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| Status |
Public on Jun 18, 2020 |
| Title |
Rph1_del_rep2 |
| Sample type |
SRA |
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| Source name |
yeast cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
genotype: rph1 deletion
treatment: none
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Low quality reads and adaptor contamination were removed by Trimmomatic v0.38
For RNA-Seq, the filtered reads were mapped to SacCer3 using STAR v2.5.3a. For ChIP-Seq, the filtered reads were aligned against SacCer3 genome using Bowtie2 v2.3.4.3 with default parameters.
For RNA-Seq, the mapped reads was quantified using featureCounts v1.6.3. Reads count normalization and differential gene expression analysis was performed using DESeq2 v1.24.0. For ChIP-Seq, MACS2 v2.2.1 with a P value threshold of 1e -5 was used to call ChIP peaks.
Genome_build: SacCer3
Supplementary_files_format_and_content: reads were quantified using featureCounts v1.6.3
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| Submission date |
Nov 26, 2019 |
| Last update date |
Jun 19, 2020 |
| Contact name |
shu Wenjie |
| E-mail(s) |
shuwenjie@whu.edu.cn
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| Phone |
17671613819
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| Organization name |
Wuhan University
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| Department |
College of Life Sciences
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| Street address |
East Lake South Road
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| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platform ID |
GPL27812 |
| Series (1) |
| GSE141034 |
Rph1 coordinates transcription of ribosomal protein gene and ribosomal RNA to control cell growth under nutrient stress conditions |
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| Relations |
| BioSample |
SAMN13389501 |
| SRA |
SRX7217629 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4192719_Rph1_0h_2_featurecount.txt.gz |
32.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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