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| Status |
Public on Nov 21, 2019 |
| Title |
A multi-omics dataset of heat-shock response in the yeast RNA transport protein Mip6 |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We studied the heat-shock response in wild-type (wt) and in absence of Mip6, an RNA binding protein with roles at multiple levels of the gene expression pathway. This study include; their transcriptome (RNA-seq), metabolome (targeted NMR) and H4K12ac epigenome (ChIP-seq) using an experimental desing that ensures that the same samples are used across all omics determinations. This facilitates data analysis approaches that can leverage fully matched, longitudinal, replicated data. These data will faciliate studies of covariation patterns across multiple molecular layers controlling and responding to RNA biogenesis.
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| Overall design |
RNA-seq, histone H4 ChIP-seq and H4K12Ac ChIP seq of four biological replicates of wt and mip6D yeast cells growth at: (i) normal conditions; (ii) 20 minutes of heat shock at 39ºC and (iii) 120 minutes of heat shock at 39ºC.
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| Contributor(s) |
Nuño-Cabanes C, Ugidos M, Tarazona S, Riquelme AF, Rodríguez-Navarro S, Conesa A |
| Citation(s) |
32109230 |
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| Submission date |
Aug 08, 2019 |
| Last update date |
Mar 09, 2020 |
| Contact name |
Susana Rodríguez Navarro |
| E-mail(s) |
[email protected]
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| Organization name |
Instituto de Biomedicina de Valencia
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| Department |
Patología y Terapia Molecular y Celular
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| Lab |
Unidad de Expresión Génica y Metabolismo de RNA
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| Street address |
Jaume Roig, 11
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| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46010 |
| Country |
Spain |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (67)
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| GSM4017981 |
BY4741 wt yeast cells, 30ºC , RNAseq 1 |
| GSM4017983 |
BY4741 wt yeast cells, 30ºC , RNAseq 2 |
| GSM4017984 |
BY4741 wt yeast cells, 39ºC 20', RNAseq 3 |
| GSM4017985 |
BY4741 wt yeast cells, 39ºC 120', RNAseq 4 |
| GSM4017986 |
BY4741 mip6D yeast cells, 30ºC , RNAseq 5 |
| GSM4017987 |
BY4741 mip6D yeast cells, 39ºC 120', RNAseq 6 |
| GSM4017989 |
BY4741 mip6D yeast cells, 39ºC 120', RNAseq 7 |
| GSM4017990 |
BY4741 mip6D yeast cells, 39ºC 20', RNAseq 8 |
| GSM4017991 |
BY4741 wt yeast cells, 39ºC 20', RNAseq 9 |
| GSM4017993 |
BY4741 wt yeast cells, 39ºC 120', RNAseq 10 |
| GSM4017994 |
BY4741 wt yeast cells, 30ºC , RNAseq 11 |
| GSM4017995 |
BY4741 wt yeast cells, 39ºC 20', RNAseq 12 |
| GSM4017997 |
BY4741 mip6D yeast cells, 39ºC 120', RNAseq 13 |
| GSM4017998 |
BY4741 mip6D yeast cells, 30ºC , RNAseq 14 |
| GSM4017999 |
BY4741 mip6D yeast cells, 39ºC 20', RNAseq 15 |
| GSM4018000 |
BY4741 mip6D yeast cells, 30ºC , RNAseq 16 |
| GSM4018002 |
BY4741 wt yeast cells, 39ºC 120', RNAseq 17 |
| GSM4018003 |
BY4741 wt yeast cells, 39ºC 20', RNAseq 18 |
| GSM4018004 |
BY4741 wt yeast cells, 39ºC 120', RNAseq 19 |
| GSM4018005 |
BY4741 wt yeast cells, 30ºC , RNAseq 20 |
| GSM4018006 |
BY4741 mip6D yeast cells, 39ºC 20', RNAseq 21 |
| GSM4018008 |
