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Sample GSM5982652 Query DataSets for GSM5982652
Status Public on Apr 17, 2024
Title RNA-seq: TEV control replicate 1, BATCH 1
Sample type SRA
 
Source name L3 animals
Organism Caenorhabditis elegans
Characteristics tissue: whole body
strain: PMW366
treatment: Heat-shock for 30 min at 34C
developmental_stage: L3 larvae
genotype: ubsSi20[hsp-16.2p::TEV::unc-54 3'UTR; Cbr-unc-119(+)] II.
Treatment protocol Synchronised L1 animals are seeded on NGM plates, incubated for 3 hours at 22℃, heat-shocked for 30 mins at 34℃. Then they are incubated again for 19 hours at 22℃. The degron strains were seeded on 1mM auxin plates and heat-shocked as described earlier. For the auxin control, the animals were seeded on plates without auxin but with ethanol. All animals were collected by washing thrice with M9 buffer.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol, treated with DNase and cleaned using RNeasy MinElute Cleanup Kit.
Illumina Stranded mRNA preparation kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description sumFR_366_B_UniqueMultiple.bw
Data processing Reads were trimmed with Cutadapt v2.5 to remove adaptors.
Counts per transcript tables were obtained by aligning trimmed reads to the WS275 version of the C. elegans protein coding transcriptome using Salmon v1.5.2 in quant mode using –seqBias –gcBias and --numBootstraps 100 options
Bigwigs were obtained by aligning trimmed reads to the WS275 C. elegans genome using STAR v2.7.9a with the options --outSAMmultNmax 1 --alignIntronMax 5000 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM. Wig files were converted to bigwigs with the wigToBigWig v2.8 from UCSCtools. After visual inspection, bigWigs of technical replicates and then biological replicates from each batch were averaged using Ensemble WiggleTools mean command for each strand separately. Finally the bigwigs of the two strands were summed using the Ensembl tool bigWigMerge v2.
Assembly: WS275
Supplementary files format and content: Salmon quant.sf files contain 5 columns: Name, Length, EffectiveLength, TPM, NumReads and one row for each transcript.
Supplementary files format and content: The bigwig files contain the pileup of reads from both strands in RPM, averaged over technical and biological replicates.
 
Submission date Mar 29, 2022
Last update date Apr 17, 2024
Contact name Peter Meister
E-mail(s) peter.meister@unibe.ch
Phone +41316844609
Organization name University of Bern
Department Institute of Cell Biology
Lab Cell Fate and Nuclear Organization
Street address Baltzerstrasse 4
City Bern
State/province Schweiz
ZIP/Postal code 3012
Country Switzerland
 
Platform ID GPL26672
Series (2)
GSE199717 Condensin I folds the C. elegans genome [RNA-seq]
GSE199723 Condensin I folds the C. elegans genome
Relations
BioSample SAMN27063241
SRA SRX14659480

Supplementary file Size Download File type/resource
GSM5982652_366_B1_L1_quant.sf.gz 573.2 Kb (ftp)(http) SF
GSM5982652_366_B1_L2_quant.sf.gz 573.5 Kb (ftp)(http) SF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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