|
| Status |
Public on Dec 04, 2017 |
| Title |
mir-71(n4115) Day 0, replicate 1 [small RNA] |
| Sample type |
SRA |
| |
|
| Source name |
whole animal, mir-71 mutant, day 0 adulthood
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/background: MT12993
genotype/variation: mir-71(n4115)
age: day 0 adulthood
tissue: whole body
|
| Growth protocol |
Animals cultured at 20C and moved shortly after L4/adult molt to plates containing 0.1mg/mL 5-fluorodeoxyuridine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole animals were collected by washing with M9 buffer and flash frozen on liquid nitrogen. RNA was extracted using TRIzol reagent followed by phenol:chloroform extraction.
RNA libraries were prepared using standard Illumina protocols following size selection.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
smRNA_m71_Day0_rep1
Small RNA-seq; size selected for small RNA.
Processed data file: small_RNA-seq_combined_counts_normalized.txt
Processed data file: small_RNA-seq_combined_counts_normalized_log2.txt
|
| Data processing |
Sequencing reads were mapped to the C. elegans genome using STAR (version 2.4.0h) (Dobin et al., Bioinformatics, 2013) using default parameters.
For small RNA-seq, miRNAs were annotated against miRBase release 20 using SeqBuster (Pantano et al., Nucleic Acids Res., 2010) and then manually curated to match annotations in miRBase release 21.
Differential expression for small RNA-seq was tested using DESeq2 (Love et al., Genome Biol., 2014). For small RNA-seq, size factor calculation was conducted against the number of sequences excluding those mapping to rRNA and repeat sequences.
Genome_build: WBcel235
Supplementary_files_format_and_content: small_RNA-seq_combined_counts_normalized.txt: Tab-delimited text file contains normalized read counts for each gene in each sample.
Supplementary_files_format_and_content: small_RNA-seq_combined_counts_normalized_log2.txt: Tab-delimited text file contains log2-transformed normalized counts for each gene in each sample.
|
| |
|
| Submission date |
Aug 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sachi Inukai |
| E-mail(s) |
sachi.inukai@yale.edu
|
| Organization name |
Yale University
|
| Street address |
219 Prospect St
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (2) |
| GSE72233 |
Deep sequencing of small RNAs from whole nematode C. elegans during aging |
| GSE72234 |
RNA-seq and small RNA-seq analysis of N2 wildtype and mir-71(n4115) C. elegans during aging |
|
| Relations |
| BioSample |
SAMN04002997 |
| SRA |
SRX1160391 |
