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| Status |
Public on Jul 01, 2024 |
| Title |
N2 CLIP |
| Sample type |
SRA |
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| Source name |
Whole worm lysate
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| Organism |
Caenorhabditis elegans |
| Characteristics |
Stage: Young adult
temperature: 25C
genotype: N2
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| Treatment protocol |
UV 1.2mJ/cm2
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| Growth protocol |
Standard NGM
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA crosslinked to affinity purified MSTR-1::FLAG
eCLIP
CLIP-seq
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| |
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
adaptor removal with Cutadapt (https://github.com/marcelm/cutadapt) on Galaxy (https://usegalaxy.eu/)
UMI extraction with UMI-tools (https://github.com/CGATOxford/UMI-tools) on Galaxy
alignment with RNA STAR (https://github.com/alexdobin/STAR) on Galaxy
deduplication with UMI-tools 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, tabular; coverage plots, bigwig
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| Submission date |
Oct 04, 2021 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Matthew Eroglu |
| E-mail(s) |
me2839@columbia.edu
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| Organization name |
Hospital for Sick Children
|
| Department |
DSCB
|
| Street address |
686 Bay St
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| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
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| Platform ID |
GPL26672 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN22046674 |
| SRA |
SRX12485767 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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