|
| Status |
Public on Oct 01, 2023 |
| Title |
RIP-Seq MSTR-1 input rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole worm lysate
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
Stage: Young adult
temperature: 25C
genotype: F22D6.2(on49[MSTR-1::3xFLAG]) I
|
| Treatment protocol |
30 min crosslink with 2% formaldehyde
|
| Growth protocol |
Standard NGM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA crosslinked to affinity purified MSTR-1::FLAG
by Donnelly Sequencing Centre, Toronto, Canada, based on a modified small RNA protocol
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MSTR-1 input rep 2
|
| Data processing |
Concatenate fastq files
alignment with RNA STAR (https://github.com/alexdobin/STAR) on Galaxy
peak calling with PEAKachu (https://github.com/tbischler/PEAKachu) on Galaxy
coverage calculated with bamcoverage deepTools2 (https://github.com/deeptools/deepTools) on Galaxy
Genome_build: WS253
Supplementary_files_format_and_content: peak files, bed; coverage plots, bigwig
|
| |
|
| Submission date |
Oct 04, 2021 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Matthew Eroglu |
| E-mail(s) |
matt.eroglu@mail.utoronto.ca
|
| Organization name |
Hospital for Sick Children
|
| Department |
DSCB
|
| Street address |
686 Bay St
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL26672 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN22046680 |
| SRA |
SRX12485743 |
