|
| Status |
Public on Jan 24, 2020 |
| Title |
Cloning pRNA |
| Sample type |
SRA |
| |
|
| Source name |
adult worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
sample type: without PIR-1
|
| Treatment protocol |
For cloning 22G-RNA, the sample is treated with 0.5 μM PIR-1 at 20 °C for 2 hours; for cloning csRNA, the sample is treated with 1 U/μl CIP at 37 °C for 1 hour, extracted, precipitated, and treated with 0.5 μM hDcp2 at 20 °C for 2 hours.
|
| Growth protocol |
N2 worms were grown on NGM plates with OP50 at 20 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted with TRIzol
RNAs were linked with Truseq LT/V1/V2 linkers using the standard 5' and 3' ligation methods. Amplicons with ~20 nt inserts were selected for sequencing. The samples were multiplexed with 8 nt indexes in the 3' linker.
5' RNA ligation and 3' RNA ligation
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
pRNA
|
| Data processing |
The samples are debarcoded using the 8 nt barcodes
The 3' AGATCGGAA and beyond are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 2 mismatches are considered
Genome_build: C. elegans WS215
Supplementary_files_format_and_content: tabbed txt file containing sequence and read number for the analysis
|
| |
|
| Submission date |
Apr 11, 2019 |
| Last update date |
Jan 24, 2020 |
| Contact name |
Weifeng Gu |
| Organization name |
University of California at Riverside
|
| Department |
Molecular, Cell and Systems Biology
|
| Lab |
Weifeng Gu
|
| Street address |
900 University Ave
|
| City |
Riverside |
| State/province |
California |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE129664 |
A unified strategy to clone modified/unmodified small RNAs and mRNAs for high throughput sequencing |
|
| Relations |
| BioSample |
SAMN11399048 |
| SRA |
SRX5669876 |
