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| Status |
Public on Jul 18, 2023 |
| Title |
Slr1p IP, AB2756, biol repl 1 |
| Sample type |
SRA |
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| Source name |
yAS99
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cell line: yAS99
cell type: fission yeast
genotype: WT
treatment: formaldehyde cross-link
antibody: Slr1p
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| Treatment protocol |
Formaldehyde cross-link
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| Growth protocol |
YES medium, 32°C, 200 rpm
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| Extracted molecule |
total RNA |
| Extraction protocol |
1 μg/μl final concentration of proteinase K (Invitrogen) solution and 0.125% final concentration of SDS solution (Bioshop) was added to immunoprecipitated RNA. Samples were then incubated at 37°C for 1 hour to digest immunoprecipitated proteins first, and 65°C for another hour to reverse crosslinking. This was followed by phenol-chloroform extraction of RNA and ethanol precipitation. Equal volumes of acidic phenol pH 4.3 (Fisher) was added to each sample which was vortexed to mix and centrifuged at 21000xg for 10 minutes at 4°C. The top aqueous layer was removed to a new tube to which equal volumes of Phenol/Chloroform/Isoamyl Alcohol (25:24:1 mixture, Fisher) was added following by vortexing and centrifugation at 21000xg for 10 minutes at 4°C. The top aqueous layer was removed to a new tube again and to this, equal volumes of Chloroform/Isoamyl Alcohol (24:1 mixture, Sigma) was added. The centrifugation step above was repeated and the top layer was removed to a new tube again. Finally, 20 μg glycogen (Sigma), 1/10th of the volume 3M NaOAc pH 5.2 (Sigma) and 1 mL ice-cold 100% absolute ethanol (Greenfield Global) was added to each RNA sample which was precipitated next at -80°C until sequencing. Input RNA samples were extracted using the hot phenol RNA extraction method and precipitated as described above until sequencing.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used for library preparations following manufacturer's protocol.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
PE 2x50bp reads
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| Data processing |
Sequencing and analysis were performed by The Centre for Applied Genomics (TCAG, Toronto, Canada).
The untrimmed reads in FASTQ format were generated using bcl2fastq2 v2.20. The quality of the data was assessed using FastQC v.0.11.5.
Adaptors were trimmed using Trim Galore, the quality of the trimmed reads was re-assessed with FastQC. The trimmed reads were also screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.10.0.
The raw trimmed reads were aligned to the reference genome using the STAR aligner, v.2.6.0c.
The filtered STAR alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2.
Assembly: Schizosaccharomyces pombe(972h-)
Supplementary files format and content: Tab delimited text files include raw counts for each sample.
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| Submission date |
Jul 17, 2023 |
| Last update date |
Jul 18, 2023 |
| Contact name |
Farnaz Mansouri-Noori |
| E-mail(s) |
[email protected]
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| Organization name |
York University
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| Department |
Biology
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| Street address |
4700 Keele Street
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| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M3J 1P3 |
| Country |
Canada |
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| Platform ID |
GPL28961 |
| Series (1) |
| GSE237526 |
The LARP1 homolog Slr1p controls the stability and expression of proto-5’TOP mRNAs in fission yeast [RIP-seq] |
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| Relations |
| BioSample |
SAMN36506839 |
| SRA |
SRX21052371 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7623265_R1_2756_htsqct.txt.gz |
32.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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