|
| Status |
Public on May 14, 2021 |
| Title |
N2_nuclear_extract |
| Sample type |
SRA |
| |
|
| Source name |
nuclear RNA
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: N2
tissue: whole worm
rna fraction: Nuclear RNA
|
| Treatment protocol |
For cloning ppp-RNAs, the sample is treated with 0.5 μM PIR-1 at 20 °C for 2 hours and for cloning only p-RNAs, no PIR-1 is required.
|
| Growth protocol |
Worms were grown on NGM or Ivermectin-containing 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. Please refer to Li L et al. RNA. 2020 Feb;26(2):218-227.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| 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 |
Jul 24, 2020 |
| Last update date |
May 15, 2021 |
| 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 |
GPL9269 |
| Series (1) |
| GSE150690 |
The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans |
|
| Relations |
| BioSample |
SAMN15638085 |
| SRA |
SRX8817759 |
