NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3586389 Query DataSets for GSM3586389
Status Public on Mar 02, 2020
Title CN3
Sample type SRA
 
Source name colorectal cancer adjacent tissue
Organism Homo sapiens
Characteristics tissue: adjacent tissue
Extracted molecule total RNA
Extraction protocol Total RNA enriched in small RNA population was extracted using miRNeasy kit (Qiagen) as per the manual’s protocol.
RNA libraries were constructed for sequencing using standard Illumina protocols
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Data processing The raw sequencing reads were subjected to the Illumina pipeline filter (Solexa 0.3), and the dataset was then further processed using an in-house program, ACGT101-miR (LC Sciences, Houston, TX, United States) to remove adapter dimers, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA), repeats in the NCBI GenBank1, Repbase2, and Rfam3) databases.
the remaining non-annotated sequences were mapped to specific species precursors in miRbase 21.04 by BLAST searches to identify known miRNAs.
On the basis of sequence similarity to human genome, these miRNA sequences were classified into subgroups 1a, 1b, 2a, 2b, and 3 with high-to-mid confidence in order
All non-annotated reads with lengths of 18–25 nt were mapped to the reference genome sequences using the Bowtie package; only perfectly matched sRNAs were used in further analyses.
Novel miRNAs were identified using the MIREAP software based on their precursors, and the hairpin RNA structures containing sequences were predicated from the flanking 120 nt sequences using RNAfold software.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample
 
Submission date Jan 31, 2019
Last update date Mar 02, 2020
Contact name Fangbin Zhou
E-mail(s) [email protected]
Phone +8618801768978
Organization name Tongji University School of Medicine
Street address Siping Road 1239
City Shanghai
State/province State...
ZIP/Postal code 200092
Country China
 
Platform ID GPL16791
Series (1)
GSE125961 Identification of miRNAs and Their targets in Colorectal Cancer (miRNA)
Relations
BioSample SAMN10853053
SRA SRX5316203

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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