|
| Status |
Public on Nov 21, 2019 |
| Title |
BY4741 mip6D yeast cells, 39ºC 20', H4K12ac ChIPseq 15 |
| Sample type |
SRA |
| |
|
| Source name |
BY4741 mip6D yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
genotype: mip6D
growth condition: 39ºC 20'
chip antibody: Histone H4K12ac antibody catalog No 39165 (Active Motif)
biological replicate: 3
|
| Growth protocol |
For all samples, yeast cells were growth until exponential phase (O.D.600 = 0.7) in rich medium (YPD). Each culture is then split in three flasks at equal amounts. One flask is maintained at 30ºC and its labeled at time point 0. The other two flasks are incubated at 39°C for 20 minutes and 120 minutes, respectively by adding preheated media to reach 39ºC instantly. These two last flasks capture the heat-shock response while the 30°C flask serves as a control of non-stress conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For RNAseq samples, a 10 mL aliquote is collected from each culture, washed twice with pure water and celular pellet was then frozen in liquid nitrogen. Total RNA was extracted with hot acid phenol protocol.
For ChIPseq samples, a crosslinking reaction was performed with 1% formaldehyde for 15 minutes and the reaction was then stopped with 125 mM glycine for then washing three times the pellet with TBS buffer and frozen in liquid nitrogen. ChIP experiment was performed with 1 microL per sample of H4 (ab10158) or H4K12ac (39165 Active Motif) antibodies bound to magnetic beads and incubated for 2 hours before IP. It followed the genomic DNA extraction with phenol protocol.
For RNA: TruSeq Stranded Total RNA Sample Prep . For ChIPseq: ChIPseq specific library
TruSeq for RNAseq and ChIPseq library for ChIPseq
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| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
CountMatrixChIPseq.xlsx
H4K12peaks.bed
|
| Data processing |
Both RNAseq and ChIPseq data were obtained after Illumina sequencing and fastq files were obtained from Macrogen server
RNAseq: Raw sequencing data quality was checked by fastqc and good overall quality was observed in all cases
RNAseq: Reads mapped to the yeast saccer3 genome with Tophat21 and genes were cuantified with HTSEQ2 intersection-option
ChIPseq: Raw sequencing data quality was checked by fastqc and good overall quality was observed in all cases
ChIPseq: Illumina adapters trimming was needed and it was performed using cutadapt
ChIPseq: Reads were mapped to the yeast saccer3 genome with Bowtie2
ChIPseq: Regions with high coverage were defined using MACS2 (peak calling step)
ChIPseq: All the regions found in H4K12ac samples were merged into a single .bed file using bedtools (H4K12peaks.bed)
ChIPseq: The .bed file was used as an annotation file to compute the counts across regions using HTSEQ2 intersection-option
Genome_build: saccer3
Supplementary_files_format_and_content: RNAseq: we provide the count matrix in which expression values for each Saccharomyces cerevisiae gene were quantified in each sample through HTSEQ2
Supplementary_files_format_and_content: ChIPseq: we provide the count matrix in which the coverage values for each region (previously defined) were quantified in each sample. H4K12peaks.bed with regions merged.
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| |
|
| Submission date |
Aug 08, 2019 |
| Last update date |
Nov 21, 2019 |
| Contact name |
Susana Rodríguez Navarro |
| E-mail(s) |
[email protected]
|
| Organization name |
Instituto de Biomedicina de Valencia
|
| Department |
Patología y Terapia Molecular y Celular
|
| Lab |
Unidad de Expresión Génica y Metabolismo de RNA
|
| Street address |
Jaume Roig, 11
|
| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46010 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE135568 |
A multi-omics dataset of heat-shock response in the yeast RNA transport protein Mip6 |
|
| Relations |
| BioSample |
SAMN12534620 |
| SRA |
SRX6678270 |
