|
| Status |
Public on Jul 26, 2014 |
| Title |
AC06_cuff_mut_sRNA |
| Sample type |
SRA |
| |
|
| Source name |
cuff[wm25]/cuff[qq37] ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: 3-10 days old
genotype/variation: cuff[wm25]/cuff[qq37]
tissue: ovary
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ovaries dissected, isolation of RNA with Ribozol Reagent
19-29nt sRNA are cloned as detail described in Le Thomas et al. (2014)
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
19-29nt small RNA squencing
|
| Data processing |
Illumina CASAVA version 1.7 used for basecalling
Mapped to the Drosophila melanogaster genome dm3
Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non-zero expression
Values were quantile-normalized allowing comparisons of the two sets using custom-built software and algorithms as described (Aravin et al., 2008; Olson et al., 2008; Tam et al., 2008)
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimted text file includes reads and their frequencies.
|
| |
|
| Submission date |
Jul 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Adrien Le Thomas |
| Organization name |
California Institute of Technology
|
| Department |
Biology and Biological Engineering
|
| Lab |
Aravin
|
| Street address |
231 South Hudson Avenue
|
| City |
Pasadena |
| State/province |
CA - California |
| ZIP/Postal code |
91101 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE59608 |
Trans-generationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing [cuff smallRNA] |
| GSE59610 |
Trans-generationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing |
|
| Relations |
| BioSample |
SAMN02940618 |
| SRA |
SRX661249 |
