|
| Status |
Public on Nov 20, 2017 |
| Title |
Drosophila pseudoobscura embryo small RNA [M059_dpse_embryo] |
| Sample type |
SRA |
| |
|
| Source name |
D. pseudoobscura embryo small RNA
|
| Organism |
Drosophila pseudoobscura |
| Characteristics |
tissue: whole embryo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Male and female bodies were isolated in bulk using sieves after sorting by sex. Animals were flash frozen in liquid nitrogen followed by vortexing. This procedure severs heads from the thorax and abdomen allowing separation of these two body parts when sifted through chilled fine mesh sieves. Here we used a .600mm sieve to collect male bodies. Total RNA was then extracted from the bodies using TRIzol according to manufacturer protocol.
For Illumina GAII Libraries: From total RNA, ~18-26 nt fraction was isolated using PAGE and cloned using ligation to adapters requiring 5' monophosphate and 3' OH.
For Illumina HiSeq Library: Libraries were created with the Illumina truseq small RNA cloning kit using a modified protocol. Small RNAs in the 18-29nt size range were first isolated from total RNA by PAGE purification before cloning. PAGE purification was also performed after ligation of RNAs to 3’ and 5’ linkers before processing in subsequent steps. All enzymatic reactions and oligos were used as indicated by manufacturer.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mixed embryos
|
| Data processing |
3' adapter sequences were trimmmed using the fastx_clipper utility
reads < 15nt in size were filtered
identical read sequences were collapsed using the fastq_collapser utility
Supplementary_files_format_and_content: read count table files (columns are read read sequence and number of reads)
|
| |
|
| Submission date |
Apr 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jaaved Mohammed |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Chemical and Systems Biology
|
| Lab |
Joanna Wysocka
|
| Street address |
265 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13310 |
| Series (1) |
| GSE98013 |
Small RNAs from 11 Drosophila species |
|
| Relations |
| BioSample |
SAMN06770090 |
| SRA |
SRX2749096 |
