|
| Status |
Public on Jul 06, 2016 |
| Title |
BE2C_50 |
| Sample type |
SRA |
| |
|
| Source name |
BE(2)C
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BE(2)C
spike-in conc.: 50
|
| Treatment protocol |
No treatments applied
|
| Growth protocol |
All cell types were grown in DMEM/F12:MEM media supplemented with 10% IFS. Cells were collected when 70% confluent
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard Trizol extraction protocol
NEBNext Multiplex Small RNA Library Prep Set for Illumina (size selected for miRNA)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
short RNA
|
| Data processing |
Alignment to small RNA transcriptome + spike in sequences with HISAT 0.1.6.
Transcript quantification using Salmon 0.3.2.
Gene-level summarization.
Natural log transform (plus one pseudocount)
Genome_build: GRCh38
|
| |
|
| Submission date |
May 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick Cahan |
| E-mail(s) |
patrick.cahan@jhmi.edu
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
ICE and Biomedical Engineering
|
| Lab |
Cahan Lab
|
| Street address |
733 North Broadway, MRB 653
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE81499 |
Multiple mechanisms disrupt let-7 miRNA biogenesis and function in neuroblastoma [shortRNA] |
| GSE81500 |
Multiple mechanisms disrupt let-7 miRNA biogenesis and function in neuroblastoma |
|
| Relations |
| BioSample |
SAMN05004541 |
| SRA |
SRX1767628 |
