|
Status |
Public on Jul 06, 2016 |
Title |
BE2C_500 |
Sample type |
SRA |
|
|
Source name |
BE(2)C
|
Organism |
Homo sapiens |
Characteristics |
cell line: BE(2)C spike-in conc.: 500
|
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 |
SAMN05004540 |
SRA |
SRX1767627 |