NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2064277 Query DataSets for GSM2064277
Status Public on Mar 17, 2016
Title DICER KO #43 (set 2)
Sample type SRA
 
Source name HCT116 cell line
Organism Homo sapiens
Characteristics genotype/variation: DICER knockout
cell line: HCT116
experimental set: set 2
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 SRX1589542
BioSample SAMN04503930

Supplementary file Size Download File type/resource
GSM2064277_DcrKO43.txt.gz 1.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap