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| Status |
Public on Mar 27, 2024 |
| Title |
FBY2578_2_WT |
| Sample type |
SRA |
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| Source name |
S. pombe cells
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: WT Rpb3-HA
genotype: h- Rpb3-3HA::hphMX6
cell type: S. pombe cells
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| Growth protocol |
Cells were grown in YES medium until mid-log phase (OD 0.5)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by the hot-phenol method, as previously described (Duval et al., 2023). Briefly, yeast cells are first resuspended in 600 µl of TES solution (10 mM Tris-HCl [pH 7.5], 10 mM EDTA [pH8.0] and 0.5% SDS) and 600 µl of phenol-chloroform-Isoamyl alcohol (125:24:1 [pH 4.5]), and then incubated at 65°C for 60 min with vortexing every 10 min. The RNA was extracted once with 550 µl of phenol-chloroform-Isoamyl alcohol (125:24:1 [pH 4.5]) and once with 450 µl of chloroform-isoamyl alcohol (24:1), and precipitated with ethanol and 2 M NaCl.
rRNA-depleted RNA-seq libraries were prepared following manufacturer's instructions using the Illumina Truseq Stranded Total RNA-sequencing kit after ribodeletion with the RiboZero Yeast ribodepletion (Epicentre). RNA-seq libraries were sequenced in paired-end (2×100nt) using Illumina technologies (HiSeq 4000) at Genome Québec.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Reads were mapped to the S. pombe genome (version ASM294v2.26) with HISAT2 (Kim et al., 2015). Gene-level read quantification was made with featureCounts (Liao et al, 2014) with options -p -B -s 2 -P -d 0 -D 5000 -C -T 4. De novo transcript discovery was performed with stringtie (Pertea et al, 2015) using stringent options (-t -f 0.1 -c 5 --rf -s 5) that are better suited to the dense yeast genome than the default. The new transcript discovered in the S2A mutant were merged in the annotation if they did not overlap other transcripts on the same strand. Differential gene expression of mutant against WT was made with DESeq2 (Love et al, 2014). Based on DESeq2 size factors, we used deepTools to generate normalized coverage files (.bigwig) with options bamCoverage --samFlagExclude 256 --maxFragmentLength 5000 --scaleFactor [1/size_factor] -bs 1 -of --filterRNAstrand [fwd/rev] bigwig.
Assembly: ASM294v2.26
Supplementary files format and content: strand-specific genome coverage files in bigWig format are provided
Supplementary files format and content: CTD_couts_GEO.txt contains the raw read counts per gene.
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| Submission date |
Dec 03, 2023 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Carlo Yague-Sanz |
| E-mail(s) |
yague.carlo@gmail.com
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| Organization name |
Namur University
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| Department |
Medecine
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| Lab |
GEMO lab
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| Street address |
61 rue de Bruxelles
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| City |
Namur |
| ZIP/Postal code |
5000 |
| Country |
Belgium |
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| Platform ID |
GPL22682 |
| Series (2) |
| GSE249235 |
Proximity-dependent biotinylation map of the RNAPII CTD reveals that the primary role of Serine 2 phosphorylation is in the suppression of pervasive antisense transcription and not in RNA 3’ end processing [RNA-seq] |
| GSE249236 |
Proximity-dependent biotinylation map of the RNAPII CTD reveals that the primary role of Serine 2 phosphorylation is in the suppression of pervasive antisense transcription and not in RNA 3’ end processing |
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| Relations |
| BioSample |
SAMN38606551 |
| SRA |
SRX22722558 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7928817_5_FB2578_fwd.bw |
15.3 Mb |
(ftp)(http) |
BW |
| GSM7928817_5_FB2578_rev.bw |
15.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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