|
| Status |
Public on Jan 05, 2024 |
| Title |
male_T1_female_TM3_piRNA_1 |
| Sample type |
SRA |
| |
|
| Source name |
adult fly ovaries total small RNA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: adult fly ovaries
chipantibody: none
reporter: T1 BX reporter
molecule subtype: total small RNA
|
| Treatment protocol |
Flies were fed with yeast for 2-3 days prior to dissection
|
| Growth protocol |
Fly stocks were maintained at 24C on standard diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total smRNA from ovary was isolated with Ribozol reagent and do size selection from 19nt to 30nt. Total smRNA from ovary was isolated with Ribozol reagent and do ribosomal RNA depeltion.
smRNA-seq libraries were made by using NEBNext® Small RNA Library Prep Set for Illumina®. Degradome-seq libraries were prepared by using protocol from Zamore lab. Libraries were sequenced on the Illumina HiSeq 2000 platform.
smRNA-seq follow NEBNext® Small RNA Library Prep Set for Illumina®
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Degradome-seq reads were trimmed by Trimmomatic (version 0.33) and cutadapt (version 1.15) and filter out those shorter than 50 bp after trimming
Ribosomal RNA removal by bowtie
The first 50bp of reads were mapped to dm6 genome and vectors sequence respectively, using STAR alignment
smRNA-seq reads were trimmed by Cutadapt to rRNA and filter out those shorter than 15 bp after trimming
Select reads size 21-22bp (siRNA) and 23-29bp (piRNA) and 21-30bp (small RNA)
mapped to dm6 genome and extracted regions 20A cluster(20A) and 42AB cluster(42A), mapped to vector maps, Ubi-GFP(UBIG), non-RMCE Ubi-GFP(originalUBIG), double-stranded GFP reporter(UBIGasG) (parameters: -v 0 -a -m 1 -t --best --strata), and plus, minus strand of genome regions and vectors were separate.
smRNA profilings were generated by Matlab after mapping
Assembly: dm3(ChIP-seq) and dm6(smRNA-seq)
Supplementary files format and content: bg4
|
| |
|
| Submission date |
Feb 16, 2023 |
| Last update date |
Jan 05, 2024 |
| Contact name |
Yicheng Luo |
| E-mail(s) |
[email protected]
|
| Phone |
5167762261
|
| Organization name |
Calfironia Institute of Technology
|
| Department |
Division of Biology and Biological Engineering
|
| Street address |
1200 E California Blvd
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE193091 |
Maternal inherited siRNA initiate piRNA cluster formation |
|
| Relations |
| BioSample |
SAMN33325497 |
| SRA |
SRX19391309 |
