|
Status |
Public on Feb 22, 2024 |
Title |
ce_smallRNA_longTC_N2_45h |
Sample type |
SRA |
|
|
Source name |
N2
|
Organism |
Caenorhabditis elegans |
Characteristics |
strain: N2 genotype: WT time (h): 45 treatment: none
|
Treatment protocol |
no treatment
|
Growth protocol |
Synchronized L1's of N2 were plated on 10 cm plates (2000 worms/plate) and kept at 25°C for the time-course. Every hour samples were collected from 5 h to 48h
|
Extracted molecule |
total RNA |
Extraction protocol |
We harvested worms from 5h to 48h in hourly interval. Worms were collected from plates and washed 3 times and resuspended in Tri Reagent (MRC, TR118) and RNA was extracted using conventional phenol extraction, as described previously (Hendriks et al., 2014). Total RNA was DNAse treated Sequencing libraries were generated using Illumina TruSeq Small RNA Library Prep Kit according to the manufacturer’s instructions. Subsequently, library was sequenced on Illumina HiSeq2500, as 51 cycles single-end reads.
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|
|
Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
The small RNA-seq fastq files were adapter trimmed (TGGAATTCTCGGGTGCCAAGG) at the 3' end using the function preprocessReads() from the R packege QuasR (version 1.26) and mapped to the C.elegans genome (ce10) with the R package QuasR (version 1.26) using the alignment algorithm Bowtie. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",maxHits=100)". For miRNA quantification, gene annotation from miRBase v22 was used and lifted over to ce10. We extended the genomic coordinates of the 5' end of each miRNA by 3bp on both sides and counted all the reads that started within those regions using the following command: "qCount(proj,matureMirsExt,orientation="same"). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Finally the count table was log2 transformed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers. Assembly: ce10 Supplementary files format and content: tab-delimited text file with raw counts for each sample Supplementary files format and content: tab-delimited text file with normalized counts for each sample
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|
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Submission date |
Oct 20, 2023 |
Last update date |
Feb 22, 2024 |
Contact name |
Dimos Gaidatzis |
E-mail(s) |
d.gaidatzis@fmi.ch
|
Organization name |
Friedrich Miescher Institute for Biomedical Research
|
Department |
Computational Biology
|
Street address |
Maulbeerstrasse 66
|
City |
Basel |
ZIP/Postal code |
4058 |
Country |
Switzerland |
|
|
Platform ID |
GPL18245 |
Series (2) |
GSE245902 |
Dynamic regulation of miRNA accumulation during C. elegans larval development [smallRNA-Seq 5] |
GSE245904 |
Dynamic regulation of miRNA accumulation during C. elegans larval development |
|
Relations |
BioSample |
SAMN37907862 |
SRA |
SRX22157606 |