|
| Status |
Public on Apr 10, 2020 |
| Title |
2_4_mat: Small RNAs from ovaries of 2.4 mat transgenic strain |
| Sample type |
SRA |
| |
|
| Source name |
ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: ovaries
strain: 2.4 mat
molecule subtype: small RNAs
|
| Growth protocol |
Flies were grown according to standard protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
smallRNA-seq: Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt).
smallRNA-seq: Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)
GRO-seq: Nuclei were purified from homogenized ovaries, and were used for run-on reacton with Br-UTP in vitro (Rozkov et al. 2013).
GRO-seq: De novo synthesized RNA was subjected to library preparation for RNA-seq.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
smallRNA-seq: Reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie2 to dm3 genome assembly and transgene sequences.
GRO-seq: Reads were clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG), reads smaller than 19 nt were discarded. Reads were mapped to the dm3/R5 genomic assembly of transgene sequence by bowtie2 and deduplexed. Only single-mapped reads were used for the construction the genomic profiles.
Genome_build: dm3
Supplementary_files_format_and_content: smallRNA-seq: Tab-delimited file include the raw counts of clipped read occurrences. GRO-seq: Genomic profiles of RPM-normalized single-mapped reads.
|
| |
|
| Submission date |
Oct 15, 2019 |
| Last update date |
Apr 11, 2020 |
| Contact name |
Pavel Komarov |
| E-mail(s) |
pkom94@img.ras.ru
|
| Organization name |
Institute of Molecular Genetics of the Russian Academy of Sciences
|
| Street address |
Kurchatov sq. 2
|
| City |
Moscow |
| ZIP/Postal code |
123182 |
| Country |
Russia |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE138886 |
Epigenetic requirements for triggering heterochromatinization and Piwi-interacting RNA production from transgenes in the Drosophila germline |
|
| Relations |
| BioSample |
SAMN13032336 |
| SRA |
SRX6995971 |
