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| Status |
Public on Sep 29, 2021 |
| Title |
Saccharomyces cerevisiae |
| Sample type |
SRA |
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| Source name |
Saccharomyces cerevisiae
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
sample type: Saccharomyces cerevisiae
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| Treatment protocol |
none
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| Growth protocol |
Please refer to the Samples section above
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were prepared using TRIzol® reagent or TRIzol LS® reagent for liquid samples (Invitrogen Life Technologies, Carlsbad, CA, USA) following the manufacturer’s recommendations. Contaminating DNA was degraded by DNase I (M0303S, New England Biolabs, MA, USA) treatment following manufacturer’s instructions. Total RNA was shipped on dry ice and analyzed by Arraystar Inc. RNA sequencing service (Rockville, MD).
The purity, quality, and concentration of total RNA samples were determined with NanoDrop ND-1000 (Thermo Fisher Scientific) and 2100 Bioanalyzer (Agilent, Santa Clara, CA). Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: (1) 3′-adapter ligation, (2) 5′-adapter ligation, (3) cDNA synthesis, (4) PCR amplification, and (5) size selection of approximately 120 to 150 bp of PCR-amplified fragments (corresponding to approximately 8 to 30 nt of small RNA). The complete libraries were quantified by Agilent 2100 Bioanalyser. Samples were diluted to a final concentration of 8 pM, denatured as single-stranded DNA, and cluster generation was performed on the Illumina cBot using TruSeq Rapid SR cluster kit (GD-402-4001, Illumina, San Diego, USA). Afterward, the clusters were sequenced for 51 cycles on Illumina HiSeq 2000 using TruSeq Rapid SBS Kits (FC-402-4002, Illumina, San Diego, USA), as per the manufacturer's instructions.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Total RNA sample from this yeast strain was generously provided by Dr. Karl Ekwall (Karolinska Institutet).
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| Data processing |
Adaptor were trimmed using Cutadapt V1.7.1
Quality Control was performed with fastqc V0.11.3
Identical sequences were collapsed into a single fasta sequence and were filtered to keep only those detected at least twice using a custom script
Genome_build: NA
Supplementary_files_format_and_content: Fasta files containing the aligned sequences that were detected at least twice in the dataset, separated in 2 groups based on the size (8-15nt and 16-30nt)
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| Submission date |
Jul 07, 2021 |
| Last update date |
Sep 29, 2021 |
| Contact name |
Tarik Moroy |
| Organization name |
IRCM
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| Street address |
110 Pine Ave W, Montreal
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| City |
Montréal |
| ZIP/Postal code |
H2W 1R7 |
| Country |
Canada |
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| Platform ID |
GPL13821 |
| Series (1) |
| GSE179677 |
Small RNA sequencing of the 8 to 30-nucleotide window from various samples |
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| Relations |
| BioSample |
SAMN20109357 |
| SRA |
SRX11375070 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5426187_S_cerevisiae_16-30nt_trimmed.tags.fa.gz |
5.0 Mb |
(ftp)(http) |
FA |
| GSM5426187_S_cerevisiae_8-15nt_trimmed.tags.fa.gz |
830.9 Kb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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