|
| Status |
Public on Sep 06, 2009 |
| Title |
Illumina sequencing of small RNAs from living one cell C. elegans embryos |
| Sample type |
SRA |
| |
|
| Source name |
Living one-cell embryo
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: one-cell embryo
strain: TX189
meoh-fixed: -
sorted: -
resorted: -
purity: ~70%
|
| Treatment protocol |
Living one cell stage embryos obtained by eFACS.
|
| Growth protocol |
Strains were maintained using standard methods (Brenner, 1974) on OP50 seeded NGM plates or in liquid culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library preparation as well as cluster generation and deep sequencing was performed according to the 5’ ligation dependent (5’monophosphate dependent) manufacturer’s protocol (Digital Gene Expression for small RNA, Illumina). Rougly 60,000 embryos (~10µg total RNA) were used for small RNA library preparation. Small RNAs were size selected between 18 and 40 nt according to the ssDNA marker in the small RNA sequencing kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Living one-cell embryos. The embryos were sorted a single time, yielding a purity of about 70%.
|
| Data processing |
Removal of 3' adapter sequences by searching for best matches of adapter prefixes up to edit distance 4.
|
| |
|
| Submission date |
Jul 14, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonas Maaskola |
| Organization name |
Max-Delbrueck Centrum Berlin-Buch
|
| Department |
Systems Biology of Gene Regulatory Elements
|
| Lab |
Rajewsky
|
| Street address |
Robert-Roessle Str. 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9269 |
| Series (1) |
| GSE17153 |
Illumina sequencing of small RNAs from C. elegans embryos |
|
| Relations |
| SRA |
SRX012406 |
| BioSample |
SAMN00004733 |
