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| Status |
Public on Feb 02, 2015 |
| Title |
Effect of Nbr on the length of piRNAs and endo-siRNAs in Drosophila |
| Organism |
Drosophila melanogaster |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
nbr/CG9247 gene regulates the length of a subset of miRNAs.
It is not clear whether Nbr affects the length of other classes of small RNAs, such as piRNAs and endo-siRNAs.
To address this, we compared small RNA population in wild-type, Df(2L)BSC312/+, nbr null (nbrf02257/Df(2L)BSC312), (nbr null; pCaSper-nbr (WT)), and (nbr null; pCaSper-nbr (D435A,E437A)).
This approach revealed that, in addition to miRNAs, piRNAs and endo-siRNAs were also affected in their length in nbr null and nbr null; pCaSper-nbr (D435A,E437A).
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| Overall design |
4-7d ovaries were dissected in PBS, and 40ug total RNA was prepared from wild-type, Df(2L)BSC312/+, nbr null (nbrf02257/Df(2L)BSC312), (nbr null; pCaSper-nbr (WT)), and (nbr null; pCaSper-nbr (D435A,E437A)), using Trizol Reagent (#15596-018, Life Technologies, Carlsbad, CA) following the manufacturer's protocol.
The small RNAs between ~16 to ~29 nt in size were purified from 15% TBE-urea gel (#EC6885BOX, Life Technologies, Carlsbad, CA).
Small RNA libraries were prepared using Illumina's TruSeq small RNA sample preparation kit (#RS-200-0012, Illumina, Inc. San Diego, CA), following the manufacturer's protocol
The libraries were sequenced on HiSeq2000 platform (Illumina).
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| Contributor(s) |
Abe M, Bonini NM, Khaladkar M, Kim J, Feltzin VL, Parisi M, Hendriks GJ |
| Citation(s) |
25754031 |
| Submission date |
Aug 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Junhyong Kim |
| Organization name |
University of Pennsylvania
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| Department |
Biology
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| Lab |
Junhyong Kim
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| Street address |
433 S University Avenue
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (5)
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| GSM1213276 |
Drosophila_4-7d_ovary_wild type |
| GSM1213277 |
Drosophila_4-7d_ovary_Df(2L)BSC312/+ |
| GSM1213278 |
Drosophila_4-7d_ovary_nbr null (nbrf02257/Df(2L)BSC312) |
| GSM1213279 |
Drosophila_4-7d_ovary_nbr null; pCaSper-nbr (WT) |
| GSM1213280 |
Drosophila_4-7d_ovary_nbr null; pCaSper-nbr (D435A,E437A) |
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| Relations |
| BioProject |
PRJNA215892 |
| SRA |
SRP028958 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE50055_RAW.tar |
277.8 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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