|
| Status |
Public on Aug 25, 2020 |
| Title |
Intestine_ALG-1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ges1p::ALG-1
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
cell type: Intestine
genotype: ALG-1
treatment: Untreated
|
| Treatment protocol |
Standard
|
| Growth protocol |
50, 000-100, 000 synchronized L4 stage worms grown at 20 degrees, were snap frozen in liquid N2 and processed for immunoprecipitation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from immunoprecipitated ALG:RNA complexes using TRIzol reagent (Invitrogen)
NextSeq libraries were constructed as per manufacturers instructions
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Immunoprecipitated small RNA
|
| Data processing |
Basecalls performed using CASAVA (v1.8).
Read quality was assessed by FastQC (v0.11.8) and sequence adapters trimmed using Cutadapt (v2.10), default parameters.
Reads were mapped to the reference genome (WBcel235) using Bowtie2, default parameters.
General genome arithmetic and index generation was performed using Samtools (v1.10).
Known and novel miRNA annotation and quanitification was performed by miRDeep2 (v2.0.0.8), only miRNAs with > 3 score were considered significant.
Custom scripts were used to determine isomiR type from miRDeep2 output.
EdgeR (v3.11) was used to assess differential expression of miRNAs and isomiRs.
Only miRNAs with a read count greater than 1CPM and isomiRs with a read count greater than 50CPM in at least two independent samples were considered for analysis.
Significance threshold for miRNAs was set at P < 0.01 and logFC > 2. Significance threshold for isomiRs was set at FDR < 0.05 and logFC > 2.
Genome_build: WBcel235 (Ensemble release 96)
Supplementary_files_format_and_content: Matrix tables with normalised read count of miRNAs and all miRNAs/isomiRs.
|
| |
|
| Submission date |
Aug 24, 2020 |
| Last update date |
Aug 25, 2020 |
| Contact name |
Steven Zuryn |
| E-mail(s) |
s.zuryn@uq.edu.au
|
| Organization name |
The University of Queensland
|
| Department |
Queensland Brain Institute
|
| Lab |
Zuryn Lab
|
| Street address |
79 Upland Road
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19757 |
| Series (2) |
| GSE156716 |
Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading [miRNA-seq] |
| GSE156721 |
Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading |
|
| Relations |
| BioSample |
SAMN15892700 |
| SRA |
SRX8997895 |
