|
| Status |
Public on Mar 17, 2016 |
| Title |
DROSHA KO #40 (set 1) replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: DROSHA knockout
cell line: HCT116
experimental set: set 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10 µg of total RNA from parental and knockout cells was extracted with TRIzol reagent (Life Technologies).
TruSeq Small RNA Sample Prep Kit (Illumina) was used for the preparation of the small RNA sequencing library. Total RNA was size-separated on a 15% urea-polyacrylamide gel. The region of the gel containing RNA with the size from 17 to 30 nucleotides was excised and eluted for adaptor ligation at both 5' and 3' ends. The ligated RNAs were reverse-transcribed with SuperScript III (Life Technologies) reverse transcriptase and amplified using Phusion High-Fidelity DNA polymerase (Thermo Scientific). The final products were sequenced by MiSeq system (Illumina).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
small RNA (17-30nt)
|
| Data processing |
FASTQ sequences produced from the sequencer were aligned to the human reference genome (GRCh38) by Bowtie2.
By comparing with genomic coordinates of miRNAs (obtained from mirbase.org), miRNA reads were chosen. Only the reads that matched perfectly with miRNA sequences were selected for further analyses.
To normalize miRNA reads, the read of miR-320a-3p was used for DROSHA and XPO5 knockouts. In the case of DICER knockout, the combined reads from rRNAs and tRNAs were used for the normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read numbers for each miRNA was calculated.
|
| |
|
| Submission date |
Feb 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Young-Kook Kim |
| E-mail(s) |
ykkim.bio@gmail.com
|
| Organization name |
Chonnam National University Medical School
|
| Department |
Department of Biochemistry
|
| Street address |
264, Seoyang-ro
|
| City |
Hwasun, Jeollanam-do |
| ZIP/Postal code |
58128 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE77989 |
Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis |
|
| Relations |
| SRA |
SRX1589538 |
| BioSample |
SAMN04503927 |
