|
| Status |
Public on Dec 01, 2019 |
| Title |
Mlh3-Myc8 ChIPseq_5h30 |
| Sample type |
SRA |
| |
|
| Source name |
SK1 meiotic cells t=5h30 (pCUP1-IME1-synchronized meiosis)
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: VBD1837
genotype/variation: Myc8
chip antibody: c-Myc monoclonal antibody (9E10, Santa Cruz)
|
| Treatment protocol |
1. 10^9 cells were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and chromatin immunoprecipitation was performed as described (De Muyt et al (2018) Genes and Development 32, 283-296)
|
| Growth protocol |
For synchronous meiosis, cells were either grown in SPS presporulation medium and transferred to 1% potassium acetate with vigorous shaking at 30˚C (for anti-Flag samples) or grown in "semi-YPD" then transferred to sporulation medium and induced to undergo meiosis upon Cu++ addition after two hours (Mlh3-Myc samples).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq procedure.
Libraries were sequenced on a HiSeq2500 apparatus generating paired-end 50 bp reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
A964C66
|
| Data processing |
Reads were aligned to the Saccer2 version (SGD June 2008) of the S. cerevisiae S288C genome, using Bowtie, allowing for 2 mismatches. Reads that matched more than once in the genome or matching to mitochondrial or ribosomal DNA were eliminated from further analysis.
Aligned and extended paires-end reads were then normalized using a custom script as follows: for normalization, for the untagged control (or spo11∆ control for Mlh3-Myc samples), the top and bottom outliers of the distribution (Q3+1.5IQR and Q1-1.5IQR, respectively) were removed. The average read number per position (coverage) of the remaining reads of the control was then normalized to 1 (scaled untagged control). Similarly, top and bottom outliers of the distribution were removed from the average read number in the samples. Average coverage for the remaining reads was then calculated for the sample and control at the same positions. This was used to compute the sample/ control ratio. Then all reads of the sample were scaled using this ratio (scaled tagged control).
Both scaled sample and control were converted to big wig format, and the scaled control was substracted from the scaled sample.
Signal smoothing was performed on the normalized and control-subtracted bigwig files using a custom script employing fast Fourier transform convolution with a sliding window of 200 bp. The script is available upon request.
Genome_build: Saccer2
Supplementary_files_format_and_content: bigwile format files (more details in the readme.txt)
|
| |
|
| Submission date |
Jun 17, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Valerie Borde |
| E-mail(s) |
valerie.borde@curie.fr
|
| Phone |
33156246700
|
| Organization name |
Institut Curie
|
| Department |
CNRSUMR3244
|
| Street address |
26 rue d'Ulm
|
| City |
PARIS |
| ZIP/Postal code |
75248 |
| Country |
France |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE132850 |
Mechanism of in vivo activation of the MutLgamma-Exo1 complex for meiotic crossover formation |
|
| Relations |
| BioSample |
SAMN12079085 |
| SRA |
SRX6078427 |
