|
| Status |
Public on Apr 17, 2024 |
| Title |
RNA-seq: sdc-3AID auxin replicate 1, BATCH 4 |
| Sample type |
SRA |
| |
|
| Source name |
L3 animals
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole body
strain: PMW822
treatment: Exposure to 1mM auxin, 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; xeSi376[eft-3p::TIR1::mRuby::unc-54 3'UTR, cbr-unc-119(+)] III; sdc-3(ubs20[N-term AID]) V.
|
| 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_822_A_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 |
SAMN27063216 |
| SRA |
SRX14659505 |
