary_files_format_and_content: gff file; "group" field contains "ACC" (miRBase accession number) and "ID" (miRBase ID)
|
| |
|
| Submission date |
Apr 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
James Francis Amatruda |
| Organization name |
UT Southwestern
|
| Department |
Pediatrics, Internal Medicine, and Molecular BIology
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL16288 |
| Series (1) |
| GSE56955 |
Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis in Wilms tumors |
|
| Relations |
| BioSample |
SAMN02731470 |
| SRA |
SRX523229 |
