|
| Status |
Public on Apr 02, 2024 |
| Title |
SCMp, IAA, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Seam cells
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Seam cells
developmental stage: Young adults
treatment: IAA 4mM
|
| Treatment protocol |
2mL of IAA 1M (or EtOH 100%) was added to 500mL of cooling NGM (between 40°C and 45°C).
|
| Growth protocol |
Worms were grown on NGM plates supplemented with EtOH 0.4% or IAA 4mM at 20°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction.
Total RNA was used with NEBNext® Multiplex Small RNA Library Prep Kit for Illumina® (E7560S) and size selected on a gel (approximatively 140bp)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
small RNA analysis
|
| Data processing |
The samples or debarcoded
The adaptors are removed and only >16nt are kept
Small RNAs are mapped to the genome and cDNA using Bowtie 0.12.7 (maximum of 3 seed mismatches)
The samples were normalized to total gene expression (geex) reads excluding structural RNA (struc) and transformed in RPM (read per million).
Assembly: C. elegans WS215
Supplementary files format and content: (PMF1-18) The raw reads were individually normalized on the total gene expression reads (geex) minus the structural reads (struct) and converted to RPM. (PMF19-PMF24) The raw reads were individually normalized on the level of ALG-1 protein immunoprecipitated.
|
| |
|
| Submission date |
Aug 16, 2023 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Pierre-Marc Frédérick |
| E-mail(s) |
pierre-marc.frederick.1@ulaval.ca
|
| Organization name |
Centre de recherche du CHU de Québec - Université Laval
|
| Street address |
9 Rue McMahon
|
| City |
Québec |
| State/province |
Québec |
| ZIP/Postal code |
G1R 3S3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL26672 |
| Series (1) |
| GSE241034 |
Modulation of the microRNA-induced silencing complex loading through a specific interaction with a J-domain co-chaperone |
|
| Relations |
| BioSample |
SAMN37008989 |
| SRA |
SRX21384701 |
