 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 07, 2023 |
| Title |
Ribo_WT_Replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: W303 F2147 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100)
|
| Extracted molecule |
polyA 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 "Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs" Gaikwad, Ghobakhlou, et al. eLife 2021;10:e64
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
As described earlier (Martin-Marcos et al. 2017), Illumina sequencing reads were trimmed to remove the constant adapter sequence, mixed sample sequences were separated by the sample barcodes followed by removal of PCR duplicates using a custom Python (3.7) script. The sequences aligned to yeast non-coding RNAs were removed using bowtie (Langmead et al., 2009) and non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae genome (R64-1-1 S288C Saccer3 Genome Assembly) using TopHat (Trapnell et al., 2009). Only uniquely mapped reads from the final genomic alignment were used for subsequent analyses. 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.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For ribosome profiling and parallel RNA-Sequencing, Raw_counts_Ribo (Ribo-sequencing) and Raw_counts_RNA (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. Foe CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads.
Library strategy: Ribosome profiling
|
| |
|
| Submission date |
Oct 28, 2022 |
| Last update date |
Feb 07, 2023 |
| Contact name |
Alan G Hinnebusch |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institutes of Health
|
| Department |
Eunice Kennedy Shriver National Institute of Child Health and Human Development
|
| Lab |
Section on Nutrient Control of Gene Expression
|
| Street address |
6 Center Drive
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE216831 |
Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability |
|
| Relations |
| BioSample |
SAMN31510074 |
| SRA |
SRX18065582 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6696314_RawCounts_Ribo_WT_Replicate_1.csv.gz |
36.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
