|
| Status |
Public on Dec 04, 2017 |
| Title |
mir-71(n4115) Day 0, replicate 2 [poly(A) 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. For RNA library construction, RNA was poly(A)-selected.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA_mir71_Day0_rep2
Poly(A) selected
Processed data file: RNA-seq_combined_counts.txt
Processed data file: RNA-seq_combined_counts_normalized_rlog.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 RNA-seq, sequence data processing and analysis were performed primarily using the bcbio-nextgen pipeline (https://bcbio-nextgen.readthedocs.org/).
Differential expression for RNA-seq was tested using DESeq2 (Love et al., Genome Biol., 2014).
Genome_build: WBcel235
Supplementary_files_format_and_content: RNA-seq_combined_counts.txt: Tab-delimited text file contains raw read counts for each gene in each sample.
Supplementary_files_format_and_content: RNA-seq_combined_counts_normalized_rlog.txt: Tab-delimited text file contains regularized log-transformed, normalized read 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) |
| GSE72232 |
Deep sequencing of poly(A)-selected 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 |
SAMN04002981 |
| SRA |
SRX1160383 |
