|
| Status |
Public on Mar 24, 2022 |
| Title |
Athos_ip1 |
| Sample type |
SRA |
| |
|
| Source name |
Ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
group: Athos
dissection: dissected 1-3 days post-eclosion
experiment: rRNA IP seq
rip antibody: IP
genotype: athos::GFP::FLAG
tissue: Ovaries
|
| Treatment protocol |
Samples in the characteristics "RIP antibody" field: those with "IP" were subected to IP with an antibody against FLAG conjugated to the protein indicated, those with "IgG" were subjected to IP using control mouse IgG, and those with "Input" consisted of 10% of the total lysate reserved for RNA extraction using Trizol.
|
| Growth protocol |
Flies were fattened on yeast prior to dissection, ovaries were dissected in 1x PBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol (Invitrogen, 15596026), treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907). mRNA-enriched libraries were obtained by treating total RNA with poly(A)tail selection beads following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08)
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were aligned to the M21017.1 NCBI Drosophila rRNA sequence record using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
For total RNA IP experiments, expression was normalized to the matched inputs and a luciferase spike-in. Enrichment was assesed compared to the IgG control.
Genome_build: M21017.1 NCBI Drosophila rRNA sequence
Supplementary_files_format_and_content: tabular file (count table)
|
| |
|
| Submission date |
Apr 01, 2021 |
| Last update date |
Mar 24, 2022 |
| Contact name |
Prashanth Rangan |
| E-mail(s) |
[email protected]
|
| Phone |
5184423485
|
| Organization name |
RNA Institute
|
| Department |
Biological Sciences
|
| Lab |
Rangan Lab
|
| Street address |
1400 Washington
|
| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12222 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE171347 |
A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis [rRNA_RIP-seq] |
| GSE171350 |
A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis |
|
| Relations |
| BioSample |
SAMN18590379 |
| SRA |
SRX10501835 |