BY4741 mip6D yeast cells, 39ºC 20', RNAseq 22 |
| GSM4018009 |
BY4741 mip6D yeast cells, 30ºC , RNAseq 23 |
| GSM4018010 |
BY4741 mip6D yeast cells, 39ºC 120', RNAseq 24 |
| GSM4018011 |
BY4741 wt yeast cells, 30ºC , H4 ChIPseq 1 |
| GSM4018012 |
BY4741 wt yeast cells, 30ºC , H4 ChIPseq 2 |
| GSM4018014 |
BY4741 wt yeast cells, 39ºC 20', H4 ChIPseq 3 |
| GSM4018015 |
BY4741 wt yeast cells, 39ºC 120', H4 ChIPseq 4 |
| GSM4018016 |
BY4741 mip6D yeast cells, 30ºC , H4 ChIPseq 5 |
| GSM4018018 |
BY4741 mip6D yeast cells, 39ºC 120', H4 ChIPseq 6 |
| GSM4018019 |
BY4741 mip6D yeast cells, 39ºC 120', H4 ChIPseq 7 |
| GSM4018020 |
BY4741 mip6D yeast cells, 39ºC 20', H4 ChIPseq 8 |
| GSM4018021 |
BY4741 wt yeast cells, 39ºC 20', H4 ChIPseq 9 |
| GSM4018023 |
BY4741 wt yeast cells, 39ºC 120', H4 ChIPseq 10 |
| GSM4018024 |
BY4741 wt yeast cells, 30ºC , H4 ChIPseq 11 |
| GSM4018025 |
BY4741 wt yeast cells, 39ºC 20', H4 ChIPseq 12 |
| GSM4018026 |
BY4741 mip6D yeast cells, 39ºC 120', H4 ChIPseq 13 |
| GSM4018028 |
BY4741 mip6D yeast cells, 30ºC , H4 ChIPseq 14 |
| GSM4018029 |
BY4741 mip6D yeast cells, 39ºC 20', H4 ChIPseq 15 |
| GSM4018030 |
BY4741 mip6D yeast cells, 30ºC , H4 ChIPseq 16 |
| GSM4018031 |
BY4741 wt yeast cells, 39ºC 120', H4 ChIPseq 17 |
| GSM4018033 |
BY4741 wt yeast cells, 39ºC 20', H4 ChIPseq 18 |
| GSM4018034 |
BY4741 wt yeast cells, 39ºC 120', H4 ChIPseq 19 |
| GSM4018035 |
BY4741 wt yeast cells, 30ºC , H4 ChIPseq 20 |
| GSM4018036 |
BY4741 mip6D yeast cells, 39ºC 20', H4 ChIPseq 21 |
| GSM4018037 |
BY4741 mip6D yeast cells, 39ºC 20', H4 ChIPseq 22 |
| GSM4018039 |
BY4741 mip6D yeast cells, 30ºC , H4 ChIPseq 23 |
| GSM4018040 |
BY4741 mip6D yeast cells, 39ºC 120', H4 ChIPseq 24 |
| GSM4018041 |
BY4741 wt yeast cells, 30ºC , H4K12ac ChIPseq 1 |
| GSM4018042 |
BY4741 wt yeast cells, 30ºC , H4K12ac ChIPseq 2 |
| GSM4018044 |
BY4741 wt yeast cells, 39ºC 20', H4K12ac ChIPseq 3 |
| GSM4018045 |
BY4741 wt yeast cells, 39ºC 120', H4K12ac ChIPseq 4 |
| GSM4018046 |
BY4741 mip6D yeast cells, 30ºC , H4K12ac ChIPseq 5 |
| GSM4018047 |
BY4741 mip6D yeast cells, 39ºC 120', H4K12ac ChIPseq 6 |
| GSM4018048 |
BY4741 mip6D yeast cells, 39ºC 120', H4K12ac ChIPseq 7 |
| GSM4018050 |
BY4741 mip6D yeast cells, 39ºC 20', H4K12ac ChIPseq 8 |
| GSM4018051 |
BY4741 wt yeast cells, 39ºC 120', H4K12ac ChIPseq 10 |
| GSM4018052 |
BY4741 wt yeast cells, 30ºC , H4K12ac ChIPseq 11 |
| GSM4018053 |
BY4741 mip6D yeast cells, 39ºC 120', H4K12ac ChIPseq 13 |
| GSM4018054 |
BY4741 mip6D yeast cells, 30ºC , H4K12ac ChIPseq 14 |
| GSM4018056 |
BY4741 mip6D yeast cells, 39ºC 20', H4K12ac ChIPseq 15 |
| GSM4018057 |
BY4741 mip6D yeast cells, 30ºC , H4K12ac ChIPseq 16 |
| GSM4018058 |
BY4741 wt yeast cells, 39ºC 120', H4K12ac ChIPseq 17 |
| GSM4018060 |
BY4741 wt yeast cells, 39ºC 120', H4K12ac ChIPseq 19 |
| GSM4018061 |
BY4741 mip6D yeast cells, 39ºC 20', H4K12ac ChIPseq 21 |
| GSM4018062 |
BY4741 mip6D yeast cells, 30ºC , H4K12ac ChIPseq 23 |
| GSM4018063 |
BY4741 mip6D yeast cells, 39ºC 120', H4K12ac ChIPseq 24 |
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| Relations |
| BioProject |
PRJNA559331 |
| SRA |
SRP217823 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135568_CountMatrixChIPseq.xlsx |
548.6 Kb |
(ftp)(http) |
XLSX |
| GSE135568_CountMatrixRNAseq.xlsx |
1012.9 Kb |
(ftp)(http) |
XLSX |
| GSE135568_H4K12peaks.bed.gz |
25.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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