|
| 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 |
| E-mail(s) |
johan.reimegard@scilifelab.se
|
| 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 |
|
| Relations |
| SRA |
SRX150812 |
| BioSample |
SAMN01001260 |
