|
| Status |
Public on Aug 25, 2020 |
| Title |
Neuron_ok304_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Nervous system
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
cell type: Neurons
genotype: alg-2 (ok304)
|
| 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 |
Cell-type spedific polysome complexes were immunoprecipitated using FLAG conjugated magnetic beads. Immunocomplexes were eluted from beads using the FLAG peptide and mRNA purified using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols adapted for low input samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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 Hisat2 (v2.2.0), default parameters.
General genome arithmetic and index generation was performed using Samtools (v1.10).
Genes were annotated using FeatureCounts (Subread v2.0.0) and assessed for differential expression using edgeR (v3.11).
Significance threshold was set at P < 0.01 and logFC > 2. Only genes with a read count greater than 1CPM in at least two independent samples were considered for analysis.
Genome_build: WBcel235 (Ensemble release 96)
Supplementary_files_format_and_content: Matrix table with normalised read count
|
| |
|
| 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 |
GPL13657 |
| Series (2) |
| GSE156717 |
Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading [RNA-seq] |
| GSE156721 |
Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading |
|
| Relations |
| BioSample |
SAMN15892686 |
| SRA |
SRX8997978 |
