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| Status |
Public on May 08, 2020 |
| Title |
Snf2- Mnase 20min |
| Sample type |
SRA |
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| Source name |
Yeast cells
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| Organism |
Candida albicans |
| Characteristics |
strain: SN 148
fusion protein: Snf2- Mnase
duration (min): 20
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| Treatment protocol |
Cells were pelleted at 3,000 g during 5 min and washed three times with 1 ml Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, one tablet Roche cOmplete EDTA-free mini protease inhibitors, 1 mM PMSF). Cells were then resuspended in 600 µl Buffer A containing 0.1% digitonin and permeabilized for 10 min at 30 °C under shaking. MNase digestions were performed by adding CaCl2 at final concentration of 5 mM and incubated at the indicated time at 30 °C. At each time point, a total of 200 µl aliquots of the ChEC digestions were transferred to a tube containing 50 µl of 250 mM EGTA to quench MNase digestions. For each factor analyzed, the timepoint “0” corresponds to a condition where MNase were not activated by CaCl2.
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| Growth protocol |
For each ChEC experiment, saturated overnight cultures of Mnase tagged and Mnase free strains were diluted to a starting OD600 of 0.1 in 50 ml YPD medium. Cells were grown at 30°C to an OD600 of 0.7–0.8
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nucleic acids were extracted using MasterPure yeast DNA purification kit (Epicentre, MPY80200) according the manufacturer’ instructions, and resuspended in 50 µl 0.1 X Tris-HCl buffer, pH 8.0. RNAs were digested with 10 µg RNase A at 37 °C for 20 min.
Libraries were prepared according to Illumina's instructions for Shotgun library preparation for ChIP samples (NEB Ultra II) Illumina Library QC
As Chip-Seq, A 50-bp paired-end sequencing of DNAs were performed using an Illumina HiSeq 4000 sequencing system.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Snf2- Mnase 20min
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| Data processing |
Sequence were trimmed to remove adapters using TRIMMOMATIC
Mapping the reads to reference genome was done using Bowtie2
ChEC alignment and track visualization using bedgraph files were performed as previously described in Zentner et al 2015.
Peaks were determined from the normalized ChEC ratio using MACS2 algorithm with a window size of 60 bp.
Analysis was done for data obtained using nomodel_extsize_200_keep-dup_all option. The assumption being removing duplicates will decrease the peak calling power of the MACS2 algorithm.
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/current/
Supplementary_files_format_and_content: peaks, bigwig
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| Submission date |
May 07, 2020 |
| Last update date |
May 08, 2020 |
| Contact name |
Faiza Tebbji |
| E-mail(s) |
t_faiza2000@yahoo.fr
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| Organization name |
CHU Québec
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| Street address |
2705 Boulevard Laurier
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| City |
Québec |
| ZIP/Postal code |
G1V 4G2 |
| Country |
Canada |
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| Platform ID |
GPL24129 |
| Series (1) |
| GSE150063 |
High resolution genome-wide occupancy in Candida species using ChEC-seq |
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| Relations |
| BioSample |
SAMN14850126 |
| SRA |
SRX8288531 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4522956_Snf2-Mnase-20min_Snf2-Mnase-20min_1.bigwig |
109.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM4522956_Snf2-Mnase-20min_Snf2-Mnase-20min_1_peaks.narrowPeak.gz |
259.8 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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