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Status |
Public on Feb 22, 2024 |
Title |
ce_mRNA_ebax_TC_mut_30h |
Sample type |
SRA |
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Source name |
HW3527
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Organism |
Caenorhabditis elegans |
Characteristics |
strain: HW3527 genotype: ebax-1(tm2321) time (h): 30 treatment: none
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Treatment protocol |
no treatment
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Growth protocol |
Synchronized L1's of N2 and HW3527 (ebax-1(tm2321) IV) were plated on 10 cm plates (2000 worms/plate) and kept at 25°C for the time-course. Every hour samples were collected from 18h to 31h
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Extracted molecule |
polyA RNA |
Extraction protocol |
We harvested worms from 18h to 31h in hourly interval. Worms were collected from plates and washed 3 times and resuspended in Tri Reagent (MRC, TR118) and RNA was extracted using Direct-zol™ RNA MicroPrep kit (Zymo Research; R2062) as per manufacturere's instructions. Total RNA was treated with DNAse on column Sequencing libraries were generated using Illumina Stranded mRNA Prep Kit according to the manufacturer’s instructions. Subsequently, library was sequenced on NovaSeq6000, as 56 cycles paired-end reads.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
The RNA-seq samples were mapped to the c.elegans genome (ce10) with the R package QuasR (version 1.26) using the spliced alignment algorithm HISAT2. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",splicedAlignment=TRUE,aligner="Rhisat2")". For gene quantification, gene annotation from WormBase was used (WS220). The command used to create the expression count table was qCount(proj,exons,orientation="opposite", useRead="first"). 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. 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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Submission date |
Oct 20, 2023 |
Last update date |
Feb 22, 2024 |
Contact name |
Dimos Gaidatzis |
E-mail(s) |
d.gaidatzis@fmi.ch
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Organization name |
Friedrich Miescher Institute for Biomedical Research
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Department |
Computational Biology
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Street address |
Maulbeerstrasse 66
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City |
Basel |
ZIP/Postal code |
4058 |
Country |
Switzerland |
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Platform ID |
GPL26672 |
Series (2) |
GSE245892 |
Dynamic regulation of miRNA accumulation during C. elegans larval development [RNA-Seq] |
GSE245904 |
Dynamic regulation of miRNA accumulation during C. elegans larval development |
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Relations |
BioSample |
SAMN37906707 |
SRA |
SRX22157196 |
Supplementary data files not provided |
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Raw data are available in SRA |
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