GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM940602 Query DataSets for GSM940602
Status Public on Aug 31, 2012
Title d24h_small RNA-seq
Sample type SRA
Source name developing multicellular cells
Organism Dictyostelium discoideum
Characteristics strain: AX4
cell type: 24 hour developing multicellular cells
Growth protocol Cell were grown in HL5 liquid media (0h) and developed in PDF buffer on nitrocellulose filters (16h and 24h)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol. Small RNA was enriched using FlashPAGE (Ambiont). The SOLiD Small RNA Expression system (Applied Biosystems) was used for preparation of cDNA and multiplexing and subsequently sequenced using the SOLiD technology.
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model AB SOLiD System 3.0
Data processing Remove adaptersequence using in-house program (available upon request)
Map reads to the genome sequence
Remove reads that are not 21 nt
Remove reads that map to more than 10 locations
Remove reads that likely come from siRNAs
Remove reads where the surrounding sequence does not correspond to a potential pre-miRNA structure
Supplementary_files_format_and_content: the count of the miRNA and their sequence
Submission date May 31, 2012
Last update date May 15, 2019
Contact name Johan Reimegård
Organization name Science for Life Laboratories
Street address Tomtebodavägen 23A
City Stockholm
State/province Solna
ZIP/Postal code 17165
Country Sweden
Platform ID GPL15636
Series (1)
GSE38361 MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs
SRA SRX150812
BioSample SAMN01001260

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