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| Status |
Public on Sep 27, 2023 |
| Title |
Ribo_ pat1D _Replicate_1 |
| Sample type |
SRA |
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| Source name |
Whole cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: W303 F2181 (MATa ura3-1 trp1-1 ade2-1 leu2-3,112 his3-11,15 {delta}pat1::HIS3)
cell type: yeast cells
fraction: Ribosome protected RNA 25-34 nt
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo" Zeidan et al., 2018 Plos Genetics 15(7): e1008299
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
For ChIP-Seq: Sequence data were aligned to the SacCer3 version of the genome sequence using Bowtie2 with parameters -X 1000 -very-sensitive, to map sequences up to 1 kb with maximum accuracy. PCR duplicates from ChIP-seq data were removed using the samtools rmdup package.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads. For Rpb1 ChIP-Seq, average occupancy file contains two columns providing: systemmatic gene name (ORF) and avg occupancy.
Library strategy: Ribo-seq
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| Submission date |
Feb 07, 2023 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Alan G Hinnebusch |
| E-mail(s) |
alanh@mail.nih.gov
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| Organization name |
National Institutes of Health
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| Department |
Eunice Kennedy Shriver National Institute of Child Health and Human Development
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| Lab |
Section on Nutrient Control of Gene Expression
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| Street address |
6 Center Drive
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL17342 |
| Series (1) |
| GSE224774 |
mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability |
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| Relations |
| BioSample |
SAMN33193320 |
| SRA |
SRX19304990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7031896_RawCounts_Ribo_pat1_Replicate_1.csv.gz |
47.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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